K. Abdelmohsen, A. Panda, M. Kang, J. Xu, R. Selimyan et al., Senescenceassociated lncRNAs: senescence-associated long noncoding RNAs, Aging Cell, vol.12, pp.890-900, 2013.

M. D. Adams, S. E. Celniker, R. A. Holt, C. A. Evans, J. D. Gocayne et al., The genome sequence of Drosophila melanogaster, Science, vol.287, pp.2185-2195, 2000.

N. Agarwal, A. , and A. , Enhancement of Transcription by a Splicing-Competent Intron Is Dependent on Promoter Directionality, PLOS Genetics, vol.12, 2016.

N. M. Aiello and Y. Kang, Context-dependent EMT programs in cancer metastasis, Journal of Experimental Medicine, vol.216, pp.1016-1026, 2019.

S. L. Ameres and P. D. Zamore, Diversifying microRNA sequence and function, Nature Reviews Molecular Cell Biology, vol.14, pp.475-488, 2013.

Y. An, K. L. Furber, J. , and S. , Pseudogenes regulate parental gene expression via ceRNA network, Journal of Cellular and Molecular Medicine, 2016.

S. Anandakumar and S. Vijayakumar, Mammalian Mitochondrial ncRNA Database. Bioinformation, vol.600, pp.512-514, 2015.

S. Anders and W. Huber, Differential expression analysis for sequence count data, Genome Biology, vol.11, p.106, 2010.

S. J. Andrews and J. A. Rothnagel, Emerging evidence for functional peptides encoded by short open reading frames, Nature Reviews Genetics, vol.15, pp.193-204, 2014.

F. Antequera and A. Bird, Number of CpG islands and genes in human and mouse, Proc. Natl. Acad. Sci. U.S.A, vol.90, pp.11995-11999, 1993.

F. Ariel, N. Romero-barrios, T. Jégu, M. Benhamed, and M. Crespi, Battles and hijacks: noncoding transcription in plants, Trends in Plant Science, vol.20, pp.362-371, 2015.
URL : https://hal.archives-ouvertes.fr/hal-02635660

R. T. Arrial, R. C. Togawa, M. Brigido, and M. De, Screening non-coding RNAs in transcriptomes from neglected species using PORTRAIT: case study of the pathogenic fungus Paracoccidioides brasiliensis, BMC Bioinformatics, vol.10, p.239, 2009.

A. C. Ayupe, A. C. Tahira, L. Camargo, F. C. Beckedorff, S. Verjovski-almeida et al., Global analysis of biogenesis, stability and sub-cellular localization of lncRNAs mapping to intragenic regions of the human genome, RNA Biology, vol.12, pp.877-892, 2015.

B. Bae, I. Tietjen, K. D. Atabay, G. D. Evrony, M. B. Johnson et al., Evolutionarily dynamic alternative splicing of GPR56 regulates regional cerebral cortical patterning, Science, vol.343, pp.764-768, 2014.

B. Balk, A. Maicher, M. Dees, J. Klermund, S. Luke-glaser et al., Telomeric RNA-DNA hybrids affect telomere-length dynamics and senescence, Nature Structural & Molecular Biology, vol.20, pp.1199-1205, 2013.

B. Balk, M. Dees, K. Bender, L. , and B. , The differential processing of telomeres in response to increased telomeric transcription and RNA-DNA hybrid accumulation, RNA Biology, vol.11, pp.95-100, 2014.

B. Banfai, H. Jia, J. Khatun, E. Wood, B. Risk et al., Long noncoding RNAs are rarely translated in two human cell lines, Genome Research, vol.22, pp.1646-1657, 2012.

J. Banyard and D. R. Bielenberg, The Role of EMT and MET in Cancer Dissemination, Connect Tissue Res, vol.56, pp.403-413, 2015.

D. P. Barlow, R. Stöger, B. G. Herrmann, K. Saito, and N. Schweifer, The mouse insulin-like growth factor type-2 receptor is imprinted and closely linked to the Tme locus, Nature, vol.349, pp.84-87, 1991.

M. S. Bartolomei, S. Zemel, and S. M. Tilghman, Parental imprinting of the mouse H19 gene, Nature, vol.351, pp.153-155, 1991.

C. Battistelli, C. Cicchini, L. Santangelo, A. Tramontano, L. Grassi et al., The Snail repressor recruits EZH2 to specific genomic sites through the enrollment of the lncRNA HOTAIR, 2016.

G. Bejerano, Ultraconserved Elements in the Human Genome, Science, vol.304, pp.1321-1325, 2004.

J. Bellmunt, Stem-Like Signature Predicting Disease Progression in Early Stage Bladder Cancer. The Role of E2F3 and SOX4, vol.6, 2018.

O. P. Berezovska, A. B. Glinskii, Z. Yang, X. Li, R. M. Hoffman et al., Essential role for activation of the Polycomb group (PcG) protein chromatin silencing pathway in metastatic prostate cancer, Cell Cycle, vol.5, pp.1886-1901, 2006.

A. J. Berk, Discovery of RNA splicing and genes in pieces, Proceedings of the National Academy of Sciences, vol.113, pp.801-805, 2016.

H. S. Bernhardt, The RNA world hypothesis: the worst theory of the early evolution of life (except for all the others)a, Biology Direct, vol.7, p.23, 2012.

J. Berretta and A. Morillon, Pervasive transcription constitutes a new level of eukaryotic genome regulation, EMBO Reports, vol.10, pp.973-982, 2009.
URL : https://hal.archives-ouvertes.fr/hal-02349854

H. Bierhoff, M. A. Dammert, D. Brocks, S. Dambacher, G. Schotta et al., Quiescence-Induced LncRNAs Trigger H4K20 Trimethylation and Transcriptional Silencing, Molecular Cell, vol.54, pp.675-682, 2014.

C. P. Bird, B. E. Stranger, M. Liu, D. J. Thomas, C. E. Ingle et al., Fast-evolving noncoding sequences in the human genome, Genome Biol, vol.8, p.118, 2007.

M. D. Blower, Centromeric Transcription Regulates Aurora-B Localization and Activation, Cell Reports, vol.15, pp.1624-1633, 2016.

G. K. Bogu, P. Vizán, L. W. Stanton, M. Beato, L. Di-croce et al., Chromatin and RNA Maps Reveal Regulatory Long Noncoding RNAs in Mouse, Molecular and Cellular Biology, vol.36, pp.809-819, 2016.

C. I. Brannan, E. C. Dees, R. S. Ingram, and S. M. Tilghman, The product of the H19 gene may function as an RNA, Molecular and Cellular Biology, vol.10, pp.28-36, 1990.

K. M. Broadbent, J. C. Broadbent, U. Ribacke, D. Wirth, J. L. Rinn et al., Strand-specific RNA sequencing in Plasmodium falciparum malaria identifies developmentally regulated long non-coding RNA and circular RNA, BMC Genomics, vol.16, 2015.

V. A. Burzio, C. Villota, J. Villegas, E. Landerer, E. Boccardo et al., Expression of a family of noncoding mitochondrial RNAs distinguishes normal from cancer cells, Proceedings of the National Academy of Sciences, vol.106, pp.9430-9434, 2009.

S. E. Butcher, The spliceosome as ribozyme hypothesis takes a second step, Proceedings of the National Academy of Sciences, vol.106, pp.12211-12212, 2009.

M. N. Cabili, M. C. Dunagin, P. D. Mcclanahan, A. Biaesch, O. Padovan-merhar et al., Localization and abundance analysis of human lncRNAs at single-cell and single-molecule resolution, Genome Biol, vol.16, p.20, 2015.

I. Cajigas, D. E. Leib, J. Cochrane, H. Luo, K. R. Swyter et al., Evf2 lncRNA/BRG1/DLX1 interactions reveal RNA-dependent inhibition of chromatin remodeling, Development, vol.142, pp.2641-2652, 2015.

E. Campeau, V. E. Ruhl, F. Rodier, C. L. Smith, B. L. Rahmberg et al., A versatile viral system for expression and depletion of proteins in mammalian cells, PLoS ONE, vol.4, p.6529, 2009.

A. Cano, M. A. Pérez-moreno, I. Rodrigo, A. Locascio, M. J. Blanco et al., The transcription factor snail controls epithelial-mesenchymal transitions by repressing E-cadherin expression, Nat. Cell Biol, vol.2, pp.76-83, 2000.

J. Carlevaro-fita, A. Rahim, R. Guigo, L. Vardy, J. et al., , 2015.

, Widespread localisation of long noncoding RNAs to ribosomes: Distinguishing features and evidence for regulatory roles

M. Carlile, D. Swan, K. Jackson, K. Preston-fayers, B. Ballester et al., Strand selective generation of endo-siRNAs from the Na/phosphate transporter gene Slc34a1 in murine tissues, Nucleic Acids Research, vol.37, pp.2274-2282, 2009.
URL : https://hal.archives-ouvertes.fr/hal-01615161

J. Carnesecchi, C. Cerutti, J. Vanacker, and C. Forcet, ERR? protein is stabilized by LSD1 in a demethylation-independent manner, PLOS ONE, vol.12, 2017.

C. Carrieri, L. Cimatti, M. Biagioli, A. Beugnet, S. Zucchelli et al., Long non-coding antisense RNA controls Uchl1 translation through an embedded SINEB2 repeat, Nature, vol.491, pp.454-457, 2012.

S. E. Castel and R. A. Martienssen, RNA interference in the nucleus: roles for small RNAs in transcription, epigenetics and beyond, Nature Reviews Genetics, vol.14, pp.100-112, 2013.

L. J. Castro-vega, K. Jouravleva, W. Liu, C. Martinez, P. Gestraud et al., Telomere crisis in kidney epithelial cells promotes the acquisition of a microRNA signature retrieved in aggressive renal cell carcinomas, Carcinogenesis, vol.34, pp.1173-1180, 2013.

T. R. Cech, STRUCTURAL BIOLOGY: Enhanced: The Ribosome Is a Ribozyme, Science, vol.289, pp.878-879, 2000.

C. L. Chaffer and R. A. Weinberg, A perspective on cancer cell metastasis, Science, vol.331, pp.1559-1564, 2011.

F. L. Chan, O. J. Marshall, R. Saffery, B. Kim, E. Earle et al., Active transcription and essential role of RNA polymerase II at the centromere during mitosis, Proceedings of the National Academy of Sciences, vol.109, pp.1979-1984, 2012.

L. Chen, Linking Long Noncoding RNA Localization and Function, Trends in Biochemical Sciences, vol.41, pp.761-772, 2016.

S. Chen, J. Yin, B. Lin, H. Su, Z. Zheng et al., Upregulated expression of long noncoding RNA SNHG15 promotes cell proliferation and invasion through regulates MMP2/MMP9 in patients with GC, Tumour Biol, vol.37, pp.6801-6812, 2016.

D. Cheng, C. Bao, X. Zhang, X. Lin, H. Huang et al., LncRNA PRNCR1 interacts with HEY2 to abolish miR-448-mediated growth inhibition in non-small cell lung cancer, Biomed. Pharmacother, vol.107, pp.1540-1547, 2018.

A. T. Chinwalla, L. L. Cook, K. D. Delehaunty, G. A. Fewell, L. A. Fulton et al., Initial sequencing and comparative analysis of the mouse genome, Nature, vol.420, pp.520-562, 2002.

H. Choudhry, A. L. Harris, and A. Mcintyre, The tumour hypoxia induced non-coding transcriptome, Molecular Aspects of Medicine, vol.47, pp.35-53, 2016.

C. Chu, C. , and H. Y. , ChIRP-MS: RNA-Directed Proteomic Discovery, Methods Mol. Biol, vol.1861, pp.37-45, 2018.

C. Chu, K. Qu, F. L. Zhong, S. E. Artandi, C. et al., Genomic maps of long noncoding RNA occupancy reveal principles of RNA-chromatin interactions, Mol. Cell, vol.44, pp.667-678, 2011.

M. B. Clark, R. L. Johnston, M. Inostroza-ponta, A. H. Fox, E. Fortini et al., Genome-wide analysis of long noncoding RNA stability, Genome Research, vol.22, pp.885-898, 2012.

M. B. Clark, A. Choudhary, M. A. Smith, R. J. Taft, and J. S. Mattick, The dark matter rises: the expanding world of regulatory RNAs, Essays Biochem, vol.54, pp.1-16, 2013.

M. Cobb, Who discovered messenger RNA?, Current Biology, vol.25, pp.526-532, 2015.

D. B. Cox, J. S. Gootenberg, O. O. Abudayyeh, B. Franklin, M. J. Kellner et al., RNA editing with CRISPR-Cas13, Science, vol.358, pp.1019-1027, 2017.

F. H. Crick, The origin of the genetic code, Journal of Molecular Biology, vol.38, pp.367-379, 1968.

H. R. Crollius, Characterization and Repeat Analysis of the Compact Genome of the Freshwater Pufferfish Tetraodon nigroviridis, Genome Research, vol.10, pp.939-949, 2000.

L. David, W. Huber, M. Granovskaia, J. Toedling, C. J. Palm et al., A high-resolution map of transcription in the yeast genome, Proceedings of the National Academy of Sciences, vol.103, pp.5320-5325, 2006.

C. Davidovich and T. R. Cech, The recruitment of chromatin modifiers by long noncoding RNAs: lessons from PRC2, RNA, vol.21, pp.2007-2022, 2015.

F. M. Davis, I. Azimi, R. A. Faville, A. A. Peters, K. Jalink et al., Induction of epithelial-mesenchymal transition (EMT) in breast cancer cells is calcium signal dependent, Oncogene, vol.33, pp.2307-2316, 2014.

Q. Deng, H. Sun, B. He, Y. Pan, T. Gao et al., Prognostic value of long non-coding RNA HOTAIR in various cancers, PLoS ONE, vol.9, 2014.

T. Derrien, R. Johnson, G. Bussotti, A. Tanzer, S. Djebali et al., The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression, Genome Research, vol.22, pp.1775-1789, 2012.
URL : https://hal.archives-ouvertes.fr/hal-01205054

M. Descrimes, Y. B. Zouari, M. Wery, R. Legendre, D. Gautheret et al., VING: a software for visualization of deep sequencing signals, BMC Res Notes, vol.8, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01199649

B. K. Dey, K. Pfeifer, and A. Dutta, The H19 long noncoding RNA gives rise to microRNAs miR-675-3p and miR-675-5p to promote skeletal muscle differentiation and regeneration, Genes & Development, vol.28, pp.491-501, 2014.

A. Dhir, S. Dhir, N. J. Proudfoot, and C. L. Jopling, Microprocessor mediates transcriptional termination of long noncoding RNA transcripts hosting microRNAs, Nature Structural & Molecular Biology, vol.22, pp.319-327, 2015.

D. Benedetto, M. Bièche, I. Deshayes, F. Vacher, S. Nouet et al., Structural organization and expression of human MTUS1, a candidate 8p22 tumor suppressor gene encoding a family of angiotensin II AT2 receptor-interacting proteins, ATIP. Gene, vol.380, pp.127-136, 2006.
URL : https://hal.archives-ouvertes.fr/pasteur-02870438

S. Diederichs, The four dimensions of noncoding RNA conservation, Trends Genet, vol.30, pp.121-123, 2014.

C. Ding, S. Cheng, Z. Yang, Z. Lv, H. Xiao et al., Long non-coding RNA HOTAIR promotes cell migration and invasion via down-regulation of RNA binding motif protein 38 in hepatocellular carcinoma cells, Int J Mol Sci, vol.15, pp.4060-4076, 2014.

M. E. Dinger, P. P. Amaral, T. R. Mercer, and J. S. Mattick, Pervasive transcription of the eukaryotic genome: functional indices and conceptual implications, Briefings in Functional Genomics and Proteomics, vol.8, pp.407-423, 2009.

S. Djebali, C. A. Davis, A. Merkel, A. Dobin, T. Lassmann et al., Landscape of transcription in human cells, Nature, vol.489, pp.101-108, 2012.
URL : https://hal.archives-ouvertes.fr/hal-01216755

R. N. Doan, B. Bae, B. Cubelos, C. Chang, A. A. Hossain et al., Mutations in Human Accelerated Regions Disrupt Cognition and Social Behavior, vol.167, pp.341-354, 2016.

L. Dong and L. Hui, HOTAIR Promotes Proliferation, Migration, and Invasion of Ovarian Cancer SKOV3 Cells Through Regulating PIK3R3, Med. Sci. Monit, vol.22, pp.325-331, 2016.

T. Dugimont, C. Montpellier, E. Adriaenssens, S. Lottin, L. Dumont et al., The H19 TATA-less promoter is efficiently repressed by wild-type tumor suppressor gene product p53, Oncogene, vol.16, pp.2395-2401, 1998.

I. Dunham, N. Shimizu, B. A. Roe, S. Chissoe, A. R. Hunt et al., The DNA sequence of human chromosome 22, Nature, vol.402, pp.489-495, 1999.

L. Duret, The Xist RNA Gene Evolved in Eutherians by Pseudogenization of a Protein-Coding Gene, Science, vol.312, pp.1653-1655, 2006.
URL : https://hal.archives-ouvertes.fr/hal-00427928

J. Durruthy-durruthy, V. Sebastiano, M. Wossidlo, D. Cepeda, J. Cui et al., The primate-specific noncoding RNA HPAT5 regulates pluripotency during human preimplantation development and nuclear reprogramming, Nature Genetics, vol.48, pp.44-52, 2015.

, An integrated encyclopedia of DNA elements in the human genome, ENCODE Project Consortium, vol.489, pp.57-74, 2012.

. Encode-project-consortium, E. Birney, J. A. Stamatoyannopoulos, A. Dutta, R. Guigó et al., Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project, Nature, vol.447, pp.799-816, 2007.

Y. Enuka, M. Lauriola, M. E. Feldman, A. Sas-chen, I. Ulitsky et al., Circular RNAs are long-lived and display only minimal early alterations in response to a growth factor, Nucleic Acids Research, vol.44, pp.1370-1383, 2016.

C. A. Espinoza, J. A. Goodrich, and J. F. Kugel, Characterization of the structure, function, and mechanism of B2 RNA, an ncRNA repressor of RNA polymerase II transcription, RNA, vol.13, pp.583-596, 2007.

A. Expósito-villén, A. Aránega, and D. Franco, Functional Role of Non-Coding RNAs during Epithelial-To-Mesenchymal Transition, Noncoding RNA, vol.4, 2018.

M. A. Faghihi, F. Modarresi, A. M. Khalil, D. E. Wood, B. G. Sahagan et al., Expression of a noncoding RNA is elevated in Alzheimer's disease and drives rapid feed-forward regulation of ?-secretase, Nature Medicine, vol.14, pp.723-730, 2008.

M. Fassan, L. Dall'olmo, M. Galasso, C. Braconi, M. Pizzi et al., Transcribed ultraconserved noncoding RNAs (T-UCR) are involved in Barrett's esophagus carcinogenesis, Oncotarget, vol.5, pp.7162-7171, 2014.

J. Feng, The Evf-2 noncoding RNA is transcribed from the Dlx-5/6 ultraconserved region and functions as a Dlx-2 transcriptional coactivator, Genes & Development, vol.20, pp.1470-1484, 2006.

J. Feng, G. Xu, J. Liu, N. Zhang, L. Li et al., Phosphorylation of LSD1 at Ser112 is crucial for its function in induction of EMT and metastasis in breast cancer, Breast Cancer Res. Treat, vol.159, pp.443-456, 2016.

J. Ferdin, N. Nishida, X. Wu, M. S. Nicoloso, M. Y. Shah et al., HINCUTs in cancer: hypoxiainduced noncoding ultraconserved transcripts, Cell Death and Differentiation, vol.20, pp.1675-1687, 2013.

G. Ferrari-amorotti, V. Fragliasso, R. Esteki, Z. Prudente, A. R. Soliera et al., Inhibiting interactions of lysine demethylase LSD1 with snail/slug blocks cancer cell invasion, Cancer Res, vol.73, pp.235-245, 2013.

S. Feuerhahn, N. Iglesias, A. Panza, A. Porro, and J. Lingner, TERRA biogenesis, turnover and implications for function, FEBS Letters, vol.584, pp.3812-3818, 2010.

R. D. Fleischmann, M. D. Adams, O. White, R. A. Clayton, E. F. Kirkness et al., Wholegenome random sequencing and assembly of Haemophilus influenzae Rd, Science, vol.269, pp.496-512, 1995.

R. A. Flynn, A. E. Almada, J. R. Zamudio, and P. A. Sharp, Antisense RNA polymerase II divergent transcripts are P-TEFb dependent and substrates for the RNA exosome, Proceedings of the National Academy of Sciences, vol.108, pp.10460-10465, 2011.

A. Fort, K. Hashimoto, D. Yamada, M. Salimullah, C. A. Keya et al., Deep transcriptome profiling of mammalian stem cells supports a regulatory role for retrotransposons in pluripotency maintenance, Nature Genetics, vol.46, pp.558-566, 2014.

K. T. Gagnon, L. Li, B. A. Janowski, and D. R. Corey, Analysis of nuclear RNA interference in human cells by subcellular fractionation and Argonaute loading, Nat Protoc, vol.9, pp.2045-2060, 2014.

S. Ganesh and P. Svoboda, Retrotransposon-associated long non-coding RNAs in mice and men, Pflügers Archiv -European Journal of Physiology, vol.468, pp.1049-1060, 2016.

T. Gebäck, M. M. Schulz, P. Koumoutsakos, and M. Detmar, TScratch: a novel and simple software tool for automated analysis of monolayer wound healing assays, BioTechniques, vol.46, pp.265-274, 2009.

Y. J. Geng, S. L. Xie, Q. Li, J. Ma, and G. Y. Wang, Large intervening noncoding RNA HOTAIR is associated with hepatocellular carcinoma progression, J. Int. Med. Res, vol.39, pp.2119-2128, 2011.

A. Giannakakis, J. Zhang, P. Jenjaroenpun, S. Nama, N. Zainolabidin et al., Contrasting expression patterns of coding and noncoding parts of the human genome upon oxidative stress, Scientific Reports, vol.5, p.9737, 2015.

L. A. Gilbert, M. A. Horlbeck, B. Adamson, J. E. Villalta, Y. Chen et al., , 2014.

, Genome-Scale CRISPR-Mediated Control of Gene Repression and Activation. Cell, vol.159, pp.647-661

M. Giovarelli, G. Bucci, A. Ramos, D. Bordo, C. J. Wilusz et al., H19 long noncoding RNA controls the mRNA decay promoting function of KSRP, Proceedings of the National Academy of Sciences, vol.111, pp.5023-5028, 2014.

A. Goffeau, B. G. Barrell, H. Bussey, R. W. Davis, B. Dujon et al., Life with 6000 genes, Science, vol.274, pp.563-567, 1996.

J. A. Gomez, O. L. Wapinski, Y. W. Yang, J. Bureau, S. Gopinath et al., The NeST Long ncRNA Controls Microbial Susceptibility and Epigenetic Activation of the Interferon-? Locus, Cell, vol.152, pp.743-754, 2013.

D. M. Gonzalez and D. Medici, Signaling mechanisms of the epithelialmesenchymal transition, Sci Signal, vol.7, p.8, 2014.

I. Gonzalez, R. Munita, E. Agirre, T. A. Dittmer, K. Gysling et al., A lncRNA regulates alternative splicing via establishment of a splicingspecific chromatin signature, Nature Structural & Molecular Biology, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01153122

A. J. Goodman, E. R. Daugharthy, K. , and J. , Pervasive Antisense Transcription Is Evolutionarily Conserved in Budding Yeast, Molecular Biology and Evolution, vol.30, pp.409-421, 2013.

S. Goossens, S. Peirs, W. Van-loocke, J. Wang, M. Takawy et al., Oncogenic ZEB2 activation drives sensitivity toward KDM1A inhibition in T-cell acute lymphoblastic leukemia, Blood, vol.129, pp.981-990, 2017.

D. Grandér, J. , and P. , Pseudogene-Expressed RNAs: Emerging Roles in Gene Regulation and Disease, Long Non-Coding RNAs in Human Disease, pp.111-126, 2015.

J. Greenwood and J. P. Cooper, Non-coding telomeric and subtelomeric transcripts are differentially regulated by telomeric and heterochromatin assembly factors in fission yeast, Nucleic Acids Research, vol.40, pp.2956-2963, 2012.

A. J. Griffiths, J. H. Miller, D. T. Suzuki, R. C. Lewontin, and W. M. Gelbart, Transcription, 2000.

C. J. Gröger, M. Grubinger, T. Waldhör, K. Vierlinger, and W. Mikulits, , 2012.

, Meta-analysis of gene expression signatures defining the epithelial to mesenchymal transition during cancer progression, PLoS ONE, vol.7, 51136.

P. M. Guenzl and D. P. Barlow, Macro lncRNAs: A new layer of cisregulatory information in the mammalian genome, RNA Biology, vol.9, pp.731-741, 2012.

C. Guerrier-takada, K. Gardiner, T. Marsh, N. Pace, and S. Altman, The RNA moiety of ribonuclease P is the catalytic subunit of the enzyme, Cell, vol.35, pp.849-857, 1983.

M. Gugnoni and A. Ciarrocchi, Long Noncoding RNA and Epithelial Mesenchymal Transition in Cancer, Int J Mol Sci, vol.20, 2019.

H. Guo, L. Zhao, B. Shi, J. Bao, D. Zheng et al., , p.5, 2018.

, uaRNA promotes gastric cancer progression through its interaction with HSP90, Oncogene, vol.37, pp.4505-4517

X. Guo, L. Gao, Y. Wang, D. K. Chiu, T. Wang et al., Advances in long noncoding RNAs: identification, structure prediction and function annotation, Briefings in Functional Genomics, 2015.

R. A. Gupta, N. Shah, K. C. Wang, J. Kim, H. M. Horlings et al., Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis, Nature, vol.464, pp.1071-1076, 2010.

M. Guttman, I. Amit, M. Garber, C. French, M. F. Lin et al., Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals, Nature, vol.458, pp.223-227, 2009.

H. Ha, J. Song, S. Wang, A. Kapusta, C. Feschotte et al., , 2014.

, A comprehensive analysis of piRNAs from adult human testis and their relationship with genes and mobile elements, BMC Genomics, vol.15, p.545

E. Hacisuleyman, C. J. Shukla, C. L. Weiner, and J. L. Rinn, Function and evolution of local repeats in the Firre locus, Nature Communications, vol.7, p.11021, 2016.

M. Hadjiargyrou and N. Delihas, The intertwining of transposable elements and non-coding RNAs, Int J Mol Sci, vol.14, pp.13307-13328, 2013.

N. Hamazaki, M. Uesaka, K. Nakashima, K. Agata, and T. Imamura, Gene activation-associated long noncoding RNAs function in mouse preimplantation development, Development, vol.142, pp.910-920, 2015.

P. Han, C. , and C. , Long non-coding RNA and chromatin remodeling, RNA Biology, vol.12, pp.1094-1098, 2015.

D. Hanahan and R. A. Weinberg, Hallmarks of Cancer: The Next Generation, Cell, vol.144, pp.646-674, 2011.

T. B. Hansen, T. I. Jensen, B. H. Clausen, J. B. Bramsen, B. Finsen et al., Natural RNA circles function as efficient microRNA sponges, Nature, vol.495, pp.384-388, 2013.

W. J. Harris, X. Huang, J. T. Lynch, G. J. Spencer, J. R. Hitchin et al., The histone demethylase KDM1A sustains the oncogenic potential of MLL-AF9 leukemia stem cells, Cancer Cell, vol.21, pp.473-487, 2012.

L. He and G. J. Hannon, MicroRNAs: small RNAs with a big role in gene regulation, Nature Reviews Genetics, vol.5, pp.522-531, 2004.

S. Van-heesch, M. Van-iterson, J. Jacobi, S. Boymans, P. B. Essers et al., Extensive localization of long noncoding RNAs to the cytosol and mono-and polyribosomal complexes, 2014.

, Genome Biology, vol.15, p.6

T. J. Heinen, F. Staubach, D. Häming, and D. Tautz, Emergence of a New Gene from an Intergenic Region, Current Biology, vol.19, pp.1527-1531, 2009.

D. G. Hendrickson, D. R. Kelley, D. Tenen, B. Bernstein, and J. L. Rinn, , 2016.

, Widespread RNA binding by chromatin-associated proteins, Genome Biol, vol.17, p.28

H. Hezroni, D. Koppstein, M. G. Schwartz, A. Avrutin, D. P. Bartel et al., Principles of Long Noncoding RNA Evolution Derived from Direct Comparison of Transcriptomes in 17 Species, Cell Reports, vol.11, pp.1110-1122, 2015.

S. Hino, K. Kohrogi, and M. Nakao, Histone demethylase LSD1 controls the phenotypic plasticity of cancer cells, Cancer Sci, vol.107, pp.1187-1192, 2016.

H. Hirata, Y. Hinoda, V. Shahryari, G. Deng, K. Nakajima et al., Long Noncoding RNA MALAT1 Promotes Aggressive Renal Cell Carcinoma through Ezh2 and Interacts with miR-205, Cancer Res, vol.75, pp.1322-1331, 2015.

D. Hnisz, B. J. Abraham, T. I. Lee, A. Lau, V. Saint-andré et al., Super-enhancers in the control of cell identity and disease, Cell, vol.155, pp.934-947, 2013.

M. Hoffmann, J. Dehn, J. Droop, G. Niegisch, C. Niedworok et al., Truncated Isoforms of lncRNA ANRIL Are Overexpressed in Bladder Cancer, But Do Not Contribute to Repression of INK4 Tumor Suppressors, Non-Coding RNA, vol.1, pp.266-284, 2015.

M. A. Horlbeck, L. A. Gilbert, J. E. Villalta, B. Adamson, R. A. Pak et al., Compact and highly active next-generation libraries for CRISPR-mediated gene repression and activation, 2016.

G. Housman and I. Ulitsky, Methods for distinguishing between proteincoding and long noncoding RNAs and the elusive biological purpose of translation of long noncoding RNAs, Biochimica et Biophysica Acta (BBA) -Gene Regulatory Mechanisms, vol.1859, pp.31-40, 2016.

H. Hu, L. He, and P. Khaitovich, Deep sequencing reveals a novel class of bidirectional promoters associated with neuronal genes, BMC Genomics, vol.15, p.457, 2014.

P. Hu, J. Yang, Y. Hou, H. Zhang, Z. Zeng et al., LncRNA expression signatures of twist-induced epithelial-tomesenchymal transition in MCF10A cells, Cell. Signal, vol.26, pp.83-93, 2014.

H. Huang, F. Chen, W. Chou, H. Hou, B. Ko et al., , 2019.

J. Huang, R. Sengupta, A. B. Espejo, M. G. Lee, J. A. Dorsey et al., , vol.449, pp.105-108, 2007.

J. Huang, M. Chen, D. Chen, X. Gao, S. Zhu et al., A Peptide Encoded by a Putative lncRNA HOXB-AS3 Suppresses Colon Cancer Growth, Mol. Cell, vol.68, pp.171-184, 2017.

M. Huarte and O. Marín-béjar, Long noncoding RNAs: from identification to functions and mechanisms, Advances in Genomics and Genetics, vol.257, 2015.

M. Huarte, M. Guttman, D. Feldser, M. Garber, M. J. Koziol et al., A Large Intergenic Noncoding RNA Induced by p53 Mediates Global Gene Repression in the p53 Response, Cell, vol.142, pp.409-419, 2010.

, Finishing the euchromatic sequence of the human genome, Human Genome Sequencing Consortium, I, vol.431, pp.931-945, 2004.

T. Hung, Y. Wang, M. F. Lin, A. K. Koegel, Y. Kotake et al., Extensive and coordinated transcription of noncoding RNAs within cell-cycle promoters, Nature Genetics, vol.43, pp.621-629, 2011.

K. Hyun, G. Koo, H. Han, J. Sohn, W. Choi et al., Epithelial-to-mesenchymal transition leads to loss of EpCAM and different physical properties in circulating tumor cells from metastatic breast cancer, Oncotarget, vol.7, pp.24677-24687, 2016.

A. Indrieri, C. Grimaldi, S. Zucchelli, R. Tammaro, S. Gustincich et al., Synthetic long non-coding RNAs [SINEUPs] rescue defective gene expression in vivo, Scientific Reports, vol.6, p.27315, 2016.

M. K. Iyer, Y. S. Niknafs, R. Malik, U. Singhal, A. Sahu et al., The landscape of long noncoding RNAs in the human transcriptome, Nat. Genet, vol.47, pp.199-208, 2015.

J. Jarroux, A. Morillon, and M. Pinskaya, History, Discovery, and Classification of lncRNAs, Adv. Exp. Med. Biol, vol.1008, pp.1-46, 2017.
URL : https://hal.archives-ouvertes.fr/hal-02349823

J. Jarroux, C. Bertrand, G. Marc, D. Foretek, Z. Saci et al., HOTAIR promotes an epithelial-to-mesenchymal transition through relocation of the histone demethylase Lsd1, 2019.

Z. Ji, R. Song, A. Regev, and K. Struhl, Many lncRNAs, 5'UTRs, and pseudogenes are translated and some are likely to express functional proteins, 2015.

L. Jiang, Z. , and L. , Identifying and functionally characterizing tissuespecific and ubiquitously expressed human lncRNAs, Oncotarget, 2016.

R. Johnson and R. Guigo, The RIDL hypothesis: transposable elements as functional domains of long noncoding RNAs, RNA, vol.20, pp.959-976, 2014.

M. K. Jolly, M. Boareto, B. Huang, D. Jia, M. Lu et al., Implications of the Hybrid Epithelial/Mesenchymal Phenotype in Metastasis, Front Oncol, vol.5, p.155, 2015.

M. K. Jolly, K. E. Ware, S. Gilja, J. A. Somarelli, and H. Levine, EMT and MET: necessary or permissive for metastasis?, Mol Oncol, vol.11, pp.755-769, 2017.

J. Joung, J. M. Engreitz, S. Konermann, O. O. Abudayyeh, V. K. Verdine et al., Genomescale activation screen identifies a lncRNA locus regulating a gene neighbourhood, Nature, vol.548, pp.343-346, 2017.

J. Joung, S. Konermann, J. S. Gootenberg, O. O. Abudayyeh, R. J. Platt et al., Genome-scale CRISPR-Cas9 knockout and transcriptional activation screening, Nat Protoc, vol.12, pp.828-863, 2017.

R. Kalluri and R. A. Weinberg, The basics of epithelial-mesenchymal transition, J. Clin. Invest, vol.119, pp.1420-1428, 2009.

H. Kambara, L. Gunawardane, E. Zebrowski, L. Kostadinova, R. Jobava et al., Regulation of Interferon-Stimulated Gene BST2 by a lncRNA Transcribed from a Shared Bidirectional Promoter, Frontiers in Immunology, vol.5, 2015.

S. Kaneko, J. Son, S. S. Shen, D. Reinberg, and R. Bonasio, PRC2 binds active promoters and contacts nascent RNAs in embryonic stem cells, Nat. Struct. Mol. Biol, vol.20, pp.1258-1264, 2013.

S. Kaneko, J. Son, R. Bonasio, S. S. Shen, and D. Reinberg, Nascent RNA interaction keeps PRC2 activity poised and in check, Genes & Development, vol.28, pp.1983-1988, 2014.

P. Kapranov, Large-Scale Transcriptional Activity in Chromosomes 21 and 22, Science, vol.296, pp.916-919, 2002.

P. Kapranov, Examples of the complex architecture of the human transcriptome revealed by RACE and high-density tiling arrays, Genome Research, vol.15, pp.987-997, 2005.

P. Kapranov, A. T. Willingham, and T. R. Gingeras, Genome-wide transcription and the implications for genomic organization, Nature Reviews Genetics, vol.8, pp.413-423, 2007.

A. Kapusta, Z. Kronenberg, V. J. Lynch, X. Zhuo, L. Ramsay et al., Transposable Elements Are Major Contributors to the Origin, Diversification, and Regulation of Vertebrate Long Noncoding RNAs, PLoS Genetics, vol.9, 2013.

S. Katayama, Y. Tomaru, T. Kasukawa, K. Waki, M. Nakanishi et al., Antisense transcription in the mammalian transcriptome, Science, vol.309, pp.1564-1566, 2005.

L. Keller, S. Werner, and K. Pantel, Biology and clinical relevance of EpCAM, Cell Stress, vol.3, pp.165-180, 2019.

L. C. Kelley, L. L. Lohmer, E. J. Hagedorn, and D. R. Sherwood, Traversing the basement membrane in vivo: a diversity of strategies, J. Cell Biol, vol.204, pp.291-302, 2014.

A. M. Khalil, M. Guttman, M. Huarte, M. Garber, A. Raj et al., Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression, Proceedings of the National Academy of Sciences, vol.106, pp.11667-11672, 2009.

K. Kim, I. Jutooru, G. Chadalapaka, G. Johnson, J. Frank et al., HOTAIR is a negative prognostic factor and exhibits prooncogenic activity in pancreatic cancer, Oncogene, vol.32, pp.1616-1625, 2013.

T. Kino, D. E. Hurt, T. Ichijo, N. Nader, and G. P. Chrousos, Noncoding RNA Gas5 Is a Growth Arrest-and Starvation-Associated Repressor of the Glucocorticoid Receptor, Science Signaling, vol.3, pp.8-8, 2010.

R. Kogo, T. Shimamura, K. Mimori, K. Kawahara, S. Imoto et al., Long noncoding RNA HOTAIR regulates polycomb-dependent chromatin modification and is associated with poor prognosis in colorectal cancers, Cancer Res, vol.71, pp.6320-6326, 2011.

S. Konermann, M. D. Brigham, A. E. Trevino, J. Joung, O. O. Abudayyeh et al., , 2015.

, Genome-scale transcriptional activation by an engineered CRISPR-Cas9 complex, Nature, vol.517, pp.583-588

Q. Kong and M. Qiu, Long noncoding RNA SNHG15 promotes human breast cancer proliferation, migration and invasion by sponging miR-211-3p, Biochem. Biophys. Res. Commun, vol.495, pp.1594-1600, 2018.

L. Kong, Y. Zhang, Z. Ye, X. Liu, S. Zhao et al., CPC: assess the protein-coding potential of transcripts using sequence features and support vector machine, Nucleic Acids Res, vol.35, pp.345-349, 2007.

A. E. Kornienko, C. P. Dotter, P. M. Guenzl, H. Gisslinger, B. Gisslinger et al., Long non-coding RNAs display higher natural expression variation than protein-coding genes in healthy humans, 2016.

, Genome Biology, vol.17

M. C. Kramer, D. Liang, D. C. Tatomer, B. Gold, Z. M. March et al., Combinatorial control of Drosophila circular RNA expression by intronic repeats, hnRNPs, and SR proteins, Genes & Development, vol.29, pp.2168-2182, 2015.

K. Kruger, P. J. Grabowski, A. J. Zaug, J. Sands, D. E. Gottschling et al., Self-splicing RNA: Autoexcision and autocyclization of the ribosomal RNA intervening sequence of tetrahymena, Cell, vol.31, pp.147-157, 1982.

V. Kumar, H. Westra, J. Karjalainen, D. V. Zhernakova, T. Esko et al., Human Disease-Associated Genetic Variation Impacts Large Intergenic Non-Coding RNA Expression, PLoS Genetics, vol.9, 2013.

M. Kwapisz, M. Ruault, E. Van-dijk, S. Gourvennec, M. Descrimes et al., Expression of Subtelomeric lncRNAs Links Telomeres Dynamics to, RNA Decay in S. cerevisiae. Non-Coding RNA, vol.1, pp.94-126, 2015.
URL : https://hal.archives-ouvertes.fr/hal-02349839

F. Lai, U. A. Orom, M. Cesaroni, M. Beringer, D. J. Taatjes et al., Activating RNAs associate with Mediator to enhance chromatin architecture and transcription, Nature, vol.494, pp.497-501, 2013.

S. Lamouille, D. Subramanyam, R. Blelloch, and R. Derynck, Regulation of epithelial-mesenchymal and mesenchymal-epithelial transitions by microRNAs, Curr. Opin. Cell Biol, vol.25, pp.200-207, 2013.

S. Lamouille, J. Xu, and R. Derynck, Molecular mechanisms of epithelialmesenchymal transition, Nat. Rev. Mol. Cell Biol, vol.15, pp.178-196, 2014.

F. Lan, R. E. Collins, R. De-cegli, R. Alpatov, J. R. Horton et al., Recognition of unmethylated histone H3 lysine 4 links BHC80 to LSD1-mediated gene repression, Nature, vol.448, pp.718-722, 2007.

F. Lan, M. Zaratiegui, J. Villén, M. W. Vaughn, A. Verdel et al., S. pombe LSD1 homologs regulate heterochromatin propagation and euchromatic gene transcription, Mol. Cell, vol.26, pp.89-101, 2007.
URL : https://hal.archives-ouvertes.fr/in2p3-00000365

H. Lan, M. Tan, Q. Zhang, F. Yang, S. Wang et al., LSD1 destabilizes FBXW7 and abrogates FBXW7 functions independent of its demethylase activity, Proceedings of the National Academy of Sciences, vol.116, pp.12311-12320, 2019.

E. S. Lander, L. M. Linton, B. Birren, C. Nusbaum, M. C. Zody et al., Initial sequencing and analysis of the human genome, Nature, vol.409, pp.860-921, 2001.

E. Landerer, J. Villegas, V. A. Burzio, L. Oliveira, C. Villota et al., Nuclear localization of the mitochondrial ncRNAs in normal and cancer cells, Cellular Oncology, vol.34, pp.297-305, 2011.

M. Latil, D. Nassar, B. Beck, S. Boumahdi, L. Wang et al., Cell-Type-Specific Chromatin States Differentially Prime Squamous Cell Carcinoma Tumor-Initiating Cells for Epithelial to Mesenchymal Transition, Cell Stem Cell, vol.20, pp.191-204, 2017.

S. Lazorthes, C. Vallot, S. Briois, M. Aguirrebengoa, J. Thuret et al., A vlincRNA participates in senescence maintenance by relieving H2AZ-mediated repression at the INK4 locus, Nature Communications, vol.6, p.5971, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01465935

R. C. Lee, R. L. Feinbaum, A. , and V. , The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14, Cell, vol.75, pp.843-854, 1993.
URL : https://hal.archives-ouvertes.fr/in2p3-00597159

S. Lee, F. Kopp, T. Chang, A. Sataluri, B. Chen et al., Noncoding RNA NORAD Regulates Genomic Stability by Sequestering PUMILIO Proteins, Cell, vol.164, pp.69-80, 2016.

C. Lepoivre, M. Belhocine, A. Bergon, A. Griffon, M. Yammine et al., Divergent transcription is associated with promoters of transcriptional regulators, BMC Genomics, vol.14, p.914, 2013.
URL : https://hal.archives-ouvertes.fr/hal-02192888

J. B. Lewis, J. F. Atkins, C. W. Anderson, P. R. Baum, and R. F. Gesteland, Mapping of late adenovirus genes by cell-free translation of RNA selected by hybridization to specific DNA fragments, PNAS, vol.72, pp.1344-1348, 1975.

C. H. Li, C. , and Y. , Targeting long non-coding RNAs in cancers: progress and prospects, Int. J. Biochem. Cell Biol, vol.45, pp.1895-1910, 2013.

F. Li, Y. Xiao, F. Huang, W. Deng, H. Zhao et al., Spatiotemporal-specific lncRNAs in the brain, colon, liver and lung of macaque during development, Mol. BioSyst, vol.11, pp.3253-3263, 2015.

H. Li, H. Yang, D. Wen, Y. Luo, C. Liang et al., Overexpression of LncRNA HOTAIR is Associated with Poor Prognosis in Thyroid Carcinoma: A Study Based on TCGA and GEO Data, Horm. Metab. Res, 2017.

J. Li, J. Yang, P. Zhou, Y. Le, C. Zhou et al., Circular RNAs in cancer: novel insights into origins, properties, functions and implications, American Journal of Cancer Research, vol.5, pp.472-480, 2015.

J. Li, L. Han, P. Roebuck, L. Diao, L. Liu et al., TANRIC: An Interactive Open Platform to Explore the Function of lncRNAs in Cancer, Cancer Res, vol.75, pp.3728-3737, 2015.

L. Li, B. Liu, O. L. Wapinski, M. Tsai, K. Qu et al., Targeted disruption of Hotair leads to homeotic transformation and gene derepression, Cell Rep, vol.5, pp.3-12, 2013.

W. Li, D. Notani, Q. Ma, B. Tanasa, E. Nunez et al., Functional roles of enhancer RNAs for oestrogendependent transcriptional activation, Nature, vol.498, pp.516-520, 2013.

W. Li, D. Notani, and M. G. Rosenfeld, Enhancers as non-coding RNA transcription units: recent insights and future perspectives, Nature Reviews Genetics, vol.17, pp.207-223, 2016.

W. Li, Z. Zhang, X. Liu, X. Cheng, Y. Zhang et al., The FOXN3-NEAT1-SIN3A repressor complex promotes progression of hormonally responsive breast cancer, J. Clin. Invest, vol.127, pp.3421-3440, 2017.

Y. Li, Z. Wang, H. Shi, H. Li, L. Li et al., HBXIP and LSD1 Scaffolded by lncRNA Hotair Mediate Transcriptional Activation by c-Myc, Cancer Res, vol.76, pp.293-304, 2016.

Z. Li, C. Huang, C. Bao, L. Chen, M. Lin et al., Exon-intron circular RNAs regulate transcription in the nucleus, Nature Structural & Molecular Biology, vol.22, pp.256-264, 2015.

H. Liang, T. Yu, Y. Han, H. Jiang, C. Wang et al., LncRNA PTAR promotes EMT and invasion-metastasis in serous ovarian cancer by competitively binding miR-101-3p to regulate ZEB1 expression, Molecular Cancer, vol.17, 2018.

L. Liang, H. Sun, W. Zhang, M. Zhang, X. Yang et al., , 2016.

, Meta-Analysis of EMT Datasets Reveals Different Types of EMT, PLoS ONE, vol.11, p.156839

J. Liao, J. Wu, Y. Wang, J. He, W. Deng et al., Deep sequencing reveals a global reprogramming of lncRNA transcriptome during EMT, Biochimica et Biophysica Acta (BBA) -Molecular Cell Research, vol.1864, pp.1703-1713, 2017.

S. Lim, A. Janzer, A. Becker, A. Zimmer, R. Schüle et al.,

, Lysine-specific demethylase 1 (LSD1) is highly expressed in ER-negative breast cancers and a biomarker predicting aggressive biology, Carcinogenesis, vol.31, pp.512-520

T. Lin, A. Ponn, X. Hu, B. K. Law, and J. Lu, Requirement of the histone demethylase LSD1 in Snai1-mediated transcriptional repression during epithelialmesenchymal transition, Oncogene, vol.29, pp.4896-4904, 2010.

Y. Lin, Y. Wu, J. Li, C. Dong, X. Ye et al., , 2010.

, The SNAG domain of Snail1 functions as a molecular hook for recruiting lysinespecific demethylase 1, EMBO J, vol.29, pp.1803-1816

B. Liu, S. Wu, J. Ma, S. Yan, Z. Xiao et al., lncRNA GAS5 Reverses EMT and Tumor Stem Cell-Mediated Gemcitabine Resistance and Metastasis by Targeting miR-221/SOCS3 in Pancreatic Cancer, Mol Ther Nucleic Acids, vol.13, pp.472-482, 2018.

K. Liu, Y. Hou, Y. Liu, and J. Zheng, LncRNA SNHG15 contributes to proliferation, invasion and autophagy in osteosarcoma cells by sponging miR-141, J. Biomed. Sci, vol.24, p.46, 2017.

S. J. Liu, M. A. Horlbeck, S. W. Cho, H. S. Birk, M. Malatesta et al., CRISPRi-based genome-scale identification of functional long noncoding RNA loci in human cells, Science, vol.355, 2017.

L. Lobos-gonzález, V. Silva, M. Araya, F. Restovic, J. Echenique et al., Targeting antisense mitochondrial ncRNAs inhibits murine melanoma tumor growth and metastasis through reduction in survival and invasion factors, Oncotarget, 2016.

A. R. Lourenço and P. J. Coffer, SOX4: Joining the Master Regulators of Epithelial-to-Mesenchymal Transition?, Trends Cancer, vol.3, pp.571-582, 2017.

R. Louro, T. El-jundi, H. I. Nakaya, E. M. Reis, and S. Verjovski-almeida, Conserved tissue expression signatures of intronic noncoding RNAs transcribed from human and mouse loci, Genomics, vol.92, pp.18-25, 2008.

B. Luo, H. W. Cheung, A. Subramanian, T. Sharifnia, M. Okamoto et al., Highly parallel identification of essential genes in cancer cells, Proc. Natl. Acad. Sci. U.S.A, vol.105, pp.20380-20385, 2008.

M. Luo, Z. Li, W. Wang, Y. Zeng, Z. Liu et al., Long non-coding RNA H19 increases bladder cancer metastasis by associating with EZH2 and inhibiting E-cadherin expression, Cancer Lett, vol.333, pp.213-221, 2013.

M. Magistri, M. A. Faghihi, G. St-laurent, and C. Wahlestedt, Regulation of chromatin structure by long noncoding RNAs: focus on natural antisense transcripts, Trends in Genetics, vol.28, pp.389-396, 2012.

A. Maiques-diaz, G. J. Spencer, J. T. Lynch, F. Ciceri, E. L. Williams et al., Enhancer Activation by Pharmacologic Displacement of LSD1 from GFI1 Induces Differentiation in Acute Myeloid Leukemia, Cell Rep, vol.22, pp.3641-3659, 2018.

A. C. Marques and C. P. Ponting, Intergenic lncRNAs and the evolution of gene expression, Current Opinion in Genetics & Development, vol.27, pp.48-53, 2014.

A. C. Marques, J. Hughes, B. Graham, M. S. Kowalczyk, D. R. Higgs et al., Chromatin signatures at transcriptional start sites separate two equally populated yet distinct classes of intergenic long noncoding RNAs, Genome Biology, vol.14, p.131, 2013.

S. Massone, E. Ciarlo, S. Vella, M. Nizzari, T. Florio et al., NDM29, a RNA polymerase III-dependent non coding RNA, promotes amyloidogenic processing of APP and amyloid ? secretion, Biochimica et Biophysica Acta (BBA) -Molecular Cell Research, vol.1823, pp.1170-1177, 2012.

I. J. Matouk, N. Degroot, S. Mezan, S. Ayesh, R. Abu-lail et al., The H19 non-coding RNA is essential for human tumor growth, PLoS ONE, vol.2, p.845, 2007.

I. J. Matouk, E. Raveh, R. Abu-lail, S. Mezan, M. Gilon et al., Oncofetal H19 RNA promotes tumor metastasis, Biochim. Biophys. Acta, vol.1843, pp.1414-1426, 2014.

A. Matsumoto, A. Pasut, M. Matsumoto, R. Yamashita, J. Fung et al., mTORC1 and muscle regeneration are regulated by the LINC00961-encoded SPAR polypeptide, Nature, vol.541, pp.228-232, 2017.

J. S. Mattick, Non-coding RNAs: the architects of eukaryotic complexity, EMBO Rep, vol.2, pp.986-991, 2001.

J. S. Mattick, Challenging the dogma: the hidden layer of non-proteincoding RNAs in complex organisms, BioEssays, vol.25, pp.930-939, 2003.

J. S. Mattick and M. J. Gagen, The evolution of controlled multitasked gene networks: the role of introns and other noncoding RNAs in the development of complex organisms, Mol. Biol. Evol, vol.18, pp.1611-1630, 2001.

A. Mayer, J. Di-iulio, S. Maleri, U. Eser, J. Vierstra et al., Native elongating transcript sequencing reveals human transcriptional activity at nucleotide resolution, Cell, vol.161, pp.541-554, 2015.

O. G. Mcdonald, H. Wu, W. Timp, A. Doi, and A. P. Feinberg, Genomescale epigenetic reprogramming during epithelial-to-mesenchymal transition, Nat. Struct. Mol. Biol, vol.18, pp.867-874, 2011.

S. Memczak, M. Jens, A. Elefsinioti, F. Torti, J. Krueger et al., Circular RNAs are a large class of animal RNAs with regulatory potency, Nature, vol.495, pp.333-338, 2013.

T. R. Mercer, D. Wilhelm, M. E. Dinger, G. Solda, D. J. Korbie et al., Expression of distinct RNAs from 3' untranslated regions, Nucleic Acids Research, vol.39, pp.2393-2403, 2011.

T. R. Mercer, D. J. Gerhardt, M. E. Dinger, J. Crawford, C. Trapnell et al., Targeted RNA sequencing reveals the deep complexity of the human transcriptome, Nature Biotechnology, vol.30, pp.99-104, 2012.

D. Meseure, S. Vacher, F. Lallemand, K. D. Alsibai, R. Hatem et al., Prognostic value of a newly identified MALAT1 alternatively spliced transcript in breast cancer, British Journal of Cancer, vol.114, pp.1395-1404, 2016.
URL : https://hal.archives-ouvertes.fr/hal-02349825

P. Mestdagh, E. Fredlund, F. Pattyn, A. Rihani, T. Van-maerken et al., An integrative genomics screen uncovers ncRNA T-UCR functions in neuroblastoma tumours, Oncogene, vol.29, pp.3583-3592, 2010.

E. Metzger, M. Wissmann, N. Yin, J. M. Müller, R. Schneider et al., LSD1 demethylates repressive histone marks to promote androgen-receptor-dependent transcription, Nature, vol.437, pp.436-439, 2005.

M. J. Milligan and L. Lipovich, Pseudogene-derived lncRNAs: emerging regulators of gene expression, Frontiers in Genetics, vol.5, 2015.

N. Mise, R. Savai, H. Yu, J. Schwarz, N. Kaminski et al., , 2012.

, Zyxin is a transforming growth factor-? (TGF-?)/Smad3 target gene that regulates lung cancer cell motility via integrin ?5?1, J. Biol. Chem, vol.287, pp.31393-31405

T. Mondal, M. Rasmussen, G. K. Pandey, A. Isaksson, and C. Kanduri, Characterization of the RNA content of chromatin, Genome Research, vol.20, pp.899-907, 2010.

T. Mondal, S. Subhash, R. Vaid, S. Enroth, S. Uday et al., MEG3 long noncoding RNA regulates the TGF-? pathway genes through formation of RNA-DNA triplex structures, Nature Communications, vol.6, p.7743, 2015.

A. Montalbano, M. C. Canver, and N. E. Sanjana, High-Throughput Approaches to Pinpoint Function within the Noncoding Genome, Mol. Cell, vol.68, pp.44-59, 2017.

M. K. Montgomery, RNA Interference, RNA Interference, Editing, and Modification, J.M. Gott, pp.3-21, 2004.

M. Morlando, M. Ballarino, A. Fatica, and I. Bozzoni, The role of long noncoding RNAs in the epigenetic control of gene expression, ChemMedChem, vol.9, pp.505-510, 2014.

K. V. Morris, S. Santoso, A. Turner, C. Pastori, and P. G. Hawkins, , 2008.

, Bidirectional Transcription Directs Both Transcriptional Gene Activation and Suppression in Human Cells, PLoS Genetics, vol.4, 1000258.

E. Mouse, . Consortium, J. A. Stamatoyannopoulos, M. Snyder, R. Hardison et al., An encyclopedia of mouse DNA elements (Mouse ENCODE), Genome Biology, vol.13, p.418, 2012.

S. S. Nair, B. C. Nair, V. Cortez, D. Chakravarty, E. Metzger et al., PELP1 is a reader of histone H3 methylation that facilitates oestrogen receptor-alpha target gene activation by regulating lysine demethylase 1 specificity, EMBO Rep, vol.11, pp.438-444, 2010.

H. I. Nakaya, P. P. Amaral, R. Louro, A. Lopes, A. A. Fachel et al., Genome mapping and expression analyses of human intronic noncoding RNAs reveal tissue-specific patterns and enrichment in genes related to regulation of transcription, Genome Biology, vol.8, p.43, 2007.

A. Necsulea, M. Soumillon, M. Warnefors, A. Liechti, T. Daish et al., The evolution of lncRNA repertoires and expression patterns in tetrapods, Nature, vol.505, pp.635-640, 2014.

B. R. Nelson, C. A. Makarewich, D. M. Anderson, B. R. Winders, C. D. Troupes et al., A peptide encoded by a transcript annotated as long noncoding RNA enhances SERCA activity in muscle, Science, vol.351, pp.271-275, 2016.

M. A. Nieto, R. Y. Huang, .. Jackson, R. A. Thiery, and J. P. , Cell, vol.166, pp.21-45, 2016.

J. H. Noh, K. M. Kim, K. Abdelmohsen, J. Yoon, A. C. Panda et al., HuR and GRSF1 modulate the nuclear export and mitochondrial localization of the lncRNA RMRP, Genes & Development, 2016.

T. Nojima, T. Gomes, A. R. Grosso, H. Kimura, M. J. Dye et al., Mammalian NET-Seq Reveals Genomewide Nascent Transcription Coupled to RNA Processing, Cell, vol.161, pp.526-540, 2015.

E. Ntini, A. I. Järvelin, J. Bornholdt, Y. Chen, M. Boyd et al., Polyadenylation site-induced decay of upstream transcripts enforces promoter directionality, Nature Structural & Molecular Biology, vol.20, pp.923-928, 2013.

S. Ochoa, A Pursuit of a Hobby, Annual Review of Biochemistry, vol.49, pp.1-31, 1980.

Y. Okazaki, M. Furuno, T. Kasukawa, J. Adachi, H. Bono et al., Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs, Nature, vol.420, pp.563-573, 2002.

L. Ombrato and I. Malanchi, The EMT universe: space between cancer cell dissemination and metastasis initiation, Crit Rev Oncog, vol.19, pp.349-361, 2014.

L. E. Orgel and F. H. Crick, Selfish DNA: the ultimate parasite, Nature, vol.284, pp.604-607, 1980.

U. A. Ørom, T. Derrien, M. Beringer, K. Gumireddy, A. Gardini et al., Long Noncoding RNAs with Enhancer-like Function in Human Cells, Cell, vol.143, pp.46-58, 2010.

V. Pachnis, A. Belayew, and S. M. Tilghman, Locus unlinked to alphafetoprotein under the control of the murine raf and Rif genes, Proc. Natl. Acad. Sci. U.S.A, vol.81, pp.5523-5527, 1984.

C. Pádua-alves, A. S. Fonseca, B. R. Muys, . De-barros-e-lima, R. Bueno et al., Brief report: The lincRNA Hotair is required for epithelial-to-mesenchymal transition and stemness maintenance of cancer cell lines, Stem Cells, vol.31, pp.2827-2832, 2013.

I. Pastushenko, A. Brisebarre, A. Sifrim, M. Fioramonti, T. Revenco et al., Identification of the tumour transition states occurring during EMT, Nature, vol.556, pp.463-468, 2018.

S. Pavan, N. Meyer-schaller, M. Diepenbruck, R. K. Kalathur, M. Saxena et al., A kinome-wide high-content siRNA screen identifies MEK5-ERK5 signaling as critical for breast cancer cell EMT and metastasis, Oncogene, vol.37, pp.4197-4213, 2018.

L. Peng, X. Yuan, L. , and G. , The emerging landscape of circular RNA ciRS-7 in cancer (Review), Oncology Reports, 2015.

M. R. Pickard and G. T. Williams, Molecular and Cellular Mechanisms of Action of Tumour Suppressor GAS5 LncRNA, Genes (Basel), vol.6, pp.484-499, 2015.

M. Pinskaya, Z. Saci, M. Gallopin, N. H. Nguyen, M. Gabriel et al., Blind exploration of the unreferenced transcriptome reveals novel RNAs for prostate cancer diagnosis, 2019.

L. Poliseno, L. Salmena, J. Zhang, B. Carver, W. J. Haveman et al., A coding-independent function of gene and pseudogene mRNAs regulates tumour biology, Nature, vol.465, pp.1033-1038, 2010.

K. S. Pollard, S. R. Salama, B. King, A. D. Kern, T. Dreszer et al., Forces shaping the fastest evolving regions in the human genome, PLoS Genet, vol.2, p.168, 2006.

K. S. Pollard, S. R. Salama, N. Lambert, M. Lambot, S. Coppens et al., An RNA gene expressed during cortical development evolved rapidly in humans, Nature, vol.443, pp.167-172, 2006.

K. Polyak and R. A. Weinberg, Transitions between epithelial and mesenchymal states: acquisition of malignant and stem cell traits, Nat. Rev. Cancer, vol.9, pp.265-273, 2009.

C. P. Ponting, P. L. Oliver, and W. Reik, Evolution and Functions of Long Noncoding RNAs, Cell, vol.136, pp.629-641, 2009.

A. Porro, S. Feuerhahn, P. Reichenbach, and J. Lingner, Molecular Dissection of Telomeric Repeat-Containing RNA Biogenesis Unveils the Presence of Distinct and Multiple Regulatory Pathways, Molecular and Cellular Biology, vol.30, pp.4808-4817, 2010.

M. Portoso, R. Ragazzini, ?. Bren?i?, A. Moiani, A. Michaud et al., PRC2 is dispensable for HOTAIR-mediated transcriptional repression, EMBO J, vol.36, pp.981-994, 2017.

A. Postepska-igielska, A. Giwojna, L. Gasri-plotnitsky, N. Schmitt, A. Dold et al., LncRNA Khps1 Regulates Expression of the Proto-oncogene SPHK1 via Triplex-Mediated Changes in Chromatin Structure, Molecular Cell, vol.60, pp.626-636, 2015.

P. Preker, J. Nielsen, S. Kammler, S. Lykke-andersen, M. S. Christensen et al., RNA Exosome Depletion Reveals Transcription Upstream of Active Human Promoters, Science, vol.322, pp.1851-1854, 2008.

P. Preker, K. Almvig, M. S. Christensen, E. Valen, C. K. Mapendano et al., PROMoter uPstream Transcripts share characteristics with mRNAs and are produced upstream of all three major types of mammalian promoters, Nucleic Acids Research, vol.39, pp.7179-7193, 2011.

J. R. Prensner, M. K. Iyer, O. A. Balbin, S. M. Dhanasekaran, Q. Cao et al., , 2011.

, Transcriptome sequencing across a prostate cancer cohort identifies PCAT-1, an unannotated lincRNA implicated in disease progression, Nature Biotechnology, vol.29, pp.742-749

J. Qiu, Y. Lin, L. Ye, J. Ding, W. Feng et al., Overexpression of long non-coding RNA HOTAIR predicts poor patient prognosis and promotes tumor metastasis in epithelial ovarian cancer, Gynecol. Oncol, vol.134, pp.121-128, 2014.

X. Qu, S. Alsager, Y. Zhuo, and B. Shan, HOX transcript antisense RNA (HOTAIR) in cancer, Cancer Lett, vol.454, pp.90-97, 2019.

D. Quénet and Y. Dalal, A long non-coding RNA is required for targeting centromeric protein A to the human centromere, 2014.

J. J. Quinn, C. , and H. Y. , Unique features of long non-coding RNA biogenesis and function, Nat. Rev. Genet, vol.17, pp.47-62, 2016.

O. Rackham, A. J. Shearwood, T. R. Mercer, S. M. Davies, J. S. Mattick et al., Long noncoding RNAs are generated from the mitochondrial genome and regulated by nuclear-encoded proteins, RNA, vol.17, pp.2085-2093, 2011.

C. M. Rands, S. Meader, C. P. Ponting, and G. Lunter, 8.2% of the Human Genome Is Constrained: Variation in Rates of Turnover across Functional Element Classes in the Human Lineage, PLoS Genetics, vol.10, 2014.

E. Raveh, I. J. Matouk, M. Gilon, and A. Hochberg, The H19 Long noncoding RNA in cancer initiation, progression and metastasis -a proposed unifying theory, Mol. Cancer, vol.14, p.184, 2015.

E. J. Richards, G. Zhang, Z. Li, J. Permuth-wey, S. Challa et al., Long non-coding RNAs (LncRNA) regulated by transforming growth factor (TGF) ?: LncRNA-hit-mediated TGF?induced epithelial to mesenchymal transition in mammary epithelia, J. Biol. Chem, vol.290, pp.6857-6867, 2015.

J. L. Rinn, M. Kertesz, J. K. Wang, S. L. Squazzo, X. Xu et al., Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs, Cell, vol.129, pp.1311-1323, 2007.

E. Rodriguez-boulan and I. G. Macara, Organization and execution of the epithelial polarity programme, Nat. Rev. Mol. Cell Biol, vol.15, pp.225-242, 2014.

S. Ro?i?, F. Köhler, and S. Erhardt, Repetitive centromeric satellite RNA is essential for kinetochore formation and cell division, The Journal of Cell Biology, vol.207, pp.335-349, 2014.

M. Roth, Z. Wang, C. , and W. Y. , SIRT1 and LSD1 competitively regulate KU70 functions in DNA repair and mutation acquisition in cancer cells, Oncotarget, vol.7, pp.50195-50214, 2016.

J. Ruiz-orera, X. Messeguer, J. A. Subirana, A. , and M. M. , Long noncoding RNAs as a source of new peptides, 2014.

M. Ruscetti, B. Quach, E. L. Dadashian, D. J. Mulholland, and H. Wu, Tracking and Functional Characterization of Epithelial-Mesenchymal Transition and Mesenchymal Tumor Cells during Prostate Cancer Metastasis, Cancer Res, vol.75, pp.2749-2759, 2015.

A. Rybak-wolf, C. Stottmeister, P. Gla?ar, M. Jens, N. Pino et al., Circular RNAs in the Mammalian Brain Are Highly Abundant, Conserved, and Dynamically Expressed, Molecular Cell, vol.58, pp.870-885, 2015.

M. Saeinasab, A. R. Bahrami, J. González, F. P. Marchese, D. Martinez et al., SNHG15 is a bifunctional MYC-regulated noncoding locus encoding a lncRNA that promotes cell proliferation, invasion and drug resistance in colorectal cancer by interacting with AIF, J. Exp. Clin. Cancer Res, vol.38, p.172, 2019.

V. Saint-andré, E. Batsché, C. Rachez, and C. Muchardt, Histone H3 lysine 9 trimethylation and HP1? favor inclusion of alternative exons, Nat. Struct. Mol. Biol, vol.18, pp.337-344, 2011.

W. A. Sakr, R. J. Zarbo, J. R. Jacobs, and J. D. Crissman, Distribution of basement membrane in squamous cell carcinoma of the head and neck, Human Pathology, vol.18, pp.1043-1050, 1987.

N. E. Sanjana, J. Wright, K. Zheng, O. Shalem, P. Fontanillas et al., High-resolution interrogation of functional elements in the noncoding genome, Science, vol.353, pp.1545-1549, 2016.

P. G. Santamaría, G. Moreno-bueno, and A. Cano, Contribution of Epithelial Plasticity to Therapy Resistance, J Clin Med, vol.8, 2019.

P. Scaruffi, S. Stigliani, S. Moretti, S. Coco, C. De-vecchi et al., Transcribed-ultra conserved region expression is associated with outcome in high-risk neuroblastoma, BMC Cancer, vol.9, 2009.

T. Schenk, W. C. Chen, S. Göllner, L. Howell, L. Jin et al., Inhibition of the LSD1 (KDM1A) demethylase reactivates the all-trans-retinoic acid differentiation pathway in acute myeloid leukemia, Nat. Med, vol.18, pp.605-611, 2012.

A. Scoumanne, C. , and X. , The lysine-specific demethylase 1 is required for cell proliferation in both p53-dependent and -independent manners, J. Biol. Chem, vol.282, pp.15471-15475, 2007.

B. S. Scruggs, D. A. Gilchrist, S. Nechaev, G. W. Muse, A. Burkholder et al., Bidirectional Transcription Arises from Two Distinct Hubs of Transcription Factor Binding and Active Chromatin, Molecular Cell, vol.58, pp.1101-1112, 2015.

A. Sehrawat, L. Gao, Y. Wang, A. Bankhead, S. K. Mcweeney et al., LSD1 activates a lethal prostate cancer gene network independently of its demethylase function, Proceedings of the National Academy of Sciences, vol.115, pp.4179-4188, 2018.

A. C. Seila, J. M. Calabrese, S. S. Levine, G. W. Yeo, P. B. Rahl et al., Divergent Transcription from Active Promoters, Science, vol.322, pp.1849-1851, 2008.

S. Sengupta, G. , and R. E. , Super-enhancer-driven Transcriptional Dependencies in Cancer, Trends Cancer, vol.3, pp.269-281, 2017.

A. Shahryari, M. S. Jazi, N. M. Samaei, and S. J. Mowla, Long non-coding RNA SOX2OT: expression signature, splicing patterns, and emerging roles in pluripotency and tumorigenesis, Frontiers in Genetics, vol.6, 2015.

S. Shi, L. Wang, B. Yu, Y. Li, Y. Jin et al., LncRNA-ATB promotes trastuzumab resistance and invasion-metastasis cascade in breast cancer, Oncotarget, vol.6, pp.11652-11663, 2015.

Y. Shi, F. Lan, C. Matson, P. Mulligan, J. R. Whetstine et al., Histone demethylation mediated by the nuclear amine oxidase homolog LSD1, Cell, vol.119, pp.941-953, 2004.

M. Shimojo, H. , and L. B. , Characterization of the REST/NRSFinteracting LIM domain protein (RILP): localization and interaction with REST/NRSF, Journal of Neurochemistry, vol.96, pp.1130-1138, 2006.

C. J. Shukla, A. L. Mccorkindale, C. Gerhardinger, K. D. Korthauer, M. N. Cabili et al., High-throughput identification of RNA nuclear enrichment sequences, EMBO J, vol.37, 2018.

A. A. Sigova, A. C. Mullen, B. Molinie, S. Gupta, D. A. Orlando et al., Divergent transcription of long noncoding RNA/mRNA gene pairs in embryonic stem cells, Proceedings of the National Academy of Sciences, vol.110, pp.2876-2881, 2013.

D. K. Singh and K. V. Prasanth, Functional insights into the role of nuclearretained long noncoding RNAs in gene expression control in mammalian cells, Chromosome Research, vol.21, pp.695-711, 2013.

N. Skrypek, S. Goossens, E. De-smedt, N. Vandamme, and G. Berx, , 2017.

, Epithelial-to-Mesenchymal Transition: Epigenetic Reprogramming Driving Cellular Plasticity, Trends Genet, vol.33, pp.943-959

S. Somarowthu, M. Legiewicz, I. Chillón, M. Marcia, F. Liu et al., , 2015.

, HOTAIR Forms an Intricate and Modular Secondary Structure, Molecular Cell, vol.58, pp.353-361

X. Song, X. Wang, S. Arai, and R. Kurokawa, Promoter-Associated Noncoding RNA from the CCND1 Promoter, pp.609-622, 2012.

Y. Song, R. Wang, L. Li, X. Liu, Y. Wang et al., Long non-coding RNA HOTAIR mediates the switching of histone H3 lysine 27 acetylation to methylation to promote epithelial-to-mesenchymal transition in gastric cancer, Int. J. Oncol, vol.54, pp.77-86, 2019.

C. F. Spurlock, J. T. Tossberg, Y. Guo, S. P. Collier, P. S. Crooke et al., Expression and functions of long noncoding RNAs during human T helper cell differentiation, Nature Communications, vol.6, p.6932, 2015.

G. St-laurent, D. Shtokalo, M. R. Tackett, Z. Yang, T. Eremina et al., , 2012.

, Intronic RNAs constitute the major fraction of the non-coding RNA in mammalian cells, BMC Genomics, vol.13, p.504

G. St-laurent, D. Shtokalo, B. Dong, M. R. Tackett, X. Fan et al., VlincRNAs controlled by retroviral elements are a hallmark of pluripotency and cancer, Genome Biology, vol.14, p.73, 2013.

W. Su, H. Xiong, and J. Fang, Natural antisense transcripts regulate gene expression in an epigenetic manner, Biochemical and Biophysical Research Communications, vol.396, pp.177-181, 2010.

Y. Sun and L. Ma, New Insights into Long Non-Coding RNA MALAT1 in Cancer and Metastasis, Cancers, vol.11, p.216, 2019.

M. Sun, F. Nie, Y. Wang, Z. Zhang, J. Hou et al., LncRNA HOXA11-AS Promotes Proliferation and Invasion of Gastric Cancer by Scaffolding the Chromatin Modification Factors PRC2, LSD1, and DNMT1, Cancer Res, vol.76, pp.6299-6310, 2016.

Q. Sun, Q. Hao, and K. V. Prasanth, Nuclear Long Noncoding RNAs: Key Regulators of Gene Expression, Trends Genet, vol.34, pp.142-157, 2018.

X. Sun, Y. Bai, C. Yang, S. Hu, Z. Hou et al., Long noncoding RNA SNHG15 enhances the development of colorectal carcinoma via functioning as a ceRNA through miR-141/SIRT1/Wnt/?-catenin axis, Artif Cells Nanomed Biotechnol, vol.47, pp.2536-2544, 2019.

M. W. Szcze?niak and I. Maka?owska, lncRNA-RNA Interactions across the Human Transcriptome, PLOS ONE, vol.11, 2016.

Y. Tay, J. Rinn, and P. P. Pandolfi, The multilayered complexity of ceRNA crosstalk and competition, Nature, vol.505, pp.344-352, 2014.

M. Terashima, S. Tange, A. Ishimura, and T. Suzuki, MEG3 Long Noncoding RNA Contributes to the Epigenetic Regulation of Epithelial-Mesenchymal Transition in Lung Cancer Cell Lines, J. Biol. Chem, vol.292, pp.82-99, 2017.

F. The and . Consortium, The Transcriptional Landscape of the Mammalian Genome, Science, vol.309, pp.1559-1563, 2005.

J. P. Thiery, Epithelial-mesenchymal transitions in tumour progression, Nat. Rev. Cancer, vol.2, pp.442-454, 2002.

D. W. Thomson and M. E. Dinger, Endogenous microRNA sponges: evidence and controversy, Nature Reviews Genetics, vol.17, pp.272-283, 2016.

J. Tong, X. Ma, H. Yu, Y. , and J. , SNHG15: a promising cancer-related long noncoding RNA, Cancer Manag Res, vol.11, pp.5961-5969, 2019.

O. Tornavaca, M. Chia, N. Dufton, L. O. Almagro, D. E. Conway et al., ZO-1 controls endothelial adherens junctions, cell-cell tension, angiogenesis, and barrier formation, The Journal of Cell Biology, vol.208, pp.821-838, 2015.

I. Trofimova, D. Chervyakova, and A. Krasikova, Transcription of subtelomere tandemly repetitive DNA in chicken embryogenesis, Chromosome Research, vol.23, pp.495-503, 2015.

M. Tsai, O. Manor, Y. Wan, N. Mosammaparast, J. K. Wang et al., Long Noncoding RNA as Modular Scaffold of Histone Modification Complexes, Science, vol.329, pp.689-693, 2010.

M. Tsai, R. C. Spitale, C. , and H. Y. , Long intergenic noncoding RNAs: new links in cancer progression, Cancer Res, vol.71, pp.3-7, 2011.

Y. Tseng, B. S. Moriarity, W. Gong, R. Akiyama, A. Tiwari et al., PVT1 dependence in cancer with MYC copy-number increase, Nature, vol.512, pp.82-86, 2014.

M. Uesaka, O. Nishimura, Y. Go, K. Nakashima, K. Agata et al., Bidirectional promoters are the major source of gene activation-associated non-coding RNAs in mammals, BMC Genomics, vol.15, p.35, 2014.

I. Ulitsky, A. Shkumatava, C. H. Jan, H. Sive, and D. P. Bartel, Conserved Function of lincRNAs in Vertebrate Embryonic Development despite Rapid Sequence Evolution, Cell, vol.147, pp.1537-1550, 2011.

C. Vannier, K. Mock, T. Brabletz, and W. Driever, Zeb1 regulates Ecadherin and Epcam (epithelial cell adhesion molecule) expression to control cell behavior in early zebrafish development, J. Biol. Chem, vol.288, pp.18643-18659, 2013.

J. C. Venter, The Sequence of the Human Genome, Science, vol.291, pp.1304-1351, 2001.
URL : https://hal.archives-ouvertes.fr/hal-00465088

S. Vidaurre, C. Fitzpatrick, V. A. Burzio, M. Briones, C. Villota et al., Downregulation of the Antisense Mitochondrial Non-coding RNAs (ncRNAs) Is a Unique Vulnerability of Cancer Cells and a Potential Target for Cancer Therapy, Journal of Biological Chemistry, vol.289, pp.27182-27198, 2014.

P. Volders, J. Anckaert, K. Verheggen, J. Nuytens, L. Martens et al., LNCipedia 5: towards a reference set of human long non-coding RNAs, Nucleic Acids Res, vol.47, pp.135-139, 2019.

J. Wang, K. Scully, X. Zhu, L. Cai, J. Zhang et al., Opposing LSD1 complexes function in developmental gene activation and repression programmes, Nature, vol.446, pp.882-887, 2007.

L. Wang, H. J. Park, S. Dasari, S. Wang, J. Kocher et al., CPAT: Coding-Potential Assessment Tool using an alignment-free logistic regression model, Nucleic Acids Res, vol.41, p.74, 2013.

P. Wang, Y. Xue, Y. Han, L. Lin, C. Wu et al., The STAT3-Binding Long Noncoding RNA lnc-DC Controls Human Dendritic Cell Differentiation, Science, vol.344, pp.310-313, 2014.

X. Wang, S. Arai, X. Song, D. Reichart, K. Du et al., Induced ncRNAs allosterically modify RNA-binding proteins in cis to inhibit transcription, Nature, vol.454, pp.126-130, 2008.

Y. Wang, W. Devereux, P. M. Woster, T. M. Stewart, A. Hacker et al., Cloning and characterization of a human polyamine oxidase that is inducible by polyamine analogue exposure, Cancer Res, vol.61, pp.5370-5373, 2001.

Y. Wang, H. Zhang, Y. Chen, Y. Sun, F. Yang et al., LSD1 Is a Subunit of the NuRD Complex and Targets the Metastasis Programs in Breast Cancer, Cell, vol.138, pp.660-672, 2009.

M. Ward, C. Mcewan, J. D. Mills, J. , and M. , Conservation and tissuespecific transcription patterns of long noncoding RNAs, Journal of Human Transcriptome, vol.1, pp.2-9, 2015.

S. Washietl, M. Kellis, and M. Garber, Evolutionary dynamics and tissue specificity of human long noncoding RNAs in six mammals, Genome Research, vol.24, pp.616-628, 2014.

M. Wassenegger, S. Heimes, L. Riedel, and H. L. Sänger, RNA-directed de novo methylation of genomic sequences in plants, Cell, vol.76, pp.567-576, 1994.

R. Waterston and J. Sulston, The genome of Caenorhabditis elegans, Proc. Natl. Acad. Sci. U.S.A, vol.92, pp.10836-10840, 1995.

K. M. Watters, K. Bryan, N. H. Foley, M. Meehan, and R. L. Stallings, Expressional alterations in functional ultra-conserved non-coding rnas in response to all-transretinoic acid -induced differentiation in neuroblastoma cells, BMC Cancer, vol.13, 2013.

W. Wei, V. Pelechano, A. I. Järvelin, and L. M. Steinmetz, Functional consequences of bidirectional promoters, Trends in Genetics, vol.27, pp.267-276, 2011.

R. A. Weinberg and S. Penman, Small molecular weight monodisperse nuclear RNA, Journal of Molecular Biology, vol.38, pp.289-304, 1968.

A. Werner, Biological functions of natural antisense transcripts, BMC Biology, vol.11, p.31, 2013.

M. S. Werner and A. J. Ruthenburg, Nuclear Fractionation Reveals Thousands of Chromatin-Tethered Noncoding RNAs Adjacent to Active Genes, Cell Reports, vol.12, pp.1089-1098, 2015.

M. S. Werner, M. A. Sullivan, R. N. Shah, R. D. Nadadur, A. T. Grzybowski et al., Chromatin-enriched lncRNAs can act as cell-type specific activators of proximal gene transcription, Nat. Struct. Mol. Biol, vol.24, pp.596-603, 2017.

M. Wery, M. Descrimes, N. Vogt, A. Dallongeville, D. Gautheret et al., Nonsense-Mediated Decay Restricts LncRNA Levels in Yeast Unless Blocked by Double-Stranded RNA Structure, Molecular Cell, vol.61, pp.379-392, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01311517

M. Wery, C. Gautier, M. Descrimes, M. Yoda, V. Migeot et al., Bases of antisense lncRNA-associated regulation of gene expression in fission yeast, PLoS Genet, vol.14, p.1007465, 2018.
URL : https://hal.archives-ouvertes.fr/hal-02349807

M. Wery, C. Gautier, M. Descrimes, M. Yoda, H. Vennin-rendos et al., Native elongating transcript sequencing reveals global anti-correlation between sense and antisense nascent transcription in fission yeast, RNA, vol.24, pp.196-208, 2018.
URL : https://hal.archives-ouvertes.fr/hal-02349817

W. A. Whyte, S. Bilodeau, D. A. Orlando, H. A. Hoke, G. M. Frampton et al., Enhancer decommissioning by LSD1 during embryonic stem cell differentiation, Nature, 2012.

B. Wightman, I. Ha, and G. Ruvkun, Posttranscriptional regulation of the heterochronic gene lin-14 by lin-4 mediates temporal pattern formation in C. elegans, Cell, vol.75, pp.855-862, 1993.

A. T. Willingham and T. R. Gingeras, TUF Love for "Junk, DNA. Cell, vol.125, pp.1215-1220, 2006.

J. E. Wilusz, S. M. Freier, and D. L. Spector, 3? End Processing of a Long Nuclear-Retained Noncoding RNA Yields a tRNA-like Cytoplasmic RNA, Cell, vol.135, pp.919-932, 2008.

J. E. Wilusz, C. K. Jnbaptiste, L. Y. Lu, C. Kuhn, L. Joshua-tor et al., A triple helix stabilizes the 3' ends of long noncoding RNAs that lack poly(A) tails, Genes & Development, vol.26, pp.2392-2407, 2012.

M. Wissmann, N. Yin, J. M. Müller, H. Greschik, B. D. Fodor et al., Cooperative demethylation by JMJD2C and LSD1 promotes androgen receptor-dependent gene expression, Nat. Cell Biol, vol.9, pp.347-353, 2007.

L. H. Wong, K. H. Brettingham-moore, L. Chan, J. M. Quach, M. A. Anderson et al., , 2007.

, Centromere RNA is a key component for the assembly of nucleoproteins at the nucleolus and centromere, Genome Research, vol.17, pp.1146-1160

E. J. Wood, K. Chin-inmanu, H. Jia, and L. Lipovich, Sense-antisense gene pairs: sequence, transcription, and structure are not conserved between human and mouse, Frontiers in Genetics, vol.4, 2013.

C. Wu, Y. Wang, B. Jin, H. Chen, B. Xie et al., Senescenceassociated Long Non-coding RNA ( SALNR ) Delays Oncogene-induced Senescence through NF90 Regulation, Journal of Biological Chemistry, vol.290, pp.30175-30192, 2015.

D. Wu, D. M. Irwin, and Y. Zhang, De Novo Origin of Human Protein-Coding Genes, PLoS Genetics, vol.7, p.1002379, 2011.

L. Wu, P. Murat, D. Matak-vinkovic, A. Murrell, and S. Balasubramanian, Binding Interactions between Long Noncoding RNA HOTAIR and PRC2 Proteins, Biochemistry, vol.52, pp.9519-9527, 2013.

G. Xu, L. Meng, D. Yuan, K. Li, Y. Zhang et al., , 2018.

, MEG3/miR-21 axis affects cell mobility by suppressing epithelial-mesenchymal transition in gastric cancer, Oncology Reports, vol.40, pp.39-48

Z. Xu, W. Wei, J. Gagneur, F. Perocchi, S. Clauder-münster et al., Bidirectional promoters generate pervasive transcription in yeast, Nature, vol.457, pp.1033-1037, 2009.

Z. Xu, Q. Yu, Y. Du, L. Yang, R. Dong et al., Knockdown of Long Non-coding RNA HOTAIR Suppresses Tumor Invasion and Reverses Epithelial-mesenchymal Transition in Gastric Cancer, International Journal of Biological Sciences, vol.9, pp.587-597, 2013.

X. Xue, Y. A. Yang, A. Zhang, K. Fong, J. Kim et al., LncRNA HOTAIR enhances ER signaling and confers tamoxifen resistance in breast cancer, Oncogene, vol.35, pp.2746-2755, 2016.

L. Yang, M. O. Duff, B. R. Graveley, G. G. Carmichael, C. et al., , 2011.

, Genomewide characterization of non-polyadenylated RNAs, Genome Biology, vol.12, p.16

Y. Yang, X. Wang, Y. Zhang, and W. Yuan, The histone demethylase LSD1 promotes renal inflammation by mediating TLR4 signaling in hepatitis B virus-associated glomerulonephritis, Cell Death & Disease, vol.10, p.278, 2019.

H. Yao, K. Brick, Y. Evrard, T. Xiao, R. D. Camerini-otero et al., Mediation of CTCF transcriptional insulation by DEAD-box RNA-binding protein p68 and steroid receptor RNA activator SRA, Genes & Development, vol.24, pp.2543-2555, 2010.

X. Ye and R. A. Weinberg, Epithelial-Mesenchymal Plasticity: A Central Regulator of Cancer Progression, Trends Cell Biol, vol.25, pp.675-686, 2015.

K. Ye, S. Wang, H. Zhang, H. Han, B. Ma et al., Long Noncoding RNA GAS5 Suppresses Cell Growth and Epithelial-Mesenchymal Transition in Osteosarcoma by Regulating the miR-221/ARHI Pathway, J. Cell. Biochem, vol.118, pp.4772-4781, 2017.

Q. Yin, L. Yang, Y. Zhang, J. Xiang, Y. Wu et al., Long Noncoding RNAs with snoRNA Ends, Molecular Cell, vol.48, pp.219-230, 2012.

L. Ying, Q. Chen, Y. Wang, Z. Zhou, Y. Huang et al., Upregulated MALAT-1 contributes to bladder cancer cell migration by inducing epithelial-tomesenchymal transition, Mol Biosyst, vol.8, pp.2289-2294, 2012.

J. Yoon, K. Abdelmohsen, J. Kim, X. Yang, J. L. Martindale et al., Scaffold function of long non-coding RNA HOTAIR in protein ubiquitination, Nature Communications, vol.4, 2013.

R. S. Young and C. P. Ponting, Identification and function of long noncoding RNAs, Essays In Biochemistry, vol.54, pp.113-126, 2013.

C. Yuan, J. Wang, A. P. Harrison, X. Meng, D. Chen et al., , 2015.

, Genome-wide view of natural antisense transcripts in Arabidopsis thaliana, DNA Research, vol.22, pp.233-243

F. Yue, Y. Cheng, A. Breschi, J. Vierstra, W. Wu et al., A comparative encyclopedia of DNA elements in the mouse genome, Nature, vol.515, pp.355-364, 2014.

C. Zang, D. E. Schones, C. Zeng, K. Cui, K. Zhao et al., A clustering approach for identification of enriched domains from histone modification ChIP-Seq data, Bioinformatics, vol.25, pp.1952-1958, 2009.

A. Zaravinos, The Regulatory Role of MicroRNAs in EMT and Cancer, J Oncol, p.865816, 2015.

M. Zeisberg and E. G. Neilson, Biomarkers for epithelial-mesenchymal transitions, J. Clin. Invest, vol.119, pp.1429-1437, 2009.

X. Zeng, M. P. Jedrychowski, Y. Chen, S. Serag, G. G. Lavery et al., Lysine-specific demethylase 1 promotes brown adipose tissue thermogenesis via repressing glucocorticoid activation, Genes Dev, vol.30, pp.1822-1836, 2016.

A. Zhang, J. C. Zhao, J. Kim, K. Fong, Y. A. Yang et al., LncRNA HOTAIR Enhances the Androgen-Receptor-Mediated Transcriptional Program and Drives Castration-Resistant Prostate Cancer, Cell Rep, vol.13, pp.209-221, 2015.

B. Zhang, L. Gunawardane, F. Niazi, F. Jahanbani, X. Chen et al.,

, A Novel RNA Motif Mediates the Strict Nuclear Localization of a Long Noncoding RNA, Molecular and Cellular Biology, vol.34, pp.2318-2329

L. Zhang, J. Carnesecchi, C. Cerutti, V. Tribollet, S. Périan et al., LSD1-ERR? complex requires NRF1 to positively regulate transcription and cell invasion, 2018.

X. Zhang, M. H. Hamblin, and K. Yin, The long noncoding RNA Malat1: Its physiological and pathophysiological functions, RNA Biol, vol.14, pp.1705-1714, 2017.

X. Zhang, W. Feng, J. Zhang, L. Ge, Y. Zhang et al., Long non-coding RNA PVT1 promotes epithelial-mesenchymal transition via the TGF-?/Smad pathway in pancreatic cancer cells, Oncol. Rep, vol.40, pp.1093-1102, 2018.

Y. Zhang, X. Zhang, T. Chen, J. Xiang, Q. Yin et al., Circular Intronic Long Noncoding RNAs, Molecular Cell, vol.51, pp.792-806, 2013.

W. Zhao, Y. An, Y. Liang, and X. Xie, Role of HOTAIR long noncoding RNA in metastatic progression of lung cancer, Eur Rev Med Pharmacol Sci, vol.18, pp.1930-1936, 2014.

D. Zheng, A. Frankish, R. Baertsch, P. Kapranov, A. Reymond et al., Pseudogenes in the ENCODE regions: Consensus annotation, 2007.

, Genome Research, vol.17, pp.839-851

R. Zheng, Z. Shen, V. Tripathi, Z. Xuan, S. M. Freier et al., Polypurine-repeat-containing RNAs: a novel class of long non-coding RNA in mammalian cells, Journal of Cell Science, vol.123, pp.3734-3744, 2010.

S. Zheng, B. Q. Vuong, B. Vaidyanathan, J. Lin, F. Huang et al., Non-coding RNA Generated following Lariat Debranching Mediates Targeting of AID to DNA, Cell, vol.161, pp.762-773, 2015.

X. Zhuang, Y. Liu, L. , and J. , Overexpression of long noncoding RNA HOXB-AS3 indicates an unfavorable prognosis and promotes tumorigenesis in epithelial ovarian cancer via Wnt/?-catenin signaling pathway, Biosci Rep, vol.39, 2019.

G. Zieve and S. Penman, Small RNA species of the HeLa cell: Metabolism and subcellular localization, Cell, vol.8, pp.19-31, 1976.

S. Zucchelli, F. Fasolo, R. Russo, L. Cimatti, L. Patrucco et al., SINEUPs are modular antisense long non-coding RNAs that increase synthesis of target proteins in cells, Frontiers in Cellular Neuroscience, vol.9, 2015.

M. Zuker, Mfold web server for nucleic acid folding and hybridization prediction, Nucleic Acids Res, vol.31, pp.3406-3415, 2003.

, Résumé en français

, le dogme central de la biologie moléculaire consistait en un flux d'information allant de l'ADN, à l'ARN-messager (ARNm) puis aux protéines, comme déterminants principaux de l'identité cellulaire. Cependant, les nouvelles techniques de séquençage à haut-débit ont révélées que parmi les 3 milliards de bases qui composent le génome humain, seules 2% codent pour des protéines. En revanche, 97% du génome humain sont transcrits en ARN, dont la grande majorité provient ainsi de régions dites « non-codantes » (nc) (Djebali et al, 2000.

, Ces lncARN sont transcrits par l'ARN Polymérase II et subissent une maturation similaire à celle des ARNm puisqu'ils sont généralement coiffés, épissés et poly-adénylés, Ils sont impliqués dans de nombreux processus biologiques, 2011.

, Grace à leur expression hautement spécifique, ces lncARN ont été proposés comme des biomarqueurs de diagnostic et classification (Li et al, 2013) ou même comme des acteurs de la cancérogénèse, 2016.

, Le travail présenté ici se concentre donc sur ces lncARN liés au cancer et plus spécifiquement sur leur association à la transition épithélio-mésenchymateuse (TEM)

, Récemment, le changement strict de l'identité épithéliale à mésenchymateuse a été remis en question et des états hybrides/intermédiaires ont été identifiés, avec notamment des phénotypes variables de caractère « souche », de plasticité cellulaire ou de capacité d'invasion et migration. Ces traits sont particulièrement importants dans le développement tumoral et sont associés à la résistance aux traitements, aux métastase et à la récurrence tumorale, Bien que les gènes codants impliqués dans la TEM aient été caractérisés dans le développement et plus récemment dans le cancer, le rôle des lncARN n'a que très peu été décrit. Il est cependant indéniable puisque dans les cinq dernières années, 2006.

. Durant-ma-thèse, des lncARN dans la régulation de la TEM en identifiant les lncARN différentiellement exprimés entre les cellules épithéliales et mésenchymateuses. J'ai d'abord caractérisé le rôle du lncARN connu HOTAIR dans la TEM (chapitre 4) puis j'ai identifié de nouveaux candidats en définissant ceux qui étaient fonctionnels au travers d'un criblage génétique par CRISPR (chapitre 5). Dans ce but, j'ai utilisé un système HEK-TEM

, qui reposent sur un modèle original provenant de cellules primaires humaines d'épithélium de rein (HEK) et dont ont été tirées une lignée cellulaire épithéliale « Epi » et une lignée mésenchymateuse « Mes

T. Le-rôle-de-hotair-dans-la,

. Avant-mon-arrivée-au-laboratoire and C. Doctorante, Comme première preuve de concept de l'étude de lncARN dans le système HEK-TEM, je me suis concentré sur le rôle de HOTAIR dans la régulation de la TEM, HOTAIR comme étant surexprimé dans les cellules Mes, 2019.

, Il a été montré que HOTAIR recrute des protéines de modifications de la chromatine, pour réprimer l'expression génique, grâce à des domaines structuraux situées à ses extrémités en 5' et 3'. Ces domaines interagissent avec les complexes PRC2 et Lsd1-CoREST-REST, respectivement. Nous avons d'abord défini l'importance de ces deux domaines dans la régulation de la TEM en surexprimant des variants tronqués de HOTAIR dans les cellules Epi