, En effet, mieux comprendre la régulation et la fonction de gènes nouveaux, en particulier des gènes à ARN long non-codants, nécessitent de combiner différentes approches de génomique afin d'aboutir à des hypothèses solides qui seront ensuite à valider expérimentalement
An unstable intermediate carrying information from genes to ribosomes for protein synthesis, Nature, vol.190, pp.576-81, 1961. ,
So much "junk" DNA in our genome, Brookhaven Symp Biol, vol.23, pp.366-70, 1972. ,
Refuge of spandrels, Curr Biol, vol.8, p.669, 1998. ,
Multiple Perspectives on Terminological Variation, 2017. ,
On "genomenclature": a comprehensive (and respectful) taxonomy for pseudogenes and other "junk DNA, Proc Natl Acad Sci USA, vol.89, pp.10706-10716, 1992. ,
Largescale transcriptional activity in chromosomes 21 and 22, Science, vol.296, pp.916-925, 2002. ,
Global identification of human transcribed sequences with genome tiling arrays, Science, vol.306, pp.2242-2248, 2004. ,
Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution, Science, vol.308, pp.1149-54, 2005. ,
, ENCODE Project Consortium. The ENCODE (ENCyclopedia Of DNA Elements) Project. Science, vol.306, pp.636-676, 2004.
The transcriptional landscape of the mammalian genome, Science, vol.309, pp.1559-63, 2005. ,
TUF love for "junk, DNA. Cell, vol.125, pp.1215-1235, 2006. ,
Functionality or transcriptional noise? Evidence for selection within long noncoding RNAs, Genome Res, vol.17, pp.556-65, 2007. ,
RNA Maps Reveal New RNA Classes and a Possible Function for Pervasive Transcription, Science, vol.316, pp.1484-1492, 2007. ,
The long and the short of RNA maps, Bioessays, vol.29, pp.1077-80, 2007. ,
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project, Nature, vol.447, pp.799-816, 2007. ,
Generations of Sequencing Technologies: From First to Next Generation, Biology and Medicine, p.9, 2017. ,
Long noncoding RNAs as enhancers of gene expression, Cold Spring Harb Symp Quant Biol, vol.75, pp.325-356, 2010. ,
Long Noncoding RNAs with Enhancer-like Function in Human Cells, Cell, vol.143, pp.46-58, 2010. ,
The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression, Genome Research, vol.22, pp.1775-89, 2012. ,
URL : https://hal.archives-ouvertes.fr/hal-01205054
The reference human genome annotation for The ENCODE Project, Genome Research, vol.22, pp.1760-74, 2012. ,
Creating reference gene annotation for the mouse C57BL6/J genome assembly, Mamm Genome, vol.26, pp.366-78, 2015. ,
Trends of long noncoding RNA research from 2007 to 2016: a bibliometric analysis, Oncotarget, vol.8, pp.83114-83141, 2017. ,
Long noncoding RNA repertoire in chicken liver and adipose tissue, Genetics Selection Evolution, vol.49, 2017. ,
URL : https://hal.archives-ouvertes.fr/hal-01431420
Livestock genome annotation: transcriptome and chromatin structure profiling in cattle, goat, chicken and pig, bioRxiv, p.316091, 2018. ,
NONCODEV5: a comprehensive annotation database for long non-coding RNAs, Nucleic Acids Res, vol.46, pp.308-322, 2018. ,
ALDB: A Domestic-Animal Long Noncoding RNA Database, PLOS ONE, vol.10, p.124003, 2015. ,
How Muscle Structure and Composition Influence Meat and Flesh Quality, ScientificWorldJournal, p.3182746, 2016. ,
URL : https://hal.archives-ouvertes.fr/hal-01285897
Fat deposition, fatty acid composition and meat quality: A review, Meat Sci, vol.78, pp.343-58, 2008. ,
Intramuscular fat content in meat-producing animals: development, genetic and nutritional control, and identification of putative markers, Animal, vol.4, pp.303-322, 2010. ,
Multi-tissue transcriptomic study reveals the main role of liver in the chicken adaptive response to a switch in dietary energy source through the transcriptional regulation of lipogenesis, BMC Genomics, vol.19, p.187, 2018. ,
URL : https://hal.archives-ouvertes.fr/hal-01727161
Regulation of bile acid, cholesterol, and fatty acid synthesis in chicken primary hepatocytes by different concentrations of T0901317, an agonist of liver X receptors ,
, Comp Biochem Physiol, Part A Mol Integr Physiol, vol.158, pp.201-207, 2011.
Physiological and molecular mechanisms involved in nutritional regulation of fatty acid synthesis, Physiol Rev, vol.75, pp.47-76, 1995. ,
Lipid metabolism in fish, Prog Lipid Res, vol.26, pp.53-85, 1987. ,
Comparative aspects of lipid metabolism: impact on contemporary research and use of animal models, J Nutr, vol.135, pp.2499-502, 2005. ,
Regulation of cholesterol and fatty acid synthesis, Cold Spring Harb Perspect Biol, vol.3, 2011. ,
Cholesterol synthesis in the lactating cow: Induced expression of candidate genes, J Steroid Biochem Mol Biol, vol.115, pp.62-69, 2009. ,
Journal d'agriculture traditionnelle et de botanique appliquée, vol.28, pp.253-261, 1981. ,
Journal d'agriculture traditionnelle et de botanique appliquée, vol.19, pp.613-62, 1939. ,
The impact of third generation genomic technologies on plant genome assembly, Curr Opin Plant Biol, vol.36, pp.64-70, 2017. ,
A molecular timescale for vertebrate evolution, Nature, vol.392, pp.917-937, 1998. ,
Vertebrate genomes compared, Science, vol.297, pp.1283-1288, 2002. ,
Principles of Long Noncoding RNA Evolution Derived from Direct Comparison of Transcriptomes in 17 Species, Cell Reports, vol.11, pp.1110-1132, 2015. ,
Long noncoding RNAs with snoRNA ends, Mol Cell, vol.48, pp.219-249, 2012. ,
On the classification of long non-coding RNAs, RNA Biol, vol.10, pp.925-958, 2013. ,
Gene regulation of mammalian long non-coding RNA, Mol Genet Genomics, vol.293, pp.1-15, 2018. ,
The role of non-coding RNAs in the regulation of stem cells and progenitors in the normal mammary gland and in breast tumors, Front Genet, vol.6, p.72, 2015. ,
The specificity of long noncoding RNA expression, Biochim Biophys Acta, vol.1859, pp.16-22, 2016. ,
Conserved Function of lincRNAs in Vertebrate Embryonic Development despite Rapid Sequence Evolution, Cell, vol.147, pp.1537-50, 2011. ,
The evolution of lncRNA repertoires and expression patterns in tetrapods, Nature, vol.505, pp.635-675, 2014. ,
Unexpected selection to retain high GC content and splicing enhancers within exons of multiexonic lncRNA loci, RNA, vol.21, pp.320-352, 2015. ,
Comparison of splice sites reveals that long noncoding RNAs are evolutionarily well conserved, RNA, vol.21, pp.801-813, 2015. ,
Conservation of the Exon-Intron Structure of Long Intergenic Non-Coding RNA Genes in Eutherian Mammals, Life ,
Long Non-coding RNA Structure and Function: Is There a Link?, Front Physiol, vol.9, p.1201, 2018. ,
Understanding the Genomic Ultraconservations: T-UCRs and Cancer, Int Rev Cell Mol Biol, vol.333, pp.159-72, 2017. ,
A comprehensive review of circRNA: from purification and identification to disease marker potential, PeerJ, vol.6, p.5503, 2018. ,
circRNA biogenesis competes with pre-mRNA splicing, Mol Cell, vol.56, pp.55-66, 2014. ,
, Translation of CircRNAs. Mol Cell, vol.66, pp.9-21, 2017.
Different roles of circular RNAs with protein coding potentials, Biochem Biophys Res Commun, vol.500, pp.907-916, 2018. ,
Circular Intronic Long Noncoding RNAs, Molecular Cell, vol.51, pp.792-806, 2013. ,
X-chromosome inactivation and evolution in marsupials and other mammals, Isozymes Curr Top Biol Med Res, vol.9, pp.201-219, 1983. ,
The Xist RNA Gene Evolved in Eutherians by Pseudogenization of a ProteinCoding Gene, Science, vol.312, pp.1653-1658, 2006. ,
URL : https://hal.archives-ouvertes.fr/hal-00427928
A subset of conserved mammalian long non-coding RNAs are fossils of ancestral protein-coding genes ,
, Genome Biol, vol.18, p.162, 2017.
A dual origin of the Xist gene from a protein-coding gene and a set of transposable elements, PLoS ONE, vol.3, p.2521, 2008. ,
Characterisation and functional predictions of canine long non-coding, RNAs. Sci Rep, vol.8, p.13444, 2018. ,
Exonization of transposed elements: A challenge and opportunity for evolution, Biochimie, vol.93, pp.1928-1962, 2011. ,
Syllogomanie moléculaire : l'ADN non codant enrichit le jeu des possibles. médecine/sciences, vol.30, pp.1177-83, 2014. ,
CircRNA-derived pseudogenes, Cell Res, vol.26, pp.747-50, 2016. ,
CPC: assess the proteincoding potential of transcripts using sequence features and support vector machine, Nucleic Acids Research, vol.35, pp.345-354, 2007. ,
CPC2: a fast and accurate coding potential calculator based on sequence intrinsic features, Nucleic Acids Res, vol.45, pp.12-18, 2017. ,
PhyloCSF: a comparative genomics method to distinguish protein coding and non-coding regions, Bioinformatics, vol.27, pp.275-282, 2011. ,
CPAT: Coding-Potential Assessment Tool using an alignment-free logistic regression model, Nucleic Acids Research, vol.41, pp.74-74, 2013. ,
Utilizing sequence intrinsic composition to classify protein-coding and long non-coding transcripts, Nucleic Acids Research, vol.41, pp.166-166, 2013. ,
PLEK: a tool for predicting long non-coding RNAs and messenger RNAs based on an improved k-mer scheme, BMC bioinformatics, vol.15, p.311, 2014. ,
A tool for Long non-coding RNAs annotation and its application to the dog transcriptome, 2016. ,
COME: a robust coding potential calculation tool for lncRNA identification and characterization based on multiple features, Nucleic Acids Res, vol.45, p.2, 2017. ,
Long noncoding RNAs in lipid metabolism, Curr Opin Lipidol, vol.29, pp.224-256, 2018. ,
Regulatory Domains and Their Mechanisms, Cold Spring Harb Symp Quant Biol, vol.80, pp.45-51, 2015. ,
Infectious long non-coding RNAs, Biochimie, vol.117, pp.37-47, 2015. ,
Long non-coding RNA TUG1 promotes migration and invasion by acting as a ceRNA of miR-335-5p in osteosarcoma cells, Cancer Sci, vol.108, pp.859-67, 2017. ,
The Long and Short Non-coding RNAs in Cancer Biology, 2016. ,
Regulation of neural macroRNAs by the transcriptional repressor REST, RNA, vol.15, pp.85-96, 2009. ,
A vlincRNA participates in senescence maintenance by relieving H2AZ-mediated repression at the INK4 locus, Nat Commun, vol.6, p.5971, 2015. ,
URL : https://hal.archives-ouvertes.fr/hal-01465935
The HUGO Gene Nomenclature Committee (HGNC), Hum Genet, vol.109, pp.678-80, 2001. ,
A uniform system for microRNA annotation, RNA, vol.9, pp.277-286, 2003. ,
Naming "junk": human non-protein coding RNA (ncRNA) gene nomenclature, Hum Genomics, vol.5, pp.90-98, 2011. ,
A short guide to long non-coding RNA gene nomenclature, Hum Genomics, vol.8, p.7, 2014. ,
Discovery and annotation of long noncoding RNAs, Nat Struct Mol Biol, vol.22, pp.5-7, 2015. ,
An update on LNCipedia: a database for annotated human lncRNA sequences, Nucleic Acids Res, pp.174-80, 2015. ,
LNCipedia: a database for annotated human lncRNA transcript sequences and structures, Nucleic Acids Res, pp.246-251, 2013. ,
, RNA Duplex Map in Living Cells Reveals Higher-Order Transcriptome Structure. Cell, vol.165, pp.1267-79, 2016.
Dawn of the in vivo RNA structurome and interactome, Biochem Soc Trans, vol.44, pp.1395-410, 2016. ,
Lingering Questions about Enhancer RNA and Enhancer Transcription-Coupled Genomic Instability, Trends Genet, vol.33, pp.143-54, 2017. ,
The Yin and Yang of R-loop biology, Curr Opin Cell Biol, vol.34, pp.39-45, 2015. ,
Headto-head antisense transcription and R-loop formation promotes transcriptional activation, Proc Natl Acad Sci U S A, vol.112, pp.5785-90, 2015. ,
Triple-helical DNA Pairing Intermediates Formed by recA Protein, J Biol Chem, pp.16898-912, 1990. ,
How Telomeres Solve the End-Protection Problem, Science, vol.326, p.948, 2009. ,
Formation of triple-helical structures by the 3'-end sequences of MALAT1 and MEN? noncoding RNAs, Proc Natl Acad Sci USA, vol.109, pp.19202-19209, 2012. ,
, Nucleic Acids Symposium Series, vol.52, pp.7-8, 2008.
Quadruplex DNA: sequence, topology and structure, Nucleic Acids Res, vol.34, pp.5402-5417, 2006. ,
The novel G-quadruplex-containing long non-coding RNA GSEC antagonizes DHX36 and modulates colon cancer cell migration, Oncogene, vol.36, pp.1191-1200, 2017. ,
Potential G-quadruplexes in the human long noncoding transcriptome, RNA Biol, vol.9, pp.81-87, 2012. ,
Crystal structures of a DNA octaplex with I-motif of G-quartets and its splitting into two quadruplexes suggest a folding mechanism of eight tandem repeats, Nucleic Acids Res, vol.32, pp.2541-2550, 2004. ,
Minor groove RNA triplex in the crystal structure of a ribosomal frameshifting viral pseudoknot, Nat Struct Biol, vol.6, pp.285-92, 1999. ,
Solution structure of an intramolecular DNA triplex linked by hexakis(ethylene glycol) units: d(AGAGAGAA-(EG)6-TTCTCTCT-(EG)6-TCTCTCTT), Biochemistry, vol.37, pp.5810-5819, 1998. ,
Structure of a lefthanded DNA G-quadruplex, Proc Natl Acad Sci USA, vol.112, pp.2729-2762, 2015. ,
URL : https://hal.archives-ouvertes.fr/hal-01140567
Structural basis of G-quadruplex unfolding by the DEAH/RHA helicase DHX36, Nature, vol.558, pp.465-474, 2018. ,
Allain FH-T. Sequence-specific binding of single-stranded RNA: is there a code for recognition?, Nucleic Acids Res, vol.34, pp.4943-59, 2006. ,
Molecular Mechanisms of Long Noncoding RNAs, Molecular Cell, vol.43, pp.904-918, 2011. ,
Long non-coding RNAs in non-small cell lung cancer as biomarkers and therapeutic targets, J Cell Mol Med, vol.18, pp.2425-2461, 2014. ,
Novel classes of non-coding RNAs and cancer, J Transl Med, vol.10, p.103, 2012. ,
The Ever-Evolving Concept of the Gene: The Use of RNA/Protein Experimental Techniques to Understand Genome Functions, Front Mol Biosci, vol.5, p.20, 2018. ,
Paraspeckles: a novel nuclear domain, Curr Biol, vol.12, pp.13-25, 2002. ,
Long noncoding RNAs: functional surprises from the RNA world, Genes Dev, vol.23, pp.1494-504, 2009. ,
Structural analyses of NEAT1 lncRNAs suggest long-range RNA interactions that may contribute to paraspeckle architecture, Nucleic Acids Res, vol.46, pp.3742-52, 2018. ,
An architectural role for a nuclear noncoding RNA: NEAT1 RNA is essential for the structure of paraspeckles, Mol Cell, vol.33, pp.717-743, 2009. ,
Critical role of vimentin phosphorylation at Ser-56 by p21-activated kinase in vimentin cytoskeleton signaling, J Biol Chem, vol.281, pp.34716-34740, 2006. ,
Long Non-Coding RNAs in Neuronal Aging, Noncoding RNA, vol.4, 2018. ,
Regulated expression of the lncRNA TERRA and its impact on telomere biology, Mechanisms of Ageing and Development, vol.167, pp.16-23, 2017. ,
Telomeric repeat-containing RNA structure in living cells, Proc Natl Acad Sci USA, vol.107, pp.14579-84, 2010. ,
The NORAD lncRNA assembles a topoisomerase complex critical for genome stability, Nature, vol.561, pp.132-138, 2018. ,
Xist and the order of silencing, EMBO Rep, vol.8, pp.34-43, 2007. ,
The multidimensional mechanisms of long noncoding RNA function, Genome Biol, vol.18, p.206, 2017. ,
LncRNA MIR100HG promotes cell proliferation in triple-negative breast cancer through triplex formation with p27 loci, Cell Death Dis, vol.9, p.805, 2018. ,
Repression of the human dihydrofolate reductase gene by a non-coding interfering transcript, Nature, vol.445, pp.666-70, 2007. ,
URL : https://hal.archives-ouvertes.fr/hal-00190957
The tissue-specific lncRNA Fendrr is an essential regulator of heart and body wall development in the mouse, Dev Cell, vol.24, pp.206-220, 2013. ,
The long non-coding RNA Fendrr links epigenetic control mechanisms to gene regulatory networks in mammalian embryogenesis, RNA Biol, vol.10, pp.1579-85, 2013. ,
MEG3 long noncoding RNA regulates the TGF-? pathway genes through formation of RNA-DNA triplex structures, Nat Commun, vol.6, p.7743, 2015. ,
LncRNA Khps1 Regulates Expression of the Proto-oncogene SPHK1 via Triplex-Mediated Changes in Chromatin Structure, Mol Cell, vol.60, pp.626-662, 2015. ,
Long noncoding RNA, polycomb, and the ghosts haunting INK4b-ARF-INK4a expression, Cancer Res, vol.71, pp.5365-5374, 2011. ,
Splicing regulation by long noncoding RNAs, Nucleic Acids Res, vol.46, pp.2169-84, 2018. ,
Long noncoding RNA Saf and splicing factor 45 increase soluble Fas and resistance to apoptosis, Oncotarget, vol.7, pp.13810-13836, 2016. ,
A natural antisense transcript regulates Zeb2/Sip1 gene expression during Snail1-induced epithelial-mesenchymal transition, Genes Dev, vol.22, pp.756-69, 2008. ,
The Nuclear-Retained Noncoding RNA MALAT1 Regulates Alternative Splicing by Modulating SR Splicing Factor Phosphorylation, Molecular Cell, vol.39, pp.925-963, 2010. ,
Mutations within the LINC-HELLP non-coding RNA differentially bind ribosomal and RNA splicing complexes and negatively affect trophoblast differentiation, Hum Mol Genet, vol.24, pp.5475-85, 2015. ,
Regulation of primiRNA processing by a long noncoding RNA transcribed from an ultraconserved region, Mol Cell, vol.55, pp.138-185, 2014. ,
Ultraconserved element uc.372 drives hepatic lipid accumulation by suppressing miR-195/miR4668 maturation, Nat Commun, vol.9, p.612, 2018. ,
Long Noncoding RNA EGFR-AS1 Promotes Cell Proliferation by Increasing EGFR mRNA Stability in Gastric Cancer, Cell Physiol Biochem, vol.49, pp.322-356, 2018. ,
Expression of a noncoding RNA is elevated in Alzheimer's disease and drives rapid feedforward regulation of beta-secretase, Nat Med, vol.14, pp.723-753, 2008. ,
A pseudogene long-noncoding-RNA network regulates PTEN transcription and translation in human cells, Nat Struct Mol Biol, vol.20, pp.440-446, 2013. ,
lncRNAs transactivate STAU1-mediated mRNA decay by duplexing with 3' UTRs via Alu elements, Nature, vol.470, pp.284-292, 2011. ,
LncRNA OIP5-AS1/cyrano suppresses GAK expression to control mitosis, Oncotarget, vol.8, pp.49409-49429, 2017. ,
Targeting the Notch-regulated non-coding RNA TUG1 for glioma treatment, Nat Commun, vol.7, 2016. ,
Integrated analysis of long noncoding RNA-associated competing endogenous RNA network in periodontitis, Journal of Periodontal Research, vol.53, pp.495-505, 2018. ,
Long Non-Coding RNA TUG1 Promotes Proliferation and Inhibits Apoptosis of Osteosarcoma Cells by Sponging miR-132-3p and Upregulating SOX4 Expression, Yonsei Med J, vol.59, pp.226-261, 2018. ,
Inhibition of long non-coding RNA TUG1 on gastric cancer cell transference and invasion through regulating and controlling the expression of miR-144/c-Met axis, Asian Pac J Trop Med, vol.9, pp.508-520, 2016. ,
The long noncoding RNA TUG1 regulates blood-tumor barrier permeability by targeting miR-144, Oncotarget, vol.6, pp.19759-79, 2015. ,
TUG1 promotes osteosarcoma tumorigenesis by upregulating EZH2 expression via miR-144-3p, Int J Oncol, vol.51, pp.1115-1138, 2017. ,
Double-negative feedback loop between long non-coding RNA TUG1 and miR-145 promotes epithelial to mesenchymal transition and radioresistance in human bladder cancer cells, FEBS Lett, vol.589, issue.20, pp.3175-81, 2015. ,
LncRNA TUG1 influences papillary thyroid cancer cell proliferation, migration and EMT formation through targeting miR-145, Acta Biochim Biophys Sin (Shanghai), vol.49, pp.588-97, 2017. ,
, Long Noncoding RNA Taurine-Upregulated Gene, vol.1
, Promotes Cell Proliferation and Invasion in Gastric Cancer via Negatively Modulating miRNA-145-5p, Oncol Res, vol.25, pp.789-98, 2017.
LncRNA TUG1 serves an important role in hypoxia-induced myocardial cell injury by regulating the miR ; 145 ; 5p ; Binp3 axis, Mol Med Rep, vol.17, pp.2422-2452, 2018. ,
TUG1 mediates methotrexate resistance in colorectal cancer via miR-186/CPEB2 axis, Biochem Biophys Res Commun, vol.491, pp.552-559, 2017. ,
LncRNA TUG1 sponges miR-204-5p to promote osteoblast differentiation through upregulating Runx2 in aortic valve calcification, Cardiovasc Res, vol.114, pp.168-79, 2018. ,
Long non-coding RNA TUG1 acts as a miR-26a sponge in human glioma cells, Biochem Biophys Res Commun, vol.477, pp.743-751, 2016. ,
Long non-coding RNA TUG1 promotes endometrial cancer development via inhibiting miR-299 and miR-34a-5p, Oncotarget, vol.8, pp.31386-94, 2017. ,
Long non-coding RNA taurine upregulated 1 enhances tumor-induced angiogenesis through inhibiting microRNA-299 in human glioblastoma, Oncogene, vol.36, pp.318-349, 2017. ,
Long non-coding RNA TUG1 promotes cell proliferation and metastasis by negatively regulating miR-300 in gallbladder carcinoma, Biomed Pharmacother, vol.88, pp.863-872, 2017. ,
Targeting long non-coding RNA-TUG1 inhibits tumor growth and angiogenesis in hepatoblastoma, Cell Death Dis, vol.7, p.2278, 2016. ,
Long noncoding RNA TUG1 alleviates extracellular matrix accumulation via mediating microRNA-377 targeting of PPAR? in diabetic nephropathy, Biochem Biophys Res Commun, vol.484, pp.598-604, 2017. ,
MiR-381 inhibits migration and invasion in human gastric carcinoma through downregulatedting SOX4, Oncol Lett, vol.14, pp.3760-3766, 2017. ,
The Lncrna-TUG1/EZH2 Axis Promotes Pancreatic Cancer Cell Proliferation, Migration and EMT Phenotype Formation Through Sponging Mir-382, Cell Physiol Biochem, vol.42, pp.2145-58, 2017. ,
TUG1 promotes lens epithelial cell apoptosis by regulating miR-421/caspase-3 axis in age-related cataract, Exp Cell Res, vol.356, pp.20-27, 2017. ,
Taurine upregulated gene 1 functions as a master regulator to coordinate glycolysis and metastasis in hepatocellular carcinoma, Hepatology, vol.67, pp.188-203, 2018. ,
LncRNA Taurine-Upregulated Gene 1 Promotes Cell Proliferation by Inhibiting MicroRNA-9 in MCF-7 Cells, J Breast Cancer, vol.19, pp.349-57, 2016. ,
LncRNA TUG1 sponges microRNA-9 to promote neurons apoptosis by up-regulated Bcl2l11 under ischemia, Biochem Biophys Res Commun, vol.485, pp.167-73, 2017. ,
Long non-coding RNA TUG1 contributes to tumorigenesis of human osteosarcoma by sponging miR-9-5p and regulating POU2F1 expression, Tumour Biol, vol.37, pp.15031-15072, 2016. ,
Circular RNAs are a large class of animal RNAs with regulatory potency, Nature, vol.495, pp.333-341, 2013. ,
LncRNA Gm2044 highly expresses in spermatocyte and inhibits Utf1 translation by interacting with Utf1 mRNA, Genes Genomics, vol.40, pp.781-788, 2018. ,
LincRNAp21 suppresses target mRNA translation, Mol Cell, vol.47, pp.648-55, 2012. ,
A strategy for probing the function of noncoding RNAs finds a repressor of NFAT, Science, vol.309, pp.1570-1573, 2005. ,
The long noncoding RNA ASNR regulates degradation of Bcl-2 mRNA through its interaction with AUF1, Sci Rep, vol.6, p.32189, 2016. ,
The LINK-A lncRNA interacts with PtdIns(3,4,5)P3 to hyperactivate AKT and confer resistance to AKT inhibitors, Nat Cell Biol, vol.19, pp.238-51, 2017. ,
Many lncRNAs, 5'UTRs, and pseudogenes are translated and some are likely to express functional proteins, Elife, vol.4, p.8890, 2015. ,
A micropeptide encoded by a putative long noncoding RNA regulates muscle performance, Cell, vol.160, pp.595-606, 2015. ,
A peptide encoded by a transcript annotated as long noncoding RNA enhances SERCA activity in muscle, Science, vol.351, pp.271-276, 2016. ,
Long non-coding RNAs as a source of new peptides, Elife, vol.3, p.3523, 2014. ,
A Peptide Encoded by a Putative lncRNA HOXB-AS3 Suppresses Colon Cancer Growth, Mol Cell, vol.68, pp.171-184, 2017. ,
Hidden Peptides Encoded by Putative Noncoding RNAs, Cell Struct Funct, vol.43, pp.75-83, 2018. ,
Protein coding genes as hosts for noncoding RNA expression, Semin Cell Dev Biol, vol.75, pp.3-12, 2018. ,
The landscape of long noncoding RNAs in the human transcriptome, Nature Genetics, vol.47, pp.199-208, 2015. ,
STAR: ultrafast universal RNA-seq aligner, Bioinformatics, vol.29, pp.15-21, 2013. ,
Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation, Nature Biotechnology, vol.28, pp.511-516, 2010. ,
featureCounts: an efficient general purpose program for assigning sequence reads to genomic features, Bioinformatics, vol.30, pp.923-953, 2014. ,
Data-based filtering for replicated highthroughput transcriptome sequencing experiments, Bioinformatics, vol.29, pp.2146-52, 2013. ,
URL : https://hal.archives-ouvertes.fr/hal-00927025
Mechanisms of long noncoding RNA function in development and disease, Cellular and Molecular Life Sciences, vol.73, pp.2491-509, 2016. ,
CAGE (cap analysis of gene expression): a protocol for the detection of promoter and transcriptional networks, Methods Mol Biol, vol.786, pp.181-200, 2012. ,
Sex chromosome dosage compensation: definitely not for everyone, Trends Genet, vol.29, pp.677-83, 2013. ,
Comparison of GENCODE and RefSeq gene annotation and the impact of reference geneset on variant effect prediction, BMC Genomics, vol.16, 2015. ,
A user's guide to the encyclopedia of DNA elements (ENCODE), PLoS Biol, vol.9, p.1001046, 2011. ,
Comparisons of computational methods for differential alternative splicing detection using RNA-seq in plant systems, BMC Bioinformatics, vol.15, p.364, 2014. ,
Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks, Nat Protoc, vol.7, pp.562-78, 2012. ,
Comparison of the transcriptional landscapes between human and mouse tissues, Proc Natl Acad Sci USA, vol.111, pp.17224-17233, 2014. ,
Informatics for RNA Sequencing: A Web Resource for Analysis on the Cloud, PLoS Comput Biol, vol.11, p.1004393, 2015. ,
Accurate inference of isoforms from multiple sample RNA-Seq data, BMC Genomics, vol.16, issue.2, p.15, 2015. ,
Modelling and simulating generic RNA-Seq experiments with the flux simulator, Nucleic Acids Res, vol.40, pp.10073-83, 2012. ,
URL : https://hal.archives-ouvertes.fr/hal-00744755
RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome, BMC Bioinformatics, vol.12, p.323, 2011. ,
The evolutionary landscape of alternative splicing in vertebrate species, Science, vol.338, pp.1587-93, 2012. ,
Evolutionary dynamics of gene and isoform regulation in Mammalian tissues, Science, vol.338, pp.1593-1602, 2012. ,
The evolution of gene expression levels in mammalian organs, Nature, vol.478, pp.343-351, 2011. ,
The UCSC genome browser and associated tools, Brief Bioinform, vol.14, pp.144-61, 2013. ,
Systematic analysis of transcription start sites in avian development, PLoS Biol, vol.15, p.2002887, 2017. ,
Analysis of long noncoding RNA and mRNA using RNA sequencing during the differentiation of intramuscular preadipocytes in chicken, PLoS ONE, vol.12, p.172389, 2017. ,
Annotating long intergenic non-coding RNAs under artificial selection during chicken domestication, BMC Evol Biol, vol.17, p.192, 2017. ,
Fatty acid metabolism and the basis of brown adipose tissue function, Adipocyte, vol.5, pp.98-118, 2016. ,
The loss of adipokine genes in the chicken genome and implications for insulin metabolism, Mol Biol Evol, vol.31, pp.2637-2683, 2014. ,
Adipocyte and adipogenesis, Eur J Cell Biol, vol.92, pp.229-265, 2013. ,
Long non-coding RNA ADNCR suppresses adipogenic differentiation by targeting miR-204, Biochim Biophys Acta, vol.1859, pp.871-82, 2016. ,
Developmental origin of fat: tracking obesity to its source, Cell, vol.131, pp.242-56, 2007. ,
Brown adipose tissue: physiological function and evolutionary significance, Biochem Syst Environ Physiol, vol.185, pp.587-606, 2015. ,
The brown adipocyte differentiation pathway in birds: an evolutionary road not taken, BMC Biol, vol.6, p.17, 2008. ,
Looking on the "brite" side exercise-induced browning of white adipose tissue, Pflugers Arch, 2018. ,
From discovery to function: the expanding roles of long noncoding RNAs in physiology and disease, Endocr Rev, vol.36, pp.25-64, 2015. ,
Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees, Nucleic Acids Res, vol.44, pp.242-245, 2016. ,
Analysis of the human tissue-specific expression by genome-wide integration of transcriptomics and antibody-based proteomics, Mol Cell Proteomics, vol.13, pp.397-406, 2014. ,
Long noncoding RNAs regulate adipogenesis, Proc Natl Acad Sci USA, vol.110, pp.3387-92, 2013. ,
Comparative epigenomic analysis of murine and human adipogenesis, Cell, vol.143, pp.156-69, 2010. ,
A quantitative model of transcriptional regulation reveals the influence of binding location on expression, PLoS Comput Biol, vol.6, p.1000773, 2010. ,
Regulatory networks of non-coding RNAs in brown/beige adipogenesis, Biosci Rep, vol.35, 2015. ,
De Novo Reconstruction of Adipose Tissue Transcriptomes Reveals Long Non-coding RNA Regulators of Brown Adipocyte Development, Cell Metab, vol.21, pp.764-76, 2015. ,
Progress and prospects of long noncoding RNAs in lipid homeostasis, Molecular Metabolism, vol.5, pp.164-70, 2016. ,
Identification of a novel lncRNA in gluteal adipose tissue and evidence for its positive effect on preadipocyte differentiation, Obesity (Silver Spring), vol.22, pp.1781-1786, 2014. ,
Long Non-Coding RNA NEAT1 Associates with SRp40 to Temporally Regulate PPAR?2 Splicing during Adipogenesis in 3T3-L1 Cells, Genes (Basel), vol.5, pp.1050-63, 2014. ,
Long noncoding RNAs in regulating adipogenesis: new RNAs shed lights on obesity, Cell Mol Life Sci, vol.73, pp.2079-87, 2016. ,
RNA-seq identified a super-long intergenic transcript functioning in adipogenesis, RNA Biol, vol.10, pp.991-1001, 2013. ,
The Roles of Long Non-Protein-Coding RNAs in OsteoAdipogenic Lineage Commitment, Int J Mol Sci, vol.18, 2017. ,
MicroRNA let-7 Regulates 3T3-L1 Adipogenesis, Mol Endocrinol, vol.23, pp.925-956, 2009. ,
, Long Noncoding RNA ADINR Regulates Adipogenesis by Transcriptionally Activating C/EBP?. Stem Cell Reports, vol.5, pp.856-65, 2015.
Adiponectin AS lncRNA inhibits adipogenesis by transferring from nucleus to cytoplasm and attenuating Adiponectin mRNA translation, Biochim Biophys Acta, vol.1863, pp.420-452, 2018. ,
Differential lncRNA expression profiles in brown and white adipose tissues, Mol Genet Genomics, vol.290, pp.699-707, 2015. ,
Long Non-Coding RNAs Associated with Metabolic Traits in Human White Adipose Tissue, EBioMedicine, vol.30, pp.248-60, 2018. ,
Long non-coding RNAs expression profile in HepG2 cells reveals the potential role of long non-coding RNAs in the cholesterol metabolism, Chin Med J, vol.128, pp.91-98, 2015. ,
A long noncoding RNA transcriptional regulatory circuit drives thermogenic adipocyte differentiation, Mol Cell, vol.55, pp.372-82, 2014. ,
Zbtb7b engages the long noncoding RNA Blnc1 to drive brown and beige fat development and thermogenesis, Proc Natl Acad Sci, vol.114, pp.7111-7131, 2017. ,
The long noncoding RNA Blnc1 orchestrates homeostatic adipose tissue remodeling to preserve metabolic health. Mol Metab, 2018. ,
Conserved function of the long noncoding RNA Blnc1 in brown adipocyte differentiation, Mol Metab, vol.6, pp.101-111, 2017. ,
The long noncoding RNA GAS5 negatively regulates the adipogenic differentiation of MSCs by modulating the miR-18a/CTGF axis as a ceRNA, Cell Death Dis, vol.9, p.554, 2018. ,
GM13133 is a negative regulator in mouse white adipocytes differentiation and drives the characteristics of brown adipocytes, J Cell Physiol, vol.233, pp.313-337, 2018. ,
LncRNA Gm15290 sponges miR-27b to promote PPAR?-induced fat deposition and contribute to body weight gain in mice, Biochem Biophys Res Commun, vol.493, pp.1168-75, 2017. ,
Long Non-coding RNA H19 Inhibits Adipocyte Differentiation of Bone Marrow Mesenchymal Stem Cells through Epigenetic Modulation of Histone Deacetylases, Sci Rep, vol.6, p.28897, 2016. ,
Long noncoding RNA H19 mediates LCoR to impact the osteogenic and adipogenic differentiation of mBMSCs in mice through sponging miR-188, J Cell Physiol, vol.233, pp.7435-7481, 2018. ,
LincRNA H19 protects from dietary obesity by constraining expression of monoallelic genes in brown fat, Nat Commun, vol.9, p.3622, 2018. ,
Transcriptome profiling in preadipocytes identifies long noncoding RNAs as Sam68 targets, Oncotarget, vol.8, pp.81994-2005, 2017. ,
Effect of lncRNA HOXA11-AS1 on adipocyte differentiation in human adipose-derived stem cells, Biochem Biophys Res Commun, vol.495, pp.1878-84, 2018. ,
Long non-coding RNA HoxA-AS3 interacts with EZH2 to regulate lineage commitment of mesenchymal stem cells, Oncotarget, vol.7, pp.63561-70, 2016. ,
Interrogation of nonconserved human adipose lincRNAs identifies a regulatory role of linc-ADAL in adipocyte metabolism, Sci Transl Med, vol.10, 2018. ,
Dynamic transcriptome changes during adipose tissue energy expenditure reveal critical roles for long noncoding RNA regulators, PLoS Biol, vol.15, p.2002176, 2017. ,
A novel brown adipocyte-enriched long non-coding RNA that is required for brown adipocyte differentiation and sufficient to drive thermogenic gene program in white adipocytes, Biochim Biophys Acta Mol Cell Biol Lipids, vol.1863, pp.409-428, 2018. ,
Long non-coding RNA MEG3 inhibits adipogenesis and promotes osteogenesis of human adipose-derived mesenchymal stem cells via miR-140-5p, Mol Cell Biochem, vol.433, pp.51-60, 2017. ,
Knockdown of lncRNA MIR31HG inhibits adipocyte differentiation of human adipose-derived stem cells via histone modification of FABP4, Sci Rep, vol.7, p.8080, 2017. ,
MicroRNA 140 Promotes Expression of Long Noncoding RNA NEAT1 in Adipogenesis, Mol Cell Biol, vol.36, pp.30-38, 2016. ,
The RBM14/CoAA-interacting, long intergenic non-coding RNA Paral1 regulates adipogenesis and coactivates the nuclear receptor PPAR?, Sci Rep, vol.7, p.14087, 2017. ,
Knockdown of PU.1 AS lncRNA inhibits adipogenesis through enhancing PU.1 mRNA translation, J Cell Biochem, vol.114, pp.2500-2512, 2013. ,
Integrated analysis of long noncoding RNA and mRNA expression profile in children with obesity by microarray analysis, Sci Rep, vol.8, p.8750, 2018. ,
LncRNA expression profiling of BMSCs in osteonecrosis of the femoral head associated with increased adipogenic and decreased osteogenic differentiation, Sci Rep, vol.8, p.9127, 2018. ,
SRA gene knockout protects against diet-induced obesity and improves glucose tolerance, J Biol Chem, vol.289, pp.13000-13009, 2014. ,
Multiple roles for the noncoding RNA SRA in regulation of adipogenesis and insulin sensitivity, PLoS ONE, vol.5, p.14199, 2010. ,
Identification and characterization of long non-coding RNAs in subcutaneous adipose tissue from castrated and intact full-sib pair Huainan male pigs, BMC Genomics, vol.18, p.542, 2017. ,
,
-? feedback loop modulates the adipogenic differentiation process in human adipose tissue-derived mesenchymal stem cells, Stem Cell Research, vol.32, pp.35-42, 2018. ,
The role and possible mechanism of lncRNA U90926 in modulating 3T3-L1 preadipocyte differentiation, Int J Obes, vol.41, pp.299-308, 2017. ,
Connective tissue growth factor regulates adipocyte differentiation of mesenchymal stromal cells and facilitates leukemia bone marrow engraftment, Blood, vol.122, pp.357-66, 2013. ,
Ligand-dependent corepressor (LCoR) represses the transcription factor C/EBP? during early adipocyte differentiation, J Biol Chem, vol.292, pp.18973-87, 2017. ,
Adipocyte SIRT1 controls systemic insulin sensitivity by modulating macrophages in adipose tissue, EMBO Rep, vol.18, pp.645-57, 2017. ,
Transcription factor PU.1 is expressed in white adipose and inhibits adipocyte differentiation, American journal of physiology Cell physiology, vol.295, 2008. ,
Down-Regulation of Type I Runx2 Mediated by Dexamethasone Is Required for 3T3-L1 Adipogenesis, Molecular endocrinology, vol.26, pp.798-808, 2012. ,
miR-155 regulates differentiation of brown and beige adipocytes via a bistable circuit, Nat Commun, vol.4, p.1769, 2013. ,
The Novel Gene CRNDE Encodes a Nuclear Peptide (CRNDEP) Which Is Overexpressed in Highly Proliferating Tissues, PLoS ONE, vol.10, p.127475, 2015. ,
Long Noncoding RNA GAS5 Suppresses 3T3-L1 Cells Adipogenesis Through miR-21a-5p/PTEN Signal Pathway, DNA Cell Biol, 2018. ,
The orphan nuclear receptor chicken ovalbumin upstream promoter-transcription factor II is a critical regulator of adipogenesis, Proc Natl Acad Sci USA, vol.105, pp.2421-2427, 2008. ,
Shortcuts to a functional adipose tissue: The role of small non-coding RNAs, Redox Biol, vol.12, pp.82-102, 2017. ,
Multiple knockout mouse models reveal lincRNAs are required for life and brain development, Elife, vol.2, p.1749, 2013. ,
Steroid Receptor RNA Activator bi-faceted genetic system: Heads or Tails?, Biochimie, vol.93, pp.1973-80, 2011. ,
The role of MAPKs in adipocyte differentiation and obesity, Biochimie, vol.87, pp.51-57, 2005. ,
URL : https://hal.archives-ouvertes.fr/inserm-00000011
SRA regulates adipogenesis by modulating p38/JNK phosphorylation and stimulating insulin receptor gene expression and downstream signaling, PLoS ONE, vol.9, p.95416, 2014. ,
Essai d'estimation directe des différents éléments de la carcasse du poulet en vue d'apprécier son rendement en viande, Ann Zootech, vol.13, pp.355-66, 1964. ,
Selecting broilers for low or high abdominal fat: Initial observations, British Poultry Science, vol.21, pp.107-120, 1980. ,
Selecting broilers for low or high abdominal fat: observations on the hens during the breeding period, Annales de zootechnie, pp.161-170, 1982. ,
URL : https://hal.archives-ouvertes.fr/hal-00888141
The Sequence Alignment/Map format and SAMtools, Bioinformatics, vol.25, pp.2078-2087, 2009. ,
FactoMineR: An R package for multivariate analysis, Journal of Statistical Software, vol.25, pp.1-18, 2008. ,
edgeR: a Bioconductor package for differential expression analysis of digital gene expression data, Bioinformatics, vol.26, pp.139-179, 2010. ,
Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing, Journal of the Royal Statistical Society, vol.57, pp.289-300, 1995. ,
Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources, Nat Protoc, vol.4, pp.44-57, 2009. ,
Ensembl BioMarts: a hub for data retrieval across taxonomic space, Database, pp.30-030, 2011. ,
Haptoglobin, a hemoglobin-binding plasma protein, is present in bony fish and mammals but not in frog and chicken, Proc Natl Acad Sci USA, vol.103, pp.4168-73, 2006. ,
Nuclear localization of aldolase A correlates with cell proliferation, Biochim Biophys Acta, vol.1833, pp.2812-2834, 2013. ,
Transcriptional profiling of liver in riboflavin-deficient chicken embryos explains impaired lipid utilization, energy depletion, massive hemorrhaging, and delayed feathering, BMC Genomics, vol.19, p.177, 2018. ,
FSP27 and PLIN1 interaction promotes the formation of large lipid droplets in human adipocytes, Biochem Biophys Res Commun, vol.432, pp.296-301, 2013. ,
Ferritin Is a Marker of Inflammation rather than Iron Deficiency in Overweight and Obese People, J Obes, 2016. ,
The matricellular protein SPARC/osteonectin as a newly identified factor up-regulated in obesity, J Biol Chem, vol.276, pp.22231-22238, 2001. ,
Insights into autotaxin: how to produce and present a lipid mediator, Nat Rev Mol Cell Biol, vol.12, pp.674-683, 2011. ,
Regulation of rat hepatic ?-amino-?-carboxymuconate-?-semialdehyde decarboxylase, a key enzyme in the tryptophan-NAD pathway, by dietary cholesterol and sterol regulatory element-binding protein-2, Eur J Nutr, vol.53, pp.469-77, 2014. ,
Integrative Genomics Viewer (IGV): highperformance genomics data visualization and exploration, Briefings in Bioinformatics, vol.14, pp.178-92, 2013. ,
The impact of amplification on differential expression analyses by RNA-seq, Sci Rep, vol.6, p.25533, 2016. ,
How to deduplicate PCR, Nat Methods, vol.14, pp.473-479, 2017. ,
Evaluating the necessity of PCR duplicate removal from next-generation sequencing data and a comparison of approaches, BMC Bioinformatics, vol.17, p.239, 2016. ,
The Ensembl Variant Effect Predictor, Genome Biology, vol.17, p.122, 2016. ,
A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff. Fly (Austin), vol.6, pp.80-92, 2012. ,
SIFT: predicting amino acid changes that affect protein function, Nucleic Acids Res, vol.31, pp.3812-3816, 2003. ,
Bidirectional expression of long ncRNA/protein-coding gene pairs in cancer, Brief Funct Genomics, vol.15, pp.167-73, 2016. ,