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, For luciferase assays, cells were cotransfected with CMV-?Gal plasmid. Luciferase activity was normalized to that of ?-galactosidase. Cells were harvested 48 h after transfection. SiRNA sequences are shown in Table S2.E R R ? deletion mut a n t sa sw e l la sE R R E-L u c i f e r a s ep l a s mids have been described elsewhere (55). Detailed materials and methods are provided in SI Materials and Methods. ACKNOWLEDGMENTS. This work was funded by, MDA-MB231 and HEK293T cells were cultured in DMEM supplemented with 10% FCS, 10 U/mL penicillin, and 10 ?g/mL streptomycin

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,

. Carnesecchi,

, Supporting Information Carnesecchi et al

, For proliferation assays, 10 4 siRNAtransfected cells were seeded in 96-well plates. Cell viability was determined 48 h after transfection using CellTiterGlo kit (Promega) under the manufacturer's recommendations. For invasion assays, 5×10 4 cells were suspended in 200 ?L DMEM/2% FCS and seeded on top of matrigel invasion chambers (Corning), SI Materials and Methods Cell Culture and Transfection

, Beads were then added to the extract and incubated for 1 h, washed 5 times with Nonidet P-40 buffer, and finally resuspended in Laemmli buffer for immunoblotting analysis. We analyzed 50 ?g of wholecell lysate as input fraction. For GST pull-down assays, GST-tagged proteins were produced from BL-21 (DE3) bacterial strain, purified on Gluthatione-Agarose beads (Sigma), and quantified by Coomassie staining, Interaction Assays. For coimmunoprecipitation assays, cells were harvested in PBS, and pellets were resuspended in Nonidet P-40 buffer (20 mM Tris, pH 7.5, 150 mM NaCl, 2 mM EDTA, 1% Nonidet P-40) supplemented with protease inhibitor mixture

;. Triton and D. Pmsf, HeLa nuclear extracts or ERR? produced in vitro with rabbit reticulocyte lysate (Promega) were subfraction. For proximity ligation assays, cells cultured on coverslips were fixed with 4% paraformaldehyde (Merck) for 10 min at room temperature, mM EDTA) supplemented with NaCl, vol.2

, Bioscience) according to the recommendations provided by the manufacturer using anti-LSD1 or anti-ERR? antibodies. Samples were Dapi-counterstained. Images were acquired using a Zeiss AxioImager microscope

, For production in insect cells, full-length ERR? (2-422) was cloned into pDEST8 vector containing a C-terminal hexahistidine tag and expressed in Sf9 or Sf21 insect cells using the baculovirus technology. For production in bacteria, full-length ERR? was cloned into pnEAvHX vector containing an N-terminal hexahistidine tag as well as a TrxA fusion moiety and expressed in BL21 Escherichia coli. For purification, harvested cells were resuspended in lysis buffer (20 mM Tris·HCl, pH 8, 400 mM NaCl, 10% glycerol, 2 mM CHAPS, 5 mM imidazole, cOmplete EDTA-free protease inhibitor mixture tablet; Roche Applied Science), sonicated, and centrifuged. The supernatant was loaded on 5 mL HisTrapp FF crude column (GE Healthcare). The protein was eluted at 250 mM imidazole and further purified by SEC on Superdex S200 (16/60 and 10/300, GE Healthcare) column. Purity and homogeneity of the protein were assessed by SDS/PAGE, and complex formation was monitored by native PAGE. For the demethylation assays, bulk histones were incubated with purified LSD1 and/or ERR? and NRF1 in the demethylase activity assay buffer (50 mM Tris, pH8.8, 50 mM KCl, 5 mM MgCl2, 0.5% BSA, 5% glycerol) for 18 h at 30 °C, Vitro Demethylation Assay. In vitro demethylation assays were performed on bulk histones (Sigma-Aldrich), using purified LSD1 (Enzo-Lifesciences; cat. no. BML-SE544) with or without ERR? translated in vitro using the reticulocyte lysate system (Promega) or recombinant ERR? produced as described (56)

, Proteins (25-50 ?g) were resolved on 8-15% SDS/PAGE, blotted onto PVDF membrane (GE-Healthcare), and probed with specific antibodies after saturation. The antibodies (and their dilution) used in this study were as follows: ERR? (GTX108166, Genetex, 1/5,000), Western Blot Analysis. For Western blot analysis, cells were lysed in Nonidet P-40 or RIPA buffer supplemented with Protease Inhibitor Mixture

, Real-time PCR was performed in a 96-well plate using the IQ SYBR Green Supermix (Biorad). Data were quantified by the ??-Ct method and normalized to 36b4 expression

, Illumina. Sequences were aligned on the human genome (hg19, GRCh37 version) using TopHat. Read counts were determined using HT-seq. Differentially expressed genes were identified with DESeq2 R package, using an adjusted P value (padj) < 0.05. Genes showing significantly modified expression in at least one siRNA experiment were gathered together for hierarchical clustering (Cluster 3.0) and heatmap representation (Java TreeView 1.1.6r4). Clustering used the euclidian distance and the average linkage method applied to log twofold changes, RNA Sequencing and Bioinformatic Analysis. RNAs were extracted from two independent replicates from MDA-MB231 cells (transfected with siRNAs) using Qiagen RNA extraction kit. RNA quality was assessed using BioAnalyzer 2100TM (Agilent Technologies), 2000.

C. , Lysates from 5 × 10 6 cells were incubated with 5 ?g of antibody overnight at 4 °C on rotation and then for 1 h with 40 ?L of Dynabead-protein G (Life Technology), We cross-linked 10 × 10 6 cells with 1% formaldehyde and quenched them for 5 min in 0.125 M Glycine

. Carnesecchi,

. Fig and . S1, RT-qPCR results are presented relative to control conditions with bars representing mean ± SEM of three independent experiments performed in triplicate. hsp90 and actin were used as a loading control in Western blots. (C) Cell viability was determined 48 h after transfection with the indicated siRNAs. Data are expressed relative to control-transfected cells. Bars represent mean ± SEM of two independent experiments in triplicate. (D) Expression of the indicated genes after siERR? or siLSD1 transfection analyzed by RT-qPCR and presented relative to control conditions. Bars represent mean ± SEM of three independent experiments performed in triplicate. (E) Cells were transfected with siLSD1 or siERR?, alone or in combination. Expression of the indicated genes was analyzed by RT-qPCR and is presented relative to control conditions. Bars represent mean ± SEM is shown for individual siRNA (siLSD1 or siERR?) relative to combined siRNA (siLSD1 + siERR?). (F) Binding of ERR? on the ERREs of the indicated genes analyzed by ChIP followed by qPCR. Percent enrichment relative to input is shown using antiERR? or IgG as a control. Bindings of ERR? on a proximal (but not distal) element of its own promoter were used as positive and negative controls, respectively. (G) Binding of ERR? on the TSSs of the indicated genes analyzed by ChIP followed by qPCR. Percent enrichment relative to input is shown using anti-ERR? or, Common transcriptional targets of ERR? and LSD1. (A and B) Cells transfected with siRNAs directed against LSD1 (A) or ERR? (B) were analyzed for expression of the indicated genes by RT-qPCR (Left) or Western blots (Right)

. Fig and . S2, Expression of the indicated genes in HEK293T cells after siERR? or siLSD1 treatment analyzed by RT-qPCR and expressed relative to 36b4. Note that all studied genes respond to ERR? and LSD1 in a similar manner in HEK293T and MDAMB231 cells with the exception of LEF1 (not regulated by either factor) and TMEM198, the expression of which was not

*. ,

*. **p-&lt;-0,

. Carnesecchi,

. Fig and . S3, Cells inactivated for LSD1 (siLSD1#1 and #2) or not (siC) were transfected with ERRE-luciferase plasmid together with increasing amounts of ERR?-encoding plasmid. Results were normalized to samples transfected by ERRE-luciferase only. Bars show the mean ± SEM of three independent experiments performed in triplicate. (B) Detection of H3K4me2 and H3K9me2 at the TSSs of the indicated genes analyzed by ChIP. IgG was used as a control. Enrichments are presented relative to total H3 with bars representing mean ± SEM of three independent experiments performed in duplicate. (C) Detection of H3K9me2 at the ERREs of the indicated gene after siRNA-mediated inactivation of ERR? or LSD1. Results are expressed relative to control conditions with bars showing the mean of two independent experiments performed in triplicate, ERR? transcriptional activity depends on LSD1 and controls for ChIP assays. (A)

*. **p-&lt;-0, 005; ns, nonsignificant. Carnesecchi et al

. Fig and . S4, ERR? mutants were detected in Western blot using flagM2 antibody. (B) In vitro demethylation assay with the same representation as Fig. 3A with supplementation by in vitro translated NRF1. (C) Control of the purity of recombinant ERR? (recERR?) used in Fig. 3B. Shown is a Coomassie blue staining of a gel loaded with the indicated amounts of recombinant ERR? or BSA used as a control. (D) Demethylation assay detecting H3K9me2 similar to Fig. 3A (for Left) and Fig. 3B (for Right) with supplementation of tranylcypromine (TCP), an LSD1 inhibitor. (E) Demethylation assay detecting H3K4me2 and H3K9me2, using recombinant LSD1 and ERR? (recHis6x-Trx-ERR?) purified from bacteria. Right shows a Coomassie blue staining of a gel loaded with the indicated amounts of recombinant ERR? and BSA used as a control. (F) Proximity ligation assays using anti-LSD1, Controls for demethylation and interaction assays. (A) Demethylation assay detecting H3K9me2 similar to Fig

. Carnesecchi,

, Significance is shown as P values above the bars. (C)S i m i l a rt oF i g .4 E using cells treated with the indicated siRNAs. (D)S i m i l a rt oF i g .4 B, analyzing the expression of MMP11 and MMP14 after treatment with the indicated siRNA. No variation (relative to control siRNA) was found significant.( E) Binding of ERR? or LSD1 on the indicated MMP1 promoter regions analyzed by ChIP. Percent enrichment is shown relative to input with IgG used as a control. Bars representmean± SEM of three independent experiments performed in duplicate. (F) Detection of H3K4me2 and H3K9me2 on the TSS of MMP1 gene. Conditions and representation are similar to Fig. S3B.(G) Expression of the indicated genes in MDA-MB231 or HEK293T cells determined by RT-qPCR is shown relative to that of the housekeeping gene 36b4, Fig. S5. ERR? and LSD1 induce cell migration in an MMP1-dependent manner. (A) Extended list of enriched GO terms in ERR?-LSD1 common targets. Numbers correspond to the representation in Fig. 4A.-log10(P value) is indicated as enrichment level

*. **p-&lt;-0,

. Scientific-reports-|, , vol.8, p.10041, 2018.

, resulting in transcriptional activation of a set of common target genes. However, how are the LSD1-TF and, in particular LSD1-ERR?, complexes determined to act at TSSs is not understood. Here we show that promoter-bound nuclear respiratory factor 1 (NRF1), but not ERR?, is essential to LSD1 recruitment at the TSSs of positive LSD1-ERR? targets. In contrast to ERR?, NRF1 does of gene expression is achieved by transcription factors (TFs) that bind to promoters and/or to discrete genomic sites (enhancers) located more or less distal, upstream or downstream, from the transcriptional start sites (TSSs) of the genes they regulate 1-3. hese TFs recruit, amongst others, co-activator proteins that modify histone tails. he latter activities are oten exerted at the TSSs of the targeted genes, and eventually lead to the induction of consistent transcriptional programs that regulate distinct physiopathological traits. How are enhancer-promoter dialogs inely regulated and, in particular, what are the determinants at the TSSs that instruct TF-Co-A complexes where to act are unclear. Lysine Speciic Demethylase 1 (LSD1; KDM1A) is an enzyme that demethylates histone and non-histone substrates and exerts dual activities on histone H3 (H3) 4-11. By demethylating mono-and dimethyl Lys4 on histone H3 (H3K4), LSD1 induces transcriptional repression. In contrast, when demethylating mono-and dimethyl H3K9, LSD1 acts as a transcriptional co-activator, promoting the expression of its target genes. LSD1 can be recruited by various TFs at their cognate response element, including in enhancer regions, and can exert its activities at enhancers and/or TSSs 12-16. he Nuclear Respiratory Factor 1 (NRF1) TF has been suggested as a key factor to tether LSD1 to TSSs and, together with LSD1, induces the expression of genes involved in oxidative phosphorylation in white adipose tissue 17,18. However, the relationships of the LSD1-NRF1 complex with upstream bound TFs are not understood. he Estrogen-Related Receptor ? (ERR?) is an orphan member of the nuclear receptor TF family 19 that regulates various physiopathological features, Lysine-speciic demethylase 1 (LSD1) exerts dual efects on histone H3, promoting transcriptional repression via Lys4 (H3K4) demethylation or transcriptional activation through Lys9 (H3K9) demethylation. These activities are often exerted at transcriptional start sites (TSSs) and depend on the type of enhancer-bound transcription factor (TFs) with which LSD1 interacts

, Correspondence and requests for materials should be addressed to

. Scientific-reports-|, For siRNA transfection, 3.10 ?5 cells per ml were seeded in 6-well plate and 25 pmol/ml of total siRNA were transfected with INTERFERin (Polyplus Transfection) according to the manufacturer's recommendations. Plasmid transfections were performed with JetPrime (Polyplus Transfection). siRNAs were from Invitrogen (ERR?, LSD1) or Eurogentec (NRF1) and sequences are shown on Supplementary Table 1. For invasion assays, 5.10 4 cells were suspended in 200 µl DMEM/2% FCS and seeded on top of matrigel invasion chambers (Corning). Cells were allowed to migrate toward the lower chamber containing DMEM/10% FCS for 48 h. Matrigel was removed using cotton buds and cells were ixed 1 h with 4% formaldehyde, coloured with 0.1% crystal violet, and microphotographed. Cell-covered surfaces were quantiied using ImageJ, | DOI:./sMethods Cells. MDA-MB231 and HEK293T cells were cultured in DMEM supplemented with 10% FCS, 10 U/ml penicillin and 10 µg/ml streptomycin, vol.8, p.10041, 2018.

, GE-Healthcare) and probed with speciic antibodies ater saturation. he antibodies (and their dilution) used in this study were: hsp90 (API-SPA-830, Protease Inhibitor Cocktail (Sigma-Aldrich). Proteins (25-50 µg) were resolved on 8 to 15% SDS-PAGE, blotted onto PVDF membrane

, centrifugation, cell pellets were resuspended in lysis bufer (1% SDS, 50 mM Tris-HCl pH8, 10 mM EDTA). used: Histone H3 (ab1791, Abcam), H3K4me2 (07-030, Millipore) and H3K9me2 (39753, ActiveMotif)

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