Project description:Using the estrogen receptor alpha (ERalpha) as a model ligand inducible transcription factor, we sought to explicitly define parameters that determine transcription factor binding site selection on a genomic scale in an inducible system that minimizes confounding chromatin effects by the transcription factor itself. By examining several genetic and epigenetic parameters, we find that an energetically favorable estrogen response element (ERE) motif sequence, evidence of occupancy of a "pioneering" transcription factor FOXA1, the presence of the enhancer mark, H3K4me1, and an open chromatin configuration (FAIRE) at the pre-ligand state provide specificity for ER binding. Genome-wide ChIP-sequencing was done in MCF-7 cancer cell line for the following histone H3 modifications: monomethylation H3K4me1, trimethylation H3K4me3, H3K9me3, H3K27me3, acetylation H3K9ac, H3K14ac. In addition sequencing of RNA Pol II was done at same treatment conditions (E2 and DMSO). In addition, we assessed the chromatin configuration of ERα binding sites by deeply sequencing fragments isolated by Formaldehyde-Assisted Isolation of Regulatory Elements (FAIRE) (Giresi et al, 2007) which enriches for nucleosome free genomic DNA in the aqueous phase of a phenol extraction. The analysis histone modifications in MCF-7 cancer cells was done by ChIP-seq data obtained either with E2 stimulation or without stimulation using vehicle as a control. Using the ERα binding sites defined by ChIP-seq (separate submission), we analyzed the population characteristics of the chromatin configuration of the ERα binding sites. To this end, we performed ChIP-seq analysis for the occupancy configuration of each of the following marks before and after E2 exposure: RNA Pol II, the activation marks H3K4me1, H3K4me3, H3K9ac and H3K14ac, and the repression marks H3K9me3 and H3K27me3. We assessed the chromatin configuration of ERα binding sites by deeply sequencing fragments isolated by Formaldehyde-Assisted Isolation of Regulatory Elements (FAIRE) (Giresi et al, 2007) which enriches for nucleosome free genomic DNA in the aqueous phase of a phenol extraction. The tag count of FAIRE fragments reflects the nucleosome depletion at any given site. RNA Pol II - Cat# ab5408, Abcam; H3K9me3 - Cat# ab8898, Abcam; H3K27me3 - Cat# 07-449, Upstate Biotechnology Inc.; H3K4me1 - Cat# ab8895, Abcam; H3K4me3 - Cat# ab8580, Abcam; H3K9ac - Cat# 07-352, Upstate Biotechnology Inc.; H3K14ac - Cat# 07-353, Upstate Biotechnology Inc.

Project description:In the cell nucleus, each chromosome is confined to a chromosome territory. This spatial organization of chromosomes plays a crucial role in gene regulation and genome stability. Recently an additional level of organization has been discovered at the chromosome scale: the spatial segregation into open and closed chromatin to form two genome-wide compartments. Although considerable progress has been made in our knowledge of chromatin organization, a fundamental issue remains the understanding of its dynamic, especially in cancer. To address this issue, we performed genome-wide mapping of intra- and interchromosomal interactions (Hi-C) over the time after estrogen (E2) stimulation of breast cancer cells. To biologically interpret these interactions, we integrated with estrogen receptor alpha (ER alpha) binding events, gene expression and multiple epigenetic marks. We show that E2 induces a global reorganization of genome. More specifically, gene-rich chromosomes as well as areas of open and highly transcribed chromatins are moved spatially closer, thus enabling genes to share transcriptional machinery and regulatory elements. At a lower scale, differentially interacting loci are enriched for cancer proliferation and E2 related genes. We also observe that these differentially interacting loci are correlated with higher ER alpha binding events and gene expression. 5 time points: before E2 (0h) and after E2 (0.5h, 1h, 4h and 24h). For each time point, there are two lanes per sample and two biological replicate samples. Please note that a processed data file corresponds to the merging of 2 replicates, and that there are 2 lanes per replicates (4 files in total per processed data file). Information about data merging is provided in the title of the sample. For instance : 0h_replicate_1_lane 1 0h_replicate_1_lane 2 0h_replicate_2_lane_1 0h_replicate_2_lane_2 are merged to generate the processed data hic_0h-all-1M.IC.csv.gz. Several bin sizes are provided for the same processed data: hic_0h-all-1M.IC.csv.gz hic_0h-all-2M.IC.csv.gz hic_0h-all-4M.IC.csv.gz hic_0h-all-500k.IC.csv.gz are the same processed data, but with different bin sizes.

Project description:Using the estrogen receptor alpha (ERalpha) as a model ligand inducible transcription factor, we sought to explicitly define parameters that determine transcription factor binding site selection on a genomic scale in an inducible system that minimizes confounding chromatin effects by the transcription factor itself. By examining several genetic and epigenetic parameters, we find that an energetically favorable estrogen response element (ERE) motif sequence, evidence of occupancy of a "pioneering" transcription factor FOXA1, the presence of the enhancer mark, H3K4me1, and an open chromatin configuration (FAIRE) at the pre-ligand state provide specificity for ER binding. Genome-wide ChIP-sequencing was done in MCF-7 cancer cell line for the following histone H3 modifications: monomethylation H3K4me1, trimethylation H3K4me3, H3K9me3, H3K27me3, acetylation H3K9ac, H3K14ac. In addition sequencing of RNA Pol II was done at same treatment conditions (E2 and DMSO). In addition, we assessed the chromatin configuration of ERα binding sites by deeply sequencing fragments isolated by Formaldehyde-Assisted Isolation of Regulatory Elements (FAIRE) (Giresi et al, 2007) which enriches for nucleosome free genomic DNA in the aqueous phase of a phenol extraction. The analysis histone modifications in MCF-7 cancer cells was done by ChIP-seq data obtained either with E2 stimulation or without stimulation using vehicle as a control. Using the ERα binding sites defined by ChIP-seq (separate submission), we analyzed the population characteristics of the chromatin configuration of the ERα binding sites. To this end, we performed ChIP-seq analysis for the occupancy configuration of each of the following marks before and after E2 exposure: RNA Pol II, the activation marks H3K4me1, H3K4me3, H3K9ac and H3K14ac, and the repression marks H3K9me3 and H3K27me3. We assessed the chromatin configuration of ERα binding sites by deeply sequencing fragments isolated by Formaldehyde-Assisted Isolation of Regulatory Elements (FAIRE) (Giresi et al, 2007) which enriches for nucleosome free genomic DNA in the aqueous phase of a phenol extraction. The tag count of FAIRE fragments reflects the nucleosome depletion at any given site. RNA Pol II - Cat# ab5408, Abcam; H3K9me3 - Cat# ab8898, Abcam; H3K27me3 - Cat# 07-449, Upstate Biotechnology Inc.; H3K4me1 - Cat# ab8895, Abcam; H3K4me3 - Cat# ab8580, Abcam; H3K9ac - Cat# 07-352, Upstate Biotechnology Inc.; H3K14ac - Cat# 07-353, Upstate Biotechnology Inc.

Dataset Information

RNAi profiling of human MCF-7 cells depleted for NMNAT1

Publications

Enzymes in the NAD+ salvage pathway regulate SIRT1 activity at target gene promoters.

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