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Series GSE87040 Query DataSets for GSE87040
Status Public on Dec 21, 2017
Title Genomic and proteomic resolution of heterochromatin and its restriction of alternate fate genes (RNA-seq)
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Heterochromatic regions in mammalian cells suppress recombination, silence transcription, and are crucial for maintaining cell differentiation. Genomic and biochemical characterization of heterochromatin has relied on the associated histone modifications H3K9me3 and H3K27me3, yet these marks are also found in euchromatic regions that permit transcription. We employed a biophysical method to isolate sonication resistant heterochromatin from human somatic cells, mapped its genomic organization compared to histone modifications, and used proteomics to reveal an extensive number of heterochromatin-bound proteins. We discriminate subtypes of H3K9me3- and H3K27me3-marked domains, in sonication-resistant heterochromatin versus euchromatin, and we present a resource of hundreds of proteins that preferentially bind heterochromatin, a set enriched for RNA-binding proteins and proteins that oppose iPS reprogramming. The sonication-resistant heterochromatin landscape includes repressed genes for alternative lineages that are resistant to activation by introduced transcription factors. Depletion of identified heterochromatin-associated proteins reduces this barrier, rendering alternative-lineage genes more competent for transcriptional activation.
Overall design This study was designed to assess the role of human SUV39H1 and RBMX/RBMXL1 in impeding the activation of heterochromatic genes by transcription factors. RNA-seq was performed in human BJ foreskin fibroblasts treated with siRNAs in two main experimental protocols: cells expressing the hepatic transcription factors FOXA3/HNF1A/HNF4A ("hepatic TF" protocol) and cells expressing no ectopic transcription factors ("no TF" protocol). There are a total of 12 RNA-seq samples: two experimental protocols, three siRNAs per protocol, and two biological replicates per siRNA/protocol. The three siRNAs are: non-targeting control siRNA, siRNA against SUV39H1, and siRNA co-targeting RBMX and RBMX/L1
Contributor(s) Becker JS, McCarthy RL, Sidoli S, Donahue G, Kaeding KE, He Z, Lin S, Garcia BA, Zaret KS
Citation(s) 29272703
Submission date Sep 16, 2016
Last update date May 15, 2019
Contact name Gregory Donahue
Organization name The University of Pennsylvania
Department Cell & Developmental Biology
Lab Zaret Lab
Street address 3400 Civic Center Blvd, Bldg 421
City Philadelphia
State/province PA
ZIP/Postal code 19104
Country USA
Platforms (1)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
Samples (12)
GSM2319585 hepaticTF-condition_control-siRNA_rep1
GSM2319586 hepaticTF-condition_control-siRNA_rep2
GSM2319587 hepaticTF-condition_RBMX-siRNA_rep1
This SubSeries is part of SuperSeries:
GSE87041 Genomic and proteomic resolution of heterochromatin and its restriction of alternate fate genes
BioProject PRJNA343265
SRA SRP090039

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Supplementary file Size Download File type/resource 129.0 Mb (ftp)(http) BW 158.4 Mb (ftp)(http) BW 133.3 Mb (ftp)(http) BW 117.3 Mb (ftp)(http) BW 129.4 Mb (ftp)(http) BW 153.4 Mb (ftp)(http) BW
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