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Series GSE90454

Query DataSets for GSE90454

Status

Public on Jan 29, 2018

Title

Genetic determinants and epigenetic effects of pioneer factor binding [ChIP-seq]

Organism

Experiment type

Genome binding/occupancy profiling by high throughput sequencing
Third-party reanalysis

Summary

Transcription factors (TFs) are the core drivers of gene regulatory networks that control developmental transitions and a complete understanding of how they access, alter and maintain specific gene expression patterns remains an important goal. To begin a systematic dissection of the molecular components that either enable or constrain TF activity, we investigated the genomic occupancy of two distinct TFs, the pioneer factor FOXA2 and the pluripotency-associated factor OCT4 (POU5F1), in both endogenous and ectopic settings. We find that, while stable binding of FOXA2 is highly cell type specific and similar to what is observed for most TFs including OCT4, pioneer activity can be distinguished by notable sampling of additional loci that are occupied in alternative lineages. In our ectopic system, FOXA2 binding can be selectively stabilized at previously sampled sites by co-expressing the lineage specific regulator GATA4. Alternatively, we observe minimal influence of chromatin state on discrete, stabilized binding choices for FOXA2 but a strong bias towards open chromatin for ectopic OCT4 targets. Finally, we demonstrate that FOXA2 binding and nucleosome remodeling at silent loci can occur when the cell cycle is halted in G1, but surprisingly subsequent changes in DNA methylation require DNA replication. Taken together, our results provide several new molecular insights that contribute to our basic understanding of gene regulation and pave the way for a more rational use of ectopic TFs for cellular reprogramming.

Overall design

In order to understand the binding dynamics of a pioneer transcription factor and its underlying chromatin environment, we performed high through-put sequencing for FOXA1 ChIP along with several histone marks. Cells were crosslinked with 1% formaldehyde for 10 minutes at room temperature, and quenched with 125mM glycine at room temperature. Chips were performed as previously described(Gifford et al., 2013) by isolating nuclei and shearing DNA to 200-600 basepair fragments using Branson sonicator.Antibody incubation with chromatin was performed overnight. ~10 million cells were used per FOXA2 ChIP with 1ug of antibody/ million cells. ~1 million cells were used for each histone ChIP. Following an overnight incubation, antibody-protein complexes were isolated using Protein G/A beads (Life Technologies) and sequencing libraries were generated. Libraries were generated as previously described (Mikkelsen et al., 2010, Gifford et al., 2013) and Libraries were sequenced on a HiSeq 2500 at 11pmol.

Please note that the processed data 'RPKM_Table.txt' was generated from all ATAC-seq and ChIP-seq studies (GSE90453, GSE90454, GSE92490, GSE92491) and is linked to the GSE90454 records.

The file MatchingSampleTable.xlsx includes a key to the column headers in RPKM_Table.txt and the sample titles from all the above-listed ATAC-seq and ChIP-seq studies. The RPKM table includes re-analyzed data and these samples are listed in Re-AnalysisTable.xlsx. Links to the re-analyzed samples can be found below.

Contributor(s)

Donaghey J, Thakurela S, Meissner A

Citation(s)

Submission date

Nov 22, 2016

Last update date

May 15, 2019

Contact name

Sudhir Thakurela

Organization name

HSCRB

Street address

7 Divinity Avenue

City

Cambridge

ZIP/Postal code

02138

Country

USA

Platforms (1)

Illumina HiSeq 2500 (Homo sapiens)

Samples (44)

More...

GSM2401446	BJ FOXA2 ChIP Rep1
GSM2401447	BJ FOXA2 ChIP Rep2
GSM2401448	BJ K27ac Rep1

This SubSeries is part of SuperSeries:

Genetic determinants and epigenetic effects of pioneer factor binding

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BioProject

SRA

Download family	Format
SOFT formatted family file(s)	SOFT
MINiML formatted family file(s)	MINiML
Series Matrix File(s)	TXT

Supplementary file	Size	Download	File type/resource
GSE90454_MatchingSampleTable.xlsx	6.3 Kb	(ftp)(http)	XLSX
GSE90454_RPKM_Table.txt.gz	10.0 Mb	(ftp)(http)	TXT
GSE90454_Re-AnalysisTable.xlsx	9.4 Kb	(ftp)(http)	XLSX
SRA Run Selector
Raw data are available in SRA
Processed data are available on Series record

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