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Series GSE67382 Query DataSets for GSE67382
Status Public on Nov 12, 2015
Title BAF controls genome accessibility
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Expression profiling by high throughput sequencing
Summary Somatic differentiation requires induction of lineage specific genes to fulfill specialized tissue functions yet the genomic control of this process is incompletely understood. Using the epidermis as a model, we show here that the BAF chromatin remodeling complex is essential to maintain a subset of open chromatin regions, which are strikingly enriched for the DNA binding motif of the stratified epithelial lineage-determining transcription factor p63 (p=1X10-1786). These p63 sites are intrinsically inaccessible. BAF is required to displace nucleosomes ~40 base pairs away from p63 motifs to enable p63 binding, to maintain active histone marks, and to recruit RNA polymerase II to promote gene expression. In this process, p63 was itself also essential for full BAF recruitment to p63 binding sites. Intrinsically, p63 binding sequences favor nucleosome occupancy. Our data therefore suggest a model where a lineage-specific transcription factor cooperates with the BAF complex to establish genome accessibility and engage tissue-specific gene expression.
Overall design We examined chromatin accessibility controlled by the cooperation between BAF and p63 using ATAC-seq and ChIP-seq. ATAC-seq was performed in differentiating primary human keratinocytes in control and Brg1/Brm knock down conditions, two replicates each. We further compared the ChIP-seq signal of H3K27me3, H3K4me1, PolII, H3K27Ac, and p300 in keratinocytes between Brg1/Brm loss versus control. To test whether p63 recruits BAF to its binding sites, we also performed BAF ChIP-seq in keratinocytes between p63 loss versus control. In addition, we performed RNA-seq in BAF loss, p63 loss, and control conditions.
Contributor(s) Bao X, Rubin A, Kun Q, Chang HY, Khavari P
Citation(s) 26683334
Submission date Mar 27, 2015
Last update date Oct 11, 2022
Contact name Douglas Porter
Organization name Stanford
Department Dermatology
Lab Khavari
Street address 269 Campus Drive
City Stanford
State/province CA
ZIP/Postal code 94305
Country USA
Platforms (1)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Samples (26)
GSM1645706 BAFi_ATAC_rep1
GSM1645707 BAFi_ATAC_rep2
GSM1645708 CTRL_ATAC_rep1
BioProject PRJNA279685
SRA SRP056637

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Supplementary file Size Download File type/resource
GSE67382_Ctrl_BAF_p63_Refseq_Norm.txt.gz 1.1 Mb (ftp)(http) TXT
GSE67382_RAW.tar 18.9 Mb (http)(custom) TAR (of BED, BROADPEAK, NARROWPEAK)
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Raw data are available in SRA
Processed data provided as supplementary file

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