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Series GSE128499 Query DataSets for GSE128499
Status Public on Jun 25, 2019
Title Pioneer factor-nucleosome binding events during differentiation are motif-encoded
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Other
Summary Though the in vitro structural and in vivo spatial characteristics of transcription factor (TF) binding are well defined, TF interactions with chromatin and other companion TFs during development are poorly understood. To analyze such interactions in vivo, we profiled several TFs across a time course of human embryonic stem cell differentiation via CUT&RUN epigenome profiling, and studied their interactions with nucleosomes and co-occurring TFs by Enhanced Chromatin Occupancy (EChO), a computational strategy for classifying TF binding characteristics across time and space. EChO shows that at different enhancer targets, the same TF can employ either direct DNA binding, or “pioneer” nucleosome binding to access them. Pioneer binding is correlated with local binding of other TFs and enhancer motif character, including degeneracy at key bases in the pioneer factor target motif. Our strategy reveals a dynamic exchange of TFs at enhancers across developmental time that is aided by pioneer nucleosome binding.
 
Overall design We used Cleavage under targets and Release using nuclease (Cut-and-Run), a chromatin profiling strategy in which antibody-targeted controlled cleavage by micrococcal nuclease releases specific protein-DNA complexes into the supernatant for paired-end DNA sequencing.
 
Contributor(s) Meers MP, Janssens DH, Henikoff S
Citation(s) 31253573
Submission date Mar 18, 2019
Last update date Sep 17, 2022
Contact name Jorja Henikoff
E-mail(s) jorja@fhcrc.org
Phone 206-667-4850
Organization name Fred Hutchinson Cancer Research Center
Department Basic Sciences
Lab Henikoff
Street address 1100 Fairview AV N, A1-162
City Seattle
State/province WA
ZIP/Postal code 98109-1024
Country USA
 
Platforms (1)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Samples (109)
GSM3677739 2d_ATACseq_(20181017_MM_Hs_0705MPM512)
GSM3677740 2d_CTCF_auto_(20181004_MPM_HsSc_678_0926)
GSM3677741 2d_CTCF_hiCa_(20180829_MM_HsSc_0817MPM577S)
Relations
BioProject PRJNA527856
SRA SRP188770

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE128499_CUT-and-RUN_Standard_protocol.rtf.gz 1.3 Kb (ftp)(http) RTF
GSE128499_CUTnRUNv2_Hi-cal-lo-salt_beads-first.rtf.gz 1.5 Kb (ftp)(http) RTF
GSE128499_Janssens_protocols.docx.gz 4.1 Mb (ftp)(http) DOCX
GSE128499_RAW.tar 5.6 Gb (http)(custom) TAR (of BED)
GSE128499_bench-top-cut-amp-tag-bcuhiwt6.pdf 480.7 Kb (ftp)(http) PDF
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
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