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Series GSE116853 Query DataSets for GSE116853
Status Public on Dec 22, 2018
Title RSC Defines MNase-sensitive Promoter Architecture in Yeast
Organism Saccharomyces cerevisiae
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary The classic view of nucleosome organization at active promoters is that two well-positioned nucleosomes flank a nucleosome-depleted region (NDR). However, this view has been recently challenged by contradictory reports as to whether a distinct set of wider (≳150 bp) NDRs instead contain unusually unstable Micrococcal Nuclease-sensitive “fragile” particles, thought to be nucleosomal because of their size. To determine the composition of fragile particles we introduce CUT&RUN.ChIP, in which targeted nuclease cleavage and release is followed by chromatin immunoprecipitation. We find that fragile particles represent the occupancy and action of the RSC nucleosome remodeler acting on dynamically unwrapped nucleosomal intermediates. We also find that general regulatory factors (GRFs) bind to partially unwrapped nucleosomal intermediates at NDRs. We propose that RSC-engagement and its action cause nucleosomes to unravel, and subsequent binding of GRFs constitute a dynamic cycle of nucleosome deposition and clearance at the subset of wide Pol II promoter NDRs.
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, followed by chromatin immunoprecipitation (ChIP).
Contributor(s) Brahma S, Henikoff S
Citation(s) 30554944
Submission date Jul 10, 2018
Last update date Feb 12, 2020
Contact name Jorja Henikoff
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)
GPL17342 Illumina HiSeq 2500 (Saccharomyces cerevisiae)
Samples (63)
GSM3262792 Abf1_H2AZ_1_(20180116_SB_ScDmSp_Abf1_H2AZ)
GSM3262793 Abf1_H2AZ_2_(20180301_SB_ScDmSp_Abf1_H2AZ)
GSM3262794 Abf1_H2B_1_(20180116_SB_ScDmSp_Abf1_H2B)
BioProject PRJNA480446
SRA SRP152937

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Supplementary file Size Download File type/resource
GSE116853_CUT_RUN.ChIP_protocol.pdf 39.8 Kb (ftp)(http) PDF
GSE116853_RAW.tar 590.7 Mb (http)(custom) TAR (of BEDGRAPH)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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