NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Series GSE72106 Query DataSets for GSE72106
Status Public on Aug 14, 2016
Title Genomic nucleosome organization reconstituted with pure proteins
Organism Saccharomyces cerevisiae
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Chromatin remodelers regulate genes by organizing nucleosomes around promoters, but their individual contributions are obfuscated by the complex in vivo milieu of factor redundancy and indirect effects. Genome-wide reconstitution of promoter nucleosome organization with purified proteins resolves this problem and is therefore a critical goal. Here we reconstitute four stages of nucleosome architecture using purified components: Yeast genomic DNA, histones, sequence-specific Abf1/Reb1, and remodelers RSC, ISW2, INO80, and ISW1a. We identify direct, specific and sufficient contributions that in vivo observations validate. First, RSC clears promoters by translating poly(dA:dT) into directional nucleosome removal. Second, partial redundancy is recapitulated where INO80 alone, or ISW2 at Abf1/Reb1sites, positions +1 nucleosomes. Third, INO80 and ISW2 each align downstream nucleosomal arrays. Fourth, ISW1a tightens the spacing to canonical repeat lengths. Such a minimal set of rules and proteins establishes core mechanisms by which promoter chromatin architecture arises through a blend of redundancy and specialization.
 
Overall design In this study, nucleosomes were assembled using Salt Gradient Dialysis (SGD) on yeast genomic DNA library. Assembled nucleosomes were either left untreated (labelled as "SGD", control), treated with whole cell extract (WCE), mutant extracts (rsc3ts WCE, isw1 isw2 chd1 WCE), purified remodelers; singly or in combinations (RSC, ISW1a, ISW1b, ISW2, INO80, CHD1, SWI/SNF), combinations of mutant extracts and chromatin remodelers or combination of General Regulatory Factors (Abf1, Reb1) and chromatin remodelers. The resulting nucleosome positions were mapped genome-wide using MNase-(anti-H3-ChIP)-Seq.
 
Contributor(s) Krietenstein N, Wal M, Watanabe S, Park B, Peterson CL, Pugh BF, Korber P
Citation(s) 27768892
NIH grant(s)
Grant ID Grant title Affiliation Name
R01 HG004160 High Resolution Mapping of Function Elements in the Yeast Genome PENNSYLVANIA STATE UNIVERSITY-UNIV PARK B FRANKLIN PUGH
Submission date Aug 14, 2015
Last update date May 15, 2019
Contact name Bongsoo Park
E-mail(s) bxp12@psu.edu
Phone 814-441-3861
Organization name Penn State University
Street address 453 North Frear Building
City University Park
State/province PA
ZIP/Postal code 16802
Country USA
 
Platforms (3)
GPL13821 Illumina HiSeq 2000 (Saccharomyces cerevisiae)
GPL18085 Illumina HiSeq 1500 (Saccharomyces cerevisiae)
GPL19756 Illumina NextSeq 500 (Saccharomyces cerevisiae)
Samples (92)
GSM1855369 SGD [MNase-ChIP-Seq] [PSU43201]
GSM1855374 isw1Δisw2Δchd1Δ WCE+ISW2+ISW1a [MNase-Seq] [PSU53204]
GSM1855375 SGD [MNase-Seq] [PSU51102]
Relations
BioProject PRJNA292928
SRA SRP062434

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
GSE72106_RAW.tar 99.3 Mb (http)(custom) TAR (of BEDGRAPH, TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap