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Series GSE65889 Query DataSets for GSE65889
Status Public on Sep 23, 2015
Title Novel nucleosomal particles containing core histones and linker DNA but no histone H1
Organisms Saccharomyces cerevisiae; Mus musculus; Synthetic plasmid
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Eukaryotic chromosomal DNA is assembled into regularly spaced nucleosomes, which play a central role in gene regulation by determining accessibility of control regions. The nucleosome contains ~147 bp of DNA wrapped ~1.7 times around a central core histone octamer. The linker histone, H1, binds both to the nucleosome, sealing the DNA coils, and to the linker DNA between nucleosomes, directing chromatin folding. Micrococcal nuclease (MNase) digests the linker to yield the chromatosome, containing H1 and ~160 bp, and then converts it to a core particle, containing ~147 bp and no H1. Sequencing of nucleosomal DNA obtained after MNase digestion (MNase-seq) generates genome-wide nucleosome maps that are important for understanding gene regulation. We present an improved MNase-seq method involving simultaneous digestion with exonuclease III, which removes linker DNA. Remarkably, we discovered two novel intermediate particles containing 154 or 161 bp, corresponding to 7 bp protruding from one or both sides of the nucleosome core. These particles are detected in yeast lacking H1 and in H1-depleted mouse chromatin. They can be reconstituted in vitro using purified core histones and DNA. We propose that these "proto-chromatosomes" are fundamental chromatin subunits, which include the H1 binding site and influence nucleosome spacing independently of H1.
 
Overall design Comparison of budding yeast nucleosome sequences obtained using micrococcal nuclease (MNase-seq) and MNase + exonuclease III (ExoIII) (MNase-ExoIII-seq): wild type cells and hho1-null cells. Nucleosome sequences from native chromatin and H1-depleted chromatin from mouse liver. Nucleosome sequences from a plasmid reconstituted into nucleosomes using recombinant yeast histones or native chicken erythrocyte histones.
 
Contributor(s) Cole HA, Ocampo J, Burke TL, Nikitina T, Nagarajavel V, Clark DJ
Citation(s) 26400169
Submission date Feb 12, 2015
Last update date May 15, 2019
Contact name David Johannes Clark
E-mail(s) clarkda@mail.nih.gov
Phone 3014966966
Organization name NICHD, NIH
Department DDB
Lab SCGE
Street address 6 Center Drive Bldg 6A Rm 2A02
City Bethesda
State/province MD
ZIP/Postal code 20892
Country USA
 
Platforms (4)
GPL9377 Illumina Genome Analyzer II (Saccharomyces cerevisiae)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
GPL13821 Illumina HiSeq 2000 (Saccharomyces cerevisiae)
Samples (31)
GSM1608382 77_MNase-1
GSM1608383 77_MNase-2
GSM1608384 77_MNase-Exo_less-digested-1
Relations
BioProject PRJNA275314
SRA SRP054975

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
GSE65889_RAW.tar 305.4 Mb (http)(custom) TAR (of BW, TXT)
GSE65889_pRS-ARG1-B_688.fa.gz 3.0 Kb (ftp)(http) FA
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Raw data are available in SRA
Processed data provided as supplementary file
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