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Series GSE168700 Query DataSets for GSE168700
Status Public on Jan 01, 2022
Title A hexasome is the preferred substrate for the INO80 chromatin remodeling complex allowing versatility of function
Organism Saccharomyces cerevisiae
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary The INO80 chromatin remodeling complex plays critical roles in transcription that are commonly attributed to INO80’s nucleosome sliding activity. Here we find that removal of INO80 in yeast cells disrupts the positions of hexasome-sized particles within genes. We show that in vitro INO80 remodels hexasomes ~60-fold faster than nucleosomes. INO80’s preference for hexasomes is highest when the linker lengths approach the ~18 bp linker lengths found in gene bodies. Our data further suggest that the module formed by the Arp5 and Ies6 subunits promotes nucleosome sliding by dislodging an H2A/H2B dimer, thereby making a nucleosome transiently resemble a hexasome. We propose a model in which the action of the Arp5/Ies6 module allows INO80 to act rapidly on both nucleosome substrates at promoters and hexasome substrates in gene bodies. Rapid repositioning of hexasomes that are generated in the wake of transcription may mitigate spurious transcription. More generally, such versatility could explain how INO80 regulates chromatin architecture during diverse processes ranging from transcription to DNA repair.
 
Overall design MNase mapping of subnucleosomal and nucleosomal fragments in S. cerevisiae WT and ∆ino80 strains with replicates
Please note that these libraries are non-traditional in the sense that the library prep is very different from standard Illumina protocols, and so the raw fastqs have been subjected to non-standard adaptor trimming + read filtration (in addition to read deduplication), generating BAM files as only processed data.
 
Contributor(s) Hsieh LJ, Gourdet MA, Moore C, Munoz EN, Gamarra N, Ramani V, Narlikar GJ
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Submission date Mar 11, 2021
Last update date Jan 03, 2022
Contact name Vijay Ramani
Organization name UCSF
Department Biochemistry & Biophysics
Lab Ramani Lab
Street address 600 16th St, GH-S312B
City San Francisco
State/province California
ZIP/Postal code 94143
Country USA
 
Platforms (1)
GPL26302 NextSeq 550 (Saccharomyces cerevisiae)
Samples (4)
GSM5159058 WT MNase Replicate 1
GSM5159059 WT MNase Replicate 2
GSM5159060 ∆ino80 MNase Replicate 1
Relations
BioProject PRJNA713560
SRA SRP310238

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
GSE168700_RAW.tar 4.8 Gb (http)(custom) TAR (of BAM)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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