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Series GSE112522 Query DataSets for GSE112522
Status Public on Aug 28, 2018
Title Asymmetric partition of parental histone (H3-H4)2 tetramers onto replicating DNA strands
Organism Saccharomyces cerevisiae
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Other
Summary In eukaryotic cells, inheritable changes in gene expression in response to environmental and developmental stimuli is associated with changes in histone modifications and relies on the passage of these changes into daughter cells during cell division, a process that remains elusive. Here, we show that parental histone (H3-H4)2 tetramers, the primary carrier of epigenetic modifications, are assembled into nucleosomes onto both replicating leading and lagging strands, with a preference for lagging strands of DNA replication forks. This asymmetric distribution of parental (H3-H4)2 is exacerbated in cells lacking Dpb3 and Dpb4, two subunits of DNA polymerase Pol ε. Dpb3-Dpb4 binds (H3-H4)2 and participates in the transfer of parental (H3-H4)2 tetramers onto leading strands of DNA replication forks. Cells lacking Dpb3 and Dpb4 exhibits defects in epigenetic inheritance. These results reveal a previously undocumented mechanism of histone segregation and a direct role for Pol ε in this poorly understood process.
 
Overall design We synchronized yeast cells (Wile type and other mutant cells) at G1 and released into early S phase in the presence of BrdU, and hydroxyurea (HU). We then performed BrdU immunoprecipitation using anti-BrdU antibodies following single-strand DNA library preparation and sequencing (ssSeq). we also performed protein ChIP followed by single-strand DNA sequencing (ChIP-ssSeq) for Dpb3, Dpb4, H3K56ac, H3K4me3, T7-tag, and HA-tag. The sequencing tag was mapped to both Watson (red) and Crick (blue) strands of the reference genome.
 
Contributor(s) Yu C, Gan H, Cardona Serra A, Zhang Z
Citation(s) 30115745
Submission date Mar 30, 2018
Last update date Mar 13, 2019
Contact name zhiguo zhang
E-mail(s) zz2401@cumc.columbia.edu
Phone 212-851-4936
Organization name Columbia University
Department Pediatric and Genetics and Development
Lab Irving Cancer Research Center
Street address 1130 St. Nicholas Avenue
City New York
State/province NY
ZIP/Postal code 10032
Country USA
 
Platforms (2)
GPL13821 Illumina HiSeq 2000 (Saccharomyces cerevisiae)
GPL19756 Illumina NextSeq 500 (Saccharomyces cerevisiae)
Samples (112)
GSM3072002 y1232: WT G1 input MNase-ssSeq repeat 1
GSM3072003 y1236: WT G1 H3K4me3 ChIP-ssSeq repeat 1
GSM3072004 y1234: WT S input MNase-ssSeq repeat 1
Relations
BioProject PRJNA448070
SRA SRP136791

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
GSE112522_RAW.tar 2.8 Gb (http)(custom) TAR (of BW)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
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