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Series GSE92846 Query DataSets for GSE92846
Status Public on May 16, 2017
Title Stem cell regulatory elements remain bookmarked by selected transcription factors and epigenetic marks during mitosis
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Purpose: We investigated the existence, nature and significance of mitotic bookmarking of Klf4, Oct4, Sox2 (KOS) and H3K27ac in mouse ESCs.
Methods: DNA-binding/epigenetic profiles of KOS and H3K27ac on asynchronous and mitotic chromatin were generated by deep sequencing following chromatin immunoprecipitation, in replicates.
Results: KOS and H3K27ac are largely maintained on mitotic chromatin. KOS bookmark critical stem cell regulatory elements during mitosis. H3K27 acetylation during mitosis is highly retained on promoters of cell cycle and homeostasis related genes and enhancers of genes important for any given cell identity.
Conclusions: The extensive mitotic occupancy that we observed is in agreement with a recent study that proposes that TF retention on mitotic chromatin may be a much broader phenomenon than previously appreciated.

Bobbie Pelham-Webb is supported by a Medical Scientist Training Program grant from the National Institute of General Medical Sciences of the NIH under award number T32GM007739 to the Weill Cornell/Rockefeller/Sloan Kettering Tri-Institutional MD-PhD Program. Additionally, this work was funded by the NIH Director s New Innovator Award ( DP2DA043813 ) to Effie Apostolou.
 
Overall design Short read signle-end ChIP-seq in V6.5 murine ESC for Klf4 (3 asynchronous and mitotic replicates, respectively ), Oct4 (1 asynchronous replicate with the additional G1 sample of GSE78073, and 2 mitotic replicates with the additional mitotic sample of GSE78073), Sox2(1 asynchronous replicate with the additional asynchronous sample of GSE44288 , and 2 mitotic replicates), H3K27ac (2 asynchronous and mitotic replicates, respectively) and whole cell extract input DNA (7 runs). Mitotic arrest was done as follows: 80-90% confluent mouse ESCs were split 1:3 on gelatinized plates the day before synchronization. Nocodazole at 100ug/ml was added in the medium for 7hr prior to collection by mitotic shake-off.
 
Contributor(s) Apostolou E
Citation(s) 28514649
Submission date Dec 22, 2016
Last update date May 15, 2019
Contact name Alison Goate
E-mail(s) alison.goate@mssm.edu
Phone 212-659-5672
Organization name Icahn School of Medicine at Mount Sinai
Department Department of Genetics and Genomic Sciences
Street address Icahn (East) Building Floor 10 Room 10-70C, 1425 Madison Ave
City New York
State/province NY
ZIP/Postal code 10029
Country USA
 
Platforms (1)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
Samples (24)
GSM2438463 EC-EA-2697-KLF4_ASYN_1
GSM2438464 EC-EA-2643-KLF4_ASYN_1
GSM2438465 EC-EA-3702-KLF4_ASYN_1
Relations
BioProject PRJNA358612
SRA SRP095560

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Supplementary file Size Download File type/resource
GSE92846_RAW.tar 4.7 Gb (http)(custom) TAR (of BW, NARROWPEAK)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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