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Series GSE168176 Query DataSets for GSE168176
Status Public on Jun 17, 2021
Title CTCF and transcription orchestrate chromatin structure re-configuration after mitosis [Hi-C]
Organism Mus musculus
Experiment type Other
Summary During mitosis, transcription is globally attenuated and chromatin architecture is dramatically reconfigured. Here we exploited the M-phase to G1-phase progression to interrogate the contributions of the architectural factor CTCF and the process of transcription to re-sculpting the genome in newborn nuclei. While CTCF appears to be dispensable for large scale post-mitotic compartmentalization, depletion of CTCF specifically during the M-phase to G1-phase transition alters the re-establishment of local short-range compartmentalization after mitosis. Without CTCF, structural loops fail to reform, leading to illegitimate contacts between cis-regulatory elements (CREs) and altered gene expression in G1-phase. Transient CRE contacts that are normally resolved after telophase persist deeply into G1-phase in CTCF depleted cells. Boundary reformation is largely disrupted upon CTCF loss. Yet, a subset (~27%) of boundaries emerges normally in the absence of CTCF and is characterized by transitions in chromatin states. Reformation of gene domains can occur prior to the full onset of transcription and can be linked to tri-methylation at lysine 36 of histone 3 (H3K36me3), a mark stable throughout mitosis. The focus on the de novo formation of nuclear architecture during G1 entry yielded novel insights into how CTCF and the process of transcription contribute to the dynamic re-configuration of chromatin architecture during the mitosis to G1 phase progression.
Overall design Uninduced G1E-ER4 (-GATA1) cells were synchronized to pro-metaphase with nocodazole treatment and treated with or without auxin to remove CTCF. Cells from both CTCF depleted and replated groups were released from nocodazole for a variety of durations. Cells at different cell cycle stages were purified with FACS. Hi-C experiments were performed on purified populations to examine chromatin structure with or without CTCF at designated cell cycle stage. 2-3 biological replicates were performed for each time point
Contributor(s) Zhang H, Lan Y, Blobel G
Citation(s) 34453048
Submission date Mar 03, 2021
Last update date Sep 16, 2021
Contact name Yemin Lan
Organization name University of Pennsylvania
Street address 3400 Civic Center Blvd
City Philadelphia
State/province PA
ZIP/Postal code 19104
Country USA
Platforms (1)
GPL19057 Illumina NextSeq 500 (Mus musculus)
Samples (22)
GSM5133376 0h_no_auxin_rep1
GSM5133377 0h_no_auxin_rep2
GSM5133378 0h_with_auxin_rep1
This SubSeries is part of SuperSeries:
GSE168251 CTCF and transcription orchestrate chromatin structure re-configuration after mitosis
BioProject PRJNA706676
SRA SRP309311

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Supplementary file Size Download File type/resource
GSE168176_RAW.tar 2.8 Gb (http)(custom) TAR (of COOL)
GSE168176_boundary_calls.csv.gz 304.9 Kb (ftp)(http) CSV
GSE168176_loop_calls.csv.gz 1.1 Mb (ftp)(http) CSV
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Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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