EXPERIMENT_TITLE: GSM5320751: ∆HDAC8 G1 Replicate 2 HiC; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: Hi-C libraries were prepared as previously described (Rao et al., 2014). The protocol was adapted slightly for G1 analyses. An asynchronous pool of cells was first crosslinked using 2% formaldehyde. Then the 10% smallest cells were sorted based on Forward Scatter and Side Scatter. 5 million cells were collected for Hi-C analysis and then processed according to protocol following crosslinking. Pulled-down DNA was end-repaired and an A-overhang was added. Sequencing adapters were ligated to the DNA samples to create sequencing libraries.
STUDY_DESCRIPTOR_STUDY_ABSTRACT: Cohesin structures the genome through the formation of chromatin loops and by holding together the sister chromatids from S-phase until mitosis. The acetylation of cohesin's SMC3 subunit is a dynamic process that involves the acetyltransferase ESCO1 and deacetylase HDAC8. Here we show that this cohesin acetylation cycle controls the 3D genome. ESCO1 restricts the length of chromatin loops and architectural stripes, while HDAC8 rather promotes the extension of such loops and stripes. This role in controlling loop length turns out to be distinct from the canonical role of cohesin acetylation that protects against WAPL-mediated DNA release. We reveal that acetylation rather controls cohesin's interaction with PDS5A to restrict chromatin loop length. Our data supports a model in which this PDS5A-bound state acts as a brake that enables the pausing and restart of loop enlargement. The cohesin acetylation cycle hereby provides punctuation in the process of genome folding. Overall design: Hi-C was performed in G1 isolated cells from the following genotypes: Wild Type, ?ESCO1, ?HDAC8, ?ESCO1/?HDAC8, ?WAPL, ?WAPL/?ESCO1, ?PDS5A, ?PDS5B and ?PDS5A/?HDAC8 cells. Hi-C replicate experiments were performed in all genotypes. Asynchronous Hi-C analysis was performed in Wild Type cells and ?HDAC8 cells.
SAMPLE_TITLE: ∆HDAC8 G1 Replicate 2 HiC
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Pool_Member_@attributes_sample_title: ∆HDAC8 G1 Replicate 2 HiC
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