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A compendium of chromatin contact maps reflecting regulation by chromatin remodelers in budding yeast

ABSTRACT: We employed in situ Hi-C with an auxin-inducible degron (AID) system to demonstrate the effect of chromatin remodeling on 3D genome organization in yeast.

ORGANISM(S): Saccharomyces cerevisiae

PROVIDER: GSE158336 | GEO | 2021/09/29

REPOSITORIES: GEO

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A compendium of chromatin contact maps reflecting regulation by chromatin remodelers in budding yeast

Project description:We herein employ in situ Hi-C with an auxin-inducible degron (AID) system to examine the effect of chromatin remodeling on 3D genome organization in yeast. Eight selected ATP-dependent chromatin remodelers representing various subfamilies contribute to 3D genome organization differently. Among the studied remodelers, the temporary depletions of Chd1p, Swr1p, and Sth1p (a catalytic subunit of the Remodeling the Structure of Chromatin [RSC] complex) cause the most significant defects in intra-chromosomal contacts, and the regulatory roles of these three remodelers in 3D genome organization differ depending on the chromosomal context and cell cycle stage. Furthermore, even though Chd1p and Isw1p are known to share functional similarities/redundancies, their depletions lead to distinct effects on 3D structures. The RSC and cohesin complexes also differentially modulate 3D genome organization within chromosome arm regions, whereas RSC appears to support the function of cohesin in centromeric clustering at G2 phase. Our work suggests that the ATP-dependent chromatin remodelers control the 3D genome organization of yeast through their chromatin-remodeling activities. The effect of ATP-dependent chromatin remodelers on 3D genome organization has not been well studied. Here the authors employ in situ Hi-C with an auxin-inducible degron system to degrade chromatin remodelers in yeast to find that the 3D structure of chromatin collapses in their absence. The chromatin remodeling can modulate 3D architecture depending on chromosomal context and cell cycle stage.

| S-EPMC8569116 | biostudies-literature

A compendium of chromatin contact maps reflecting regulation by chromatin remodelers in budding yeast

Project description:A compendium of chromatin contact maps reflecting regulation by chromatin remodelers in budding yeast

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A Compendium of Chromatin Contact Maps Reveals Spatially Active Regions in the Human Genome.

Project description:The three-dimensional configuration of DNA is integral to all nuclear processes in eukaryotes, yet our knowledge of the chromosome architecture is still limited. Genome-wide chromosome conformation capture studies have uncovered features of chromatin organization in cultured cells, but genome architecture in human tissues has yet to be explored. Here, we report the most comprehensive survey to date of chromatin organization in human tissues. Through integrative analysis of chromatin contact maps in 21 primary human tissues and cell types, we find topologically associating domains highly conserved in different tissues. We also discover genomic regions that exhibit unusually high levels of local chromatin interactions. These frequently interacting regions (FIREs) are enriched for super-enhancers and are near tissue-specifically expressed genes. They display strong tissue-specificity in local chromatin interactions. Additionally, FIRE formation is partially dependent on CTCF and the Cohesin complex. We further show that FIREs can help annotate the function of non-coding sequence variants.

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Genome-wide maps of chromatin state in HCT116 colorectal cancer cell (HiC)

Project description:Identification of the genome-wide pair-wise chromatin interaction in Auxin untreated and Auxin treated HCT116 CTCF Degron cells.

2022-01-04 | GSE179542 | GEO

Genome-wide maps of chromatin state in HCT116 colorectal cancer cell. [RNA-Seq]

Project description:Identification of the genome-wide gene transcription in Auxin untreated and Auxin treated HCT116 CTCF Degron cells.

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Genome-wide maps of chromatin state in HCT116 colorectal cancer cell (ChIP-Seq)

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One-step generation of auxin-inducible degron cells with high-efficiency homozygous tagging

Project description:Auxin-inducible degron (AID) technology is powerful for chemogenetic control of proteolysis. However, generation of human cell lines to deplete endogenous proteins with AID remains challenging. Typically, homozygous degron-tagging efficiency is low and overexpression of an auxin receptor requires additional engineering steps. Here, we establish a one-step genome editing procedure with high-efficiency homozygous tagging and auxin receptor expression. We demonstrate its application in 5 human cell lines, including embryonic stem (ES) cells. The method allowed isolation of AID single-cell clones in 10 days for 11 target proteins with >80% average homozygous degron-tagging efficiency in A431 cells, and >50% efficiency for 5 targets in H9 ES cells. The tagged endogenous proteins were inducibly degraded in all cell lines, including ES cells and ES-cell derived neurons, with robust expected functional readouts. This method facilitates the application of AID for studying endogenous protein functions in human cells, especially in stem cells.

2024-01-31 | GSE243637 | GEO

Members of an array of zinc finger proteins specify distinct Hox chromatin boundaries [ChIP-Seq2]

Project description:In this experiment, we sought to identify how the distribution of CTCF, MAZ, and RAD21 change in CTCF-degron (no auxin), CTCF-degron (auxin), CTCF-degron MAZ KO (no auxin), and CTCF-degron MAZ KO (auxin) backgrounds in mouse embryonic stem cells (ESCs).

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RING1B calibrated ChIP-seq (cChIPseq) datasets for control mESCs and an Scc1-AID auxin-inducible degron.

Project description:We examined 3D chromatin structure in the absence of cohesin (Scc1-AID auxin-inducible degron) and a control line (E14-Tir1) and found that PRC1 core promoter component RING1B was one of the most enriched proteins. Hence, we performed calibrated ChIP-seq experiments on the control (E14-Tir1) and the Scc1-AID mESC lines with a spike in of HEK293 human cells to further study this relationship.

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