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O-GlcNAcylation of CTCF regulates 3D chromatin structure [ATAC-seq]

ABSTRACT: The goal of this study is to test whether the O-GlcNAcylation of CTCF plays a role in regulating chromatin structure.

ORGANISM(S): Mus musculus

PROVIDER: GSE255855 | GEO | 2024/03/04

REPOSITORIES: GEO

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O-GlcNAcylation of CTCF regulates 3D chromatin structure [HiC]

Project description:The goal of this study is to test whether the O-GlcNAcylation of CTCF plays a role in regulating chromatin structure.

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O-GlcNAcylation of CTCF regulates 3D chromatin structure [ChIP-seq]

Project description:The goal of this study is to test whether the O-GlcNAcylation of CTCF plays a role in regulating chromatin structure.

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O-GlcNAcylation of CTCF regulates 3D chromatin structure [RNA-seq]

Project description:The goal of this study is to test whether the O-GlcNAcylation of CTCF plays a role in regulating chromatin structure.

2024-03-04 | GSE255854 | GEO

O-GlcNAcylation of CTCF regulates 3D chromatin structure

Project description:O-GlcNAcylation of CTCF regulates 3D chromatin structure

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O-GlcNAcylation of CTCF regulates 3D chromatin structure

Project description:This SuperSeries is composed of the SubSeries listed below.

2024-03-04 | GSE255897 | GEO

Establishment of 3D chromatin structure after fertilization and the metabolic switch at the morula-to-blastocyst transition require CTCF [RNA-seq]

Project description:The eukaryotic genome is tightly packed inside the nucleus, where it is organized in 3D at different scales. This structure is driven and maintained by different chromatin states and by architectural factors that bind DNA, such as the multi-zinc finger protein CTCF. Zygotic genome structure is established de novo after fertilization, but the impact of such structure on genome function during the first stages of mammalian development is still unclear. Here, we show that deletion of the Ctcf gene in mouse embryos impairs the correct establishment of chromatin structure, but initial lineage decisions take place and embryos are viable until the late blastocyst stage. Furthermore, we observe that maternal CTCF is not necessary for development. Transcriptomic analyses of mutant embryos show that the changes in metabolic and protein homeostasis programs that occur during the progression from the morula to the blastocyst depend on CTCF. Yet, these changes in gene expression do not correlate with disruption of chromatin structure, but mainly with proximal binding of CTCF to the promoter region of genes downregulated in mutants. Our results show that CTCF regulates both 3D genome organization and transcription during mouse preimplantation development, but mostly as independent processes.

2022-10-07 | GSE180306 | GEO

Establishment of 3D chromatin structure after fertilization and the metabolic switch at the morula-to-blastocyst transition require CTCF [Hi-C]

2022-10-07 | GSE180305 | GEO

GlcNAcylation of histone H2B facilitates its monoubiquitination

Project description:This SuperSeries is composed of the following subset Series: GSE33049: GlcNAcylation of histone H2B facilitates its monoubiquitination [Illumina Genome Analyzer data] GSE33050: GlcNAcylation of histone H2B facilitates its monoubiquitination [Affymetrix data] Refer to individual Series

2011-10-26 | E-GEOD-33051 | biostudies-arrayexpress

GlcNAcylation of histone H2B facilitates its monoubiquitination [Illumina Genome Analyzer data]

Project description:We report that histone GlcNAcylation of H2B S112 is a vital histone modification which facilitates histone monoubiquitination (ub). In a genome-wide analysis, H2B S112 GlcNAcylation sites were observed widely distributed over entire chromosomes including transcribed gene loci, together with co-localization of H2B S112 GlcNAcylation and K120 ub. Examination of H2B S112 GlcNAc and H2B K120 ub in HeLa S3 cells

2011-10-27 | E-GEOD-33049 | biostudies-arrayexpress

CTCF binding polarity determines chromatin looping [4C]

Project description:CCCTC-binding factor (CTCF) is an architectural protein involved in the three-dimensional organization of chromatin. In this study, we systematically assayed the 3D genomic contact profiles of hundreds of CTCF binding sites in multiple tissues with high-resolution 4C-seq. We find both developmentally stable and dynamic chromatin loops. As recently reported, our data also suggest that chromatin loops preferentially form between CTCF binding sites oriented in a convergent manner. To directly test this, we used CRISPR-Cas9 genome editing to delete core CTCF binding sites in three loci, including the CTCF site in the Sox2 super-enhancer. In all instances, CTCF and cohesin recruitment were lost, and chromatin loops with distal CTCF sites were disrupted or destabilized. Re-insertion of oppositely oriented CTCF recognition sequences restored CTCF and cohesin recruitment, but did not re-establish chromatin loops. We conclude that CTCF binding polarity plays a functional role in the formation of higher order chromatin structure. 4C-seq was performed on a large number of viewpoints in E14 embryonic stem cells, neural precursor cells and primary fetal liver cells

2015-10-29 | E-GEOD-72539 | biostudies-arrayexpress

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