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FACT depletion demonstrates a role for nucleosome organization in TAD formation

ABSTRACT: FACT depletion demonstrates a role for nucleosome organization in TAD formation

PROVIDER: PRJNA1199541 | ENA |

REPOSITORIES: ENA

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FACT depletion demonstrates a role for nucleosome organization in TAD formation [1]

Project description:Mammalian genomes are organized into distinct chromatin structures, which include small-scale nucleosome arrays and large-scale topologically associating domains (TADs). The mechanistic interplay between chromatin structures across scales is poorly understood. Here, we investigate how changes in nucleosome architecture impact TAD organization by studying the role of the histone chaperone facilitates chromatin transcription (FACT) in 3D genome organization. We show that FACT depletion perturbs TADs, causing decreased insulation and weaker CTCF loops. These changes in TAD structure cannot be attributed to changes in chromatin occupancy of CTCF or cohesin and occur specifically in transcribed regions of the genome where we observe perturbed nucleosome organization in absence of FACT. FACT depletion therefore allows us to separate the role of CTCF binding from nucleosome architecture and to demonstrate that the organization of nucleosomes at TAD boundaries directly contributes to TAD formation.

2025-08-29 | GSE284532 | GEO

FACT depletion demonstrates a role for nucleosome organization in TAD formation [2]

2025-08-29 | GSE284529 | GEO

FACT depletion demonstrates a role for nucleosome organization in TAD formation [2]

Project description:FACT depletion demonstrates a role for nucleosome organization in TAD formation [2]

| PRJNA1199476 | ENA

FACT depletion demonstrates a role for nucleosome organization in TAD formation [1]

Project description:FACT depletion demonstrates a role for nucleosome organization in TAD formation [1]

| PRJNA1199472 | ENA

FACT depletion demonstrates a role for nucleosome organization in TAD formation

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

2025-08-29 | GSE284561 | GEO

Pervasive RNA Binding Protein Enrichment on TAD Boundaries Regulates TAD Organization

Project description:Pervasive RNA Binding Protein Enrichment on TAD Boundaries Regulates TAD Organization

| PRJNA1018867 | ENA

Pervasive RNA Binding Protein Enrichment on TAD Boundaries Regulates TAD Organization [RNA-seq]

Project description:Mammalian genome is hierarchically organized by CTCF and cohesin through loop extrusion mechanism to facilitate the organization of topologically associating domains (TADs). Mounting evidence suggests additional factors/mechanisms exist to orchestrate TAD formation and maintenance. In this study, we investigate the potential role of RNA binding proteins (RBPs) in TAD organization. By integrated analyses of global RBP binding and 3D genome mapping profiles from both K562 and HepG2 cells, our study unveils the prevalent enrichment of RBPs on TAD boundaries and define boundary associated RBPs (baRBPs). We found that baRBP binding is correlated with enhanced TAD insulation strength and in a CTCF independent manner. Moreover, baRBP binding is associated with nascent promoter transcription. Additional experimental testing was performed using RBFox2 as a paradigm. Knockdown of RBFox2 in K562 cells causes moderate TAD reorganization. Moreover, RBFox2 enrichment on TAD boundaries is a conserved phenomenon in C2C12 myoblast (MB) cells. RBFox2 is down-regulated and its bound boundaries are remodeled during MB differentiation into myotubes (MTs). Finally, transcriptional inhibition indeed decreases RBFox2 binding and disrupts TAD boundary insulation. Altogether, our findings demonstrate that RBPs can play active role in modulating TAD organization through co-transcriptional association and synergistic action with nascent promoter transcripts.

2025-02-12 | GSE277220 | GEO

Nucleosome organization in mouse embryonic stem cells

Project description:The position of nucleosomes influences DNA accessibility to DNA-binding proteins. Genome-wide nucleosome profiles often report the observation of a canonical nucleosome organization at gene promoters where arrays of well-positioned nucleosomes emanate from nucleosome-depleted regions. It is unclear how this canonical promoter nucleosome organization forms and how it is related to transcription activation and the establishment of histone marks during development. Here we report the genome-wide organization of nucleosomes during zebrafish embryogenesis and show that well-positioned nucleosome arrays appear in thousands of promoters during the activation of the zygotic genome. The formation of canonical promoter nucleosome organization cannot be explained by DNA sequence preference, and is independent of transcription and the presence of RNA polymerase II, but strongly correlates with the presence of Histone H3 Lysine 4 trimethylation (H3K4me3). Our study further suggests that promoter nucleosome structure primes genes to future transcription activation. To determine whether the occlusions are consistent in mammalian pluripotent cells, we performed the same analyses in mouse embryonic stem cells and found similar relationships. MNase-seq to generate nucleosome organization in mouse embryonic stem cell (J1)

2013-10-29 | E-GEOD-51766 | biostudies-arrayexpress

Pervasive RNA Binding Protein Enrichment on TAD Boundaries Regulates TAD Organization [RNA-seq]

Project description:Pervasive RNA Binding Protein Enrichment on TAD Boundaries Regulates TAD Organization [RNA-seq]

| PRJNA1161385 | ENA

Pervasive RNA Binding Protein Enrichment on TAD Boundaries Regulates TAD Organization [Hi-C]

Project description:Pervasive RNA Binding Protein Enrichment on TAD Boundaries Regulates TAD Organization [Hi-C]

| PRJNA1018870 | ENA