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FACT depletion demonstrates a role for nucleosome organization in TAD formation

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Homo sapiens

PROVIDER: GSE284561 | GEO | 2025/08/29

REPOSITORIES: GEO

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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

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

| PRJNA1199541 | 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 [2]

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

| PRJNA1199476 | ENA

Pervasive RNA Binding Protein Enrichment on TAD Boundaries Regulates TAD Organization

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

2024-12-21 | GSE243534 | GEO

Role of Fft3 in nuclear organization

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2015-03-02 | E-GEOD-58013 | biostudies-arrayexpress

In vitro reconstitution of chromatin domains shows a role for nucleosome positioning in 3D genome organization

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

2023-11-23 | GSE220647 | GEO

Reconstituted TAD-size chromatin fibers feature heterogeneous nucleosome clusters.

Project description:Large topologically associated domains (TADs) contain irregularly spaced nucleosome clutches, and interactions between such clutches are thought to aid the compaction of these domains. Here, we reconstituted TAD-sized chromatin fibers containing hundreds of nucleosomes on native source human and lambda-phage DNA and compared their mechanical properties at the single-molecule level with shorter '601' arrays with various nucleosome repeat lengths. Fluorescent imaging showed increased compaction upon saturation of the DNA with histones and increasing magnesium concentration. Nucleosome clusters and their structural fluctuations were visualized in confined nanochannels. Force spectroscopy revealed not only similar mechanical properties of the TAD-sized fibers as shorter fibers but also large rupture events, consistent with breaking the interactions between distant clutches of nucleosomes. Though the arrays of native human DNA, lambda-phage and '601' DNA featured minor differences in reconstitution yield and nucleosome stability, the fibers' global structural and mechanical properties were similar, including the interactions between nucleosome clutches. These single-molecule experiments quantify the mechanical forces that stabilize large TAD-sized chromatin domains consisting of disordered, dynamically interacting nucleosome clutches and their effect on the condensation of large chromatin domains.

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A role for Snf2-related nucleosome-spacing enzymes in genome-wide nucleosome organization.

Project description:The positioning of nucleosomes within the coding regions of eukaryotic genes is aligned with respect to transcriptional start sites. This organization is likely to influence many genetic processes, requiring access to the underlying DNA. Here, we show that the combined action of Isw1 and Chd1 nucleosome-spacing enzymes is required to maintain this organization. In the absence of these enzymes, regular positioning of the majority of nucleosomes is lost. Exceptions include the region upstream of the promoter, the +1 nucleosome, and a subset of locations distributed throughout coding regions where other factors are likely to be involved. These observations indicate that adenosine triphosphate-dependent remodeling enzymes are responsible for directing the positioning of the majority of nucleosomes within the Saccharomyces cerevisiae genome.

| S-EPMC3428865 | biostudies-literature

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