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SATB1 Regulates 3D Genome Architecture in T cells by Constraining Chromatin Interactions surrounding CTCF-binding sites

ABSTRACT: SATB1, a nuclear matrix-associated protein, has long been proposed to function as a global chromatin loop organizer in T cells. However, the precise roles of SATB1 in chromatin organization remain elusive. Here we show that the depletion of SATB1 in immortalized T cells led to pronounced changes in gene expression, particularly for genes involved in cell proliferation and T cell activation, as well as 3D genome architecture at multiple scales, including the A/B compartment, topologically associating domains (TADs), and loops. Importantly, SATB1 extensively colocalizes with CTCF throughout the genome. Depletion of SATB1 led to increased association among the SATB1/CTCF co-occupied sites, as well as increased chromatin contacts across these sites, thereby altering the genome-wide chromatin loop landscape. SATB1 does not regulate genome architecture by modulating CTCF occupancy. Rather, the topological effects imposed by SATB1 may be attributed to SATB1-dependent anchoring of CTCF to the salt extraction-resistant nuclear matrix. Together, our findings suggest that the functional interplay between nuclear matrix and CTCF plays a critical role in orchestrating 3D genome organization.

ORGANISM(S): Mus musculus Homo sapiens

PROVIDER: GSE199007 | GEO | 2023/03/05

REPOSITORIES: GEO

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SATB1 Regulates 3D Genome Architecture in T cells by Constraining Chromatin Interactions surrounding CTCF-binding sites

Project description:SATB1, a nuclear matrix-associated protein, has long been proposed to function as a global chromatin loop organizer in T cells. However, the precise roles of SATB1 in chromatin organization remain elusive. Here we show that the depletion of SATB1 in immortalized T cells led to pronounced changes in gene expression, particularly for genes involved in cell proliferation and T cell activation, as well as 3D genome architecture at multiple scales, including the A/B compartment, topologically associating domains (TADs), and loops. Importantly, SATB1 extensively colocalizes with CTCF throughout the genome. Depletion of SATB1 led to increased association among the SATB1/CTCF co-occupied sites, as well as increased chromatin contacts across these sites, thereby altering the genome-wide chromatin loop landscape. SATB1 does not regulate genome architecture by modulating CTCF occupancy. Rather, the topological effects imposed by SATB1 may be attributed to SATB1-dependent anchoring of CTCF to the salt extraction-resistant nuclear matrix. Together, our findings suggest that the functional interplay between nuclear matrix and CTCF plays a critical role in orchestrating 3D genome organization.

2023-03-05 | GSE199006 | GEO

SATB1 Regulates 3D Genome Architecture in T cells by Constraining Chromatin Interactions surrounding CTCF-binding sites [CUT&Tag]

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SATB1 Regulates 3D Genome Architecture in T cells by Constraining Chromatin Interactions surrounding CTCF-binding sites [Hi-C]

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SATB1 Regulates 3D Genome Architecture in T cells by Constraining Chromatin Interactions surrounding CTCF-binding sites [RNA-seq]

Project description:Spatial genome organization is critical for precise gene regulation during development. Special AT-rich sequence binding protein 1 (SATB1) has long been proposed to act as a global chromatin loop organizer in T cells. However, the exact functions of SATB1 in genome organization remain elusive. Here we show that the depletion of SATB1 in human and murine T cells led to transcriptional dysregulation for genes involved in T cell activation, as well as alterations of 3D genome architecture at multiple scales, including the A/B compartment, topologically associating domains (TADs), and loops. Importantly, SATB1 extensively colocalizes with CTCF throughout the genome. Depletion of SATB1 led to increased chromatin contacts among and across the SATB1/CTCF co-occupied sites, thereby affecting the transcription of critical genes involved in T cell activation. The loss of SATB1 did not affect the genome-wide occupancy of CTCF, but significantly reduced the retention of CTCF in the nuclear matrix. Collectively, our data reveal that SATB1 constrains chromatin topology surrounding CTCF-binding sites by tethering CTCF to the nuclear matrix, and suggest that the functional interplay between SATB1 and CTCF contributes to 3D genome organization.

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SATB1 Regulates 3D Genome Architecture in T cells by Constraining Chromatin Interactions surrounding CTCF-binding sites [CUT&Tag]

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The nuclear matrix associating protein HNRNPU functions as a key regulator of 3D genome architecture [ChIP-Seq 2]

Project description:Here we show that HNRNPU, the major nuclear matrix attachment factor, is necessary to maintain proper nuclear architecture in mouse hepatocytes. Upon HNRNPU depletion, the interactions between chromatin and nuclear lamina have been changed dramatically；chromatin organization is globally changed; boundaries of topologically associating domains (TADs) become weaker; inter-TAD interactions are increased; thousands of genes are significantly altered coincident with 3D chromatin changes. Mechanically, HNRNPU interacts with CTCF and RAD21, which affects the binding of RAD21 to the chromatin significantly, whereas CTCF bindings are almost unchanged, what’ more, the decrease of binding strengths are highly correlated with the weakness of loop bounded by Rad21. Taken together, we identify HNRNPU as a key regulator of chromatin architecture, and our data suggest the importance of nuclear matrix associating factors in 3D genome organization.

2017-12-03 | GSE104098 | GEO

The 3D enhancer network of the developing T cell genome is controlled by SATB1 [Hi-C]

Project description:Mechanisms of tissue-specific gene expression regulation, particularly via spatial coordination of gene promoters and their regulatory elements are poorly understood. Here we investigated the 3D genome organization of developing murine T cells. We identified a tissue-specific genome organizer SATB1 as a factor enriched at the anchors of promoter-enhancer chromatin loops. To unravel its functions in T cells, we generated Satb1fl/flCd4-Cre+ (Satb1 cKO) conditional knockout animals. Satb1 cKO animals suffer from severe autoimmunity so we sought to investigate a potential link between the autoimmunity and putatively deregulated nuclear architecture caused by SATB1 depletion. This series of Hi-C and HiChIP experiments is a part of SuperSeries including also RNA-Seq and ATAC-Seq experiments to fully understand the deregulation of Satb1 cKO thymocytes and to unravel the roles of SATB1 in T cell chromatin organization. Utilizing the HiChIP data, we compared SATB1 and CTCF-mediated chromatin loops, revealing that SATB1 builds a more refined layer of genome organization upon the CTCF scaffold. Moreover, H3K27ac HiChIP and Hi-C experiments in WT and Satb1 cKO thymocytes helped us to assess the functional impact of SATB1 and its underlying genome-wide regulome. SATB1 primarily mediates promoter-enhancer loops affecting a number of master regulator genes whose deregulation in knockout animals may comprise a cell-intrinsic mechanism of the autoimmunity. Our findings indicate a possible existence of a special class of genome organizers controlling tissue and/or time-specific transcriptional programs via spatial chromatin arrangements that are complementary to the function of conventional ubiquitously expressed genome organizers.

2022-09-23 | GSE173446 | GEO

The 3D enhancer network of the developing T cell genome is controlled by SATB1 [RNA-seq]

Project description:Mechanisms of tissue-specific gene expression regulation, particularly via spatial coordination of gene promoters and their regulatory elements are poorly understood. Here we investigated the 3D genome organization of developing murine T cells. We identified a tissue-specific genome organizer SATB1 as a factor enriched at the anchors of promoter-enhancer chromatin loops. To unravel its functions in T cells, we generated Satb1fl/flCd4-Cre+ (Satb1 cKO) conditional knockout animals. Satb1 cKO animals suffer from severe autoimmunity so we sought to investigate a potential link between the autoimmunity and putatively deregulated nuclear architecture caused by SATB1 depletion. This series of RNA-Seq experiments is a part of SuperSeries including also ATAC-Seq, Hi-C and HiChIP experiments to fully understand the deregulation of Satb1 cKO thymocytes and to unravel the roles of SATB1 in T cell chromatin organization. RNA-Seq experiments supported the repressive nature of Satb1 cKO nuclear environment and together with the other datasets it showed that SATB1 functions primarily as an activator. SATB1 mediates promoter-enhancer chromatin loops affecting a number of master regulator genes whose deregulation in knockout animals may comprise a cell-intrinsic mechanism of the autoimmunity. Our findings indicate a possible existence of a special class of genome organizers controlling tissue and/or time-specific transcriptional programs via spatial chromatin arrangements that are complementary to the function of conventional and ubiquitously expressed genome organizers.

2022-09-23 | GSE173470 | GEO

The 3D enhancer network of the developing T cell genome is controlled by SATB1 [ATAC-seq]

Project description:Mechanisms of tissue-specific gene expression regulation, particularly via spatial coordination of gene promoters and their regulatory elements are poorly understood. Here we investigated the 3D genome organization of developing murine T cells. We identified a tissue-specific genome organizer SATB1 as a factor enriched at the anchors of promoter-enhancer chromatin loops. To unravel its functions in T cells, we generated Satb1fl/flCd4-Cre+ (Satb1 cKO) conditional knockout animals. Satb1 cKO animals suffer from severe autoimmunity so we sought to investigate a potential link between the autoimmunity and putatively deregulated nuclear architecture caused by SATB1 depletion. This series of ATAC-Seq experiments is a part of SuperSeries including also RNA-Seq, Hi-C and HiChIP experiments to fully understand the deregulation of Satb1 cKO thymocytes and to unravel the roles of SATB1 in T cell chromatin organization. ATAC-Seq experiments supported the repressive nature of Satb1 cKO nuclear environment and together with the other datasets it showed that SATB1 functions primarily as an activator. SATB1 mediates promoter-enhancer chromatin loops affecting a number of master regulator genes whose deregulation in knockout animals may comprise a cell-intrinsic mechanism of the autoimmunity. Our findings indicate a possible existence of a special class of genome organizers controlling tissue and/or time-specific transcriptional programs via spatial chromatin arrangements that are complementary to the function of conventional and ubiquitously expressed genome organizers.

2022-09-23 | GSE173445 | GEO

The 3D enhancer network of the developing T cell genome is shaped by SATB1

Project description:Mechanisms of tissue-specific gene expression regulation via 3D genome organization are poorly understood. Here we uncover the regulatory chromatin network of developing T cells and identify SATB1, a tissue-specific genome organizer, enriched at the anchors of promoter-enhancer loops. We have generated a T-cell specific Satb1 conditional knockout mouse which allows us to infer the molecular mechanisms responsible for the deregulation of its immune system. H3K27ac HiChIP and Hi-C experiments indicate that SATB1-dependent promoter-enhancer loops regulate expression of master regulator genes (such as Bcl6), the T cell receptor locus and adhesion molecule genes, collectively being critical for cell lineage specification and immune system homeostasis. SATB1-dependent regulatory chromatin loops represent a more refined layer of genome organization built upon a high-order scaffold provided by CTCF and other factors. Overall, our findings unravel the function of a tissue-specific factor that controls transcription programs, via spatial chromatin arrangements complementary to the chromatin structure imposed by ubiquitously expressed genome organizers.

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