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CTCF facilitates subset-specific chromatin interactions to limit the formation of memory CD8+ T cells [RNA-Seq]

ABSTRACT: CD8+ T cells provide protection from infection and tumor growth, and many current immunotherapies target molecules that enhance CD8+ T cell function and differentiation. The transcriptional programs orchestrating CD8+ T cell differentiation in response to infection has been described, but the changes in spatial chromatin organization accompanying effector and memory CD8+ T cell differentiation is unknown, despite research showing the importance of long-range chromatin interactions for transcriptional regulation in various cell types. Here, we studied how genome organization is integrated with CD8+ T cell differentiation and investigated the role of CTCF, a key factor that regulates genome organization through blocking or facilitating chromatin interactions, in regulating CD8+ T cell fates. We observed T cell subset-specific changes in chromatin organization and CTCF binding, and revealed weak-affinity CTCF binding is needed to promote terminal differentiation of CD8+ T cells by coordinating chromatin interactions that regulate transcriptional programs driving CD8+ T cell differentiation.

ORGANISM(S): Mus musculus

PROVIDER: GSE205079 | GEO | 2023/04/21

REPOSITORIES: GEO

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CTCF facilitates subset-specific chromatin interactions to limit the formation of memory CD8+ T cells [HiC]

Project description:CD8+ T cells provide protection from infection and tumor growth, and many current immunotherapies target molecules that enhance CD8+ T cell function and differentiation. The transcriptional programs orchestrating CD8+ T cell differentiation in response to infection has been described, but the changes in spatial chromatin organization accompanying effector and memory CD8+ T cell differentiation is unknown, despite research showing the importance of long-range chromatin interactions for transcriptional regulation in various cell types. Here, we studied how genome organization is integrated with CD8+ T cell differentiation and investigated the role of CTCF, a key factor that regulates genome organization through blocking or facilitating chromatin interactions, in regulating CD8+ T cell fates. We observed T cell subset-specific changes in chromatin organization and CTCF binding, and revealed weak-affinity CTCF binding is needed to promote terminal differentiation of CD8+ T cells by coordinating chromatin interactions that regulate transcriptional programs driving CD8+ T cell differentiation.

2023-04-21 | GSE205081 | GEO

CTCF facilitates subset-specific chromatin interactions to limit the formation of memory CD8+ T cells [ChIP-Seq]

2023-04-21 | GSE205077 | GEO

CTCF facilitates subset-specific chromatin interactions to limit the formation of memory CD8+ T cells [ATAC-Seq]

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Inner nuclear protein Matrin-3 coordinates cell differentiation by stabilizing chromatin architecture

Project description:Precise control of gene expression during differentiation relies on the interplay of chromatin and nuclear structure. Despite an established contribution of nuclear membrane proteins to developmental gene regulation, little is known regarding the role of inner nuclear proteins. Here we demonstrate that loss of the nuclear scaffolding protein Matrin-3 (Matr3) in erythroid cells leads to morphological and gene expression changes characteristic of accelerated maturation, as well as broad alterations in chromatin organization similar to those accompanying differentiation. Matr3 protein interacts with CTCF and the cohesin complex, and its loss perturbs their occupancy at a subset of sites. Destabilization of CTCF and cohesin binding correlates with altered transcription and accelerated differentiation. This association is conserved in embryonic stem cells. Our findings indicate Matr3 negatively affects cell fate transitions and demonstrate that a critical inner nuclear protein impacts occupancy of architectural factors, culminating in broad effects on chromatin organization and cell differentiation.

2021-11-11 | PXD028867 | Pride

CTCF-dependent chromatin architecture and SUZ12/PRC2 complex recruitment are required for peripheral myelination and repair

Project description:Chromatin organization is critical for cell growth, differentiation, and disease development, however, its functions in peripheral myelination and myelin repair remain elusive. Here we observed a global diminution of chromatin accessibility during Schwann cell differentiation and demonstrated that the chromatin organizer CCCTC-binding factor (CTCF) is critical for Schwann cell myelination and myelin regeneration after nerve injury. Inhibition of Ctcf or its deletion blocked Schwann cell differentiation at the pre-myelinating stage, whereas overexpression of CTCF promoted the myelination program. CTCF establishes the chromatin interaction loop between promoters and regulatory elements to promote expression of key pro-myelinogenic factors such as EGR2. In addition, CTCF interacts with SUZ12, a component of polycomb-repressive-complex 2, to repress expression of immature Schwann cell-associated regulators including HES1, RSPO2, and CALCA. Together, our findings reveal the dual role of CTCF-dependent chromatin organization in promoting myelinogenic programs and recruiting chromatin-repressive complexes to block differentiation inhibitors to control peripheral myelination and myelin repair.

2020-06-22 | GSE138117 | GEO

Cohesin and CTCF Differentially Affect the Chromatin Architecture and Gene Expression in Human Cells

Project description:Recent studies of genome-wide chromatin interactions have revealed that the human genome is partitioned into many self-associating topological domains. The boundary sequences are enriched for binding sites of CTCF and the cohesin complex, implicating these two factors in the establishment or maintenance of topological domains. To determine the role of cohesin and CTCF in higher order chromatin architecture in human cells, we proteolytically cleaved the cohesin complex from interphase chromatin and examined changes in chromosomal organization as well as transcriptome. We observed a general loss of local chromosomal interactions upon disruption of cohesin complex, but the topological domains remain intact. However, we found that depletion of CTCF by RNA interference in these cells not only reduced intra-domain interactions but also increased inter-domain interactions. Further more, distinct groups of genes become mis-regulated upon depletion of cohesin and CTCF. Taken together, these observations suggest that CTCF and cohesin contribute in different ways to chromatin organization and gene regulation. Hi-C and mRNA-seq experiments in Cohesin and CTCF depleted HEK293 cells

2013-12-16 | E-GEOD-44267 | biostudies-arrayexpress

Architectural protein subclasses shape 3-D organization of genomes during lineage commitment

Project description:Understanding the topological configurations of chromatin can reveal valuable insights into how the genome and epigenome act in concert to control cell fate during development. Here we generate high-resolution architecture maps across seven genomic loci in embryonic stem cells and neural progenitor cells. We observe a hierarchy of 3-D interactions that undergo marked reorganization at the sub-Mb scale during differentiation. Distinct combinations of CTCF, Mediator, and cohesin show widespread enrichment in architecture at different length scales. CTCF/cohesin anchor long-range constitutive interactions that might form the topological basis for invariant sub-domains. Conversely, Mediator/cohesin together with pioneer factors bridge short-range enhancer-promoter interactions within and between larger sub-domains. Knockdown of Smc1 or Med12 in ES cells results in disruption of spatial architecture and down-regulation of genes found in cohesin-mediated interactions. We conclude that cell type-specific chromatin organization occurs at the sub-Mb scale and that architectural proteins shape the genome in hierarchical length scales. Analysis of higher-order chromatin chromatin architecture in mouse ES cells and ES-derived NPCs. Analysis of CTCF and Smc1 occupied sites in ES-derived NPCs.

2013-05-24 | E-GEOD-36203 | biostudies-arrayexpress

Transient Pairing of Homologous Oct4 Alleles Accompanies the Onset of Embryonic Stem Cell Differentiation

Project description:The relationship between chromatin organization and transcriptional regulation is an area of intense investigation. We have characterized the spatial relationships between alleles of the Oct4, Sox2, and Nanog genes in single cells during the earliest stages of mouse embryonic stem cell (ESC) differentiation and during embryonic development. We describe homologous pairing of the Oct4 alleles during ESC differentiation and embryogenesis, and present evidence that pairing is correlated with the kinetics of ESC differentiation. Importantly, we identify critical DNA elements within the Oct4 promoter/enhancer region that mediate pairing of Oct4 alleles. Finally, we show that mutation of OCT4/SOX2 binding sites within this region abolishes inter-chromosomal interactions and affects accumulation of the repressive H3K9me2 modification at the Oct4 enhancer. Our findings demonstrate that chromatin organization and transcriptional programs are intimately connected in ESCs, and that the dynamic positioning of the Oct4 alleles is associated with the transition from pluripotency to lineage specification. Examination of chromatin contacts between Oct4 alleles using PE-4Cseq

2015-02-03 | E-GEOD-65510 | biostudies-arrayexpress

Reorganization of nuclear lamina – genome interactions upon differentiation of embryonic stem cells.

Project description:The three-dimensional organization of chromosomes within the nucleus and its dynamics during differentiation are largely unknown. We present a genome-wide analysis of the interactions between chromatin and the nuclear lamina during differentiation of mouse embryonic stem cells (ESCs) into lineage-committed neural precursor cells (NPCs) and terminally differentiated astrocytes. Chromatin in each of these cell types shows a similar organization into large lamina associated domains (LADs), which represent a transcriptionally repressive environment. During sequential differentiation steps, lamina interactions are progressively modified at hundreds of genomic locations. This remodeling is typically confined to individual transcription units and involves many genes that determine cellular identity. From ESCs to NPCs, the majority of genes that move away from the lamina are concomitantly activated. Strikingly, a significant amount remain inactive yet become primed for activation by further differentiation. These results suggest that lamina-genome interactions are widely involved in the control of gene expression programs during lineage commitment and terminal differentiation. laminB1-chromatin interactions were assayed in 4 different mouse cell-types. For each cell-type there were 2 biological replicates, that were hybridized in a dye-swap design.

2010-05-27 | E-GEOD-17051 | biostudies-arrayexpress

Regulation of cohesin loop extrusion underlies changes in enhancer-promoter interactions during pancreatic cell differentiation

Project description:Transcriptional reprogramming during cell fate determination involves precise targeting of enhancers to tissue-specific genes. Enhancer-promoter interactions are regulated by different types of 3D chromatin organization, including compartmental domains and CTCF loops. To understand the contribution of these different levels of chromatin organization in cell lineage commitment, we analyzed changes in 3D organization during the differentiation of human embryonic stem cells (hESCs) into pancreatic islet organoids. We find that major events in chromatin reorganization, including decompaction of transposon-enriched heterochromatin, breakdown of poised enhancer-promoter interaction networks, gain or loss of CTCF loops and establishment of novel enhancer-promoter contacts, occur either sequentially or simultaneously. Transcriptionally activated transposons released from unstable heterochromatin compartments recruit CTCF to form new loops. In contrast, when released from poised long-range interaction networks, enhancers and genes crucial for cell differentiation recruit tissue-specific transcription factors by either direct binding or indirect 3D contacts containing RNA Polymerase II. Activation of stage-specific genes correlates with gain of CTCF binding at anchors of extended CTCF loops, suggesting changes in loop extrusion capacity. In agreement with this, we find a global increase in cohesin loading leading to longer residency on extended CTCF loops encompassing tissue-specific genes. Our findings provide new insights into how distinct types of chromatin organization affect the reprogramming of gene expression patterns to regulate cell lineage commitment.

2023-09-19 | GSE211101 | GEO

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