SRF is a new player in 3D genome organization and stem cell pluripotency
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Q Exactive HF
ORGANISM(S): Mus Musculus (mouse)
TISSUE(S): Embryonic Stem Cell
SUBMITTER: 
David Meierhofer
LAB HEAD: Bernhard Herrmann
PROVIDER: PXD049365 | Pride | 2024-10-14
REPOSITORIES: Pride
Dataset's files
Similar Datasets
Project description:Serum response factor (SRF) is a transcription factor essential for cell proliferation, differentiation, and migration, and is required for primitive streak and mesoderm formation in the embryo. The canonical roles of SRF are mediated by a diverse set of context-dependent cofactors. Here we show that SRF physically interacts with CTCF and cohesin subunits at TAD boundaries and loop anchors. SRF reinforces the insulation of TADs and promotes the formation of long-range chromatin loops. In ES cells, SRF associates with Oct4, Sox2, and Nanog and contributes to the formation of 3D pluripotency hubs. Our findings reveal new roles of SRF in higher-order chromatin organization.
2024-10-09 | GSE255733 | GEO
Project description:The genome is partitioned into Topologically Associating Domains (TADs). About half of the boundaries of these TADs exhibit transcriptional activity and are correlated with better TAD insulation. However, the association between these transcripts and TAD insulation, enhancer:promoter interactions and transcription of genes remains unknown. Here we investigate the functional roles of these bRNAs (boundary-RNA) in boundary insulation and consequent effects on enhancer-promoter interactions and TAD transcription genome-wide and more specifically on the disease relevant INK4a/ARF TAD. Using a series of CTCF site deletions and bRNA knockdown experiments at this TAD boundary, we show a direct association of CTCF with the bidirectional bRNAs where the loss of bRNA triggers the concomitant loss of: CTCF at the TAD boundary, its insulation, enhancer:promoter interactions and gene transcription within the targeted TAD. We used another series of enhancer deletions and CRISPRi on promoters within INK4a/ARF TAD to better understand the regulation and origins of bRNA itself. We observe that the enhancers interact with boundaries and positively regulate the bRNA transcription at TAD boundaries. In return, the bRNAs recruit/stabilize the CTCF even on weak motifs within these boundaries and supports CTCF binding in clusters, therefore enhancing TAD insulation. This favors the intra-TAD enhancer:promoter interactions and leads to robust gene transcription. Functionally, bRNAs are more stable than eRNAs and their knockdown exactly mimics the CTCF site deletion. Furthermore, transcribing boundaries exhibit high TAD transcription in TCGA tumour datasets. Together, these results show that active enhancers directly mediate better insulation of TADs by activating the transcription at TAD boundaries triggering CTCF clustering at the boundary which results in better insulation and favours robust intra-TAD enhancer:promoter interactions to activate the gene transcription.
2022-12-28 | GSE180659 | GEO
Project description:Insulators play a critical role in spatiotemporal gene expression in metazoans by separating active and repressive chromatin domains and preventing inappropriate enhancer-promoter contacts. The evolutionarily conserved CCCTC-binding factor (CTCF) is required for insulator function in mammals, but not all of its binding sites act as insulators. Here, we explore the sequence requirements of CTCF-mediated transcriptional insulation with the use of a sensitive insulator reporter assay in mouse embryonic stem cells. We find that potent insulation is provided by multiple CTCF binding sites. Furthermore, CTCF-mediated insulation is dependent on DNA sequences adjacent to its core binding motifs, and CTCF binding sites from topologically associating domains (TAD) boundaries are more likely to function as insulators than those outside TAD boundaries independent of binding strength. Using chromosomal conformation capture assays and high resolution chromatin imaging techniques, we demonstrate that insulators reduce enhancer-promoter contacts by forming local chromatin domains. Taken together, our results provide strong genetic, molecular and imaging evidence connecting chromatin topology to action of insulators in the mammalian genome.
2020-11-25 | GSE162101 | GEO
Project description:Insulators play a critical role in spatiotemporal gene expression in metazoans by separating active and repressive chromatin domains and preventing inappropriate enhancer-promoter contacts. The evolutionarily conserved CCCTC-binding factor (CTCF) is required for insulator function in mammals, but not all of its binding sites act as insulators. Here, we explore the sequence requirements of CTCF-mediated transcriptional insulation with the use of a sensitive insulator reporter assay in mouse embryonic stem cells. We find that potent insulation is provided by multiple CTCF binding sites. Furthermore, CTCF-mediated insulation is dependent on DNA sequences adjacent to its core binding motifs, and CTCF binding sites from topologically associating domains (TAD) boundaries are more likely to function as insulators than those outside TAD boundaries independent of binding strength. Using chromosomal conformation capture assays and high resolution chromatin imaging techniques, we demonstrate that insulators reduce enhancer-promoter contacts by forming local chromatin domains. Taken together, our results provide strong genetic, molecular and imaging evidence connecting chromatin topology to action of insulators in the mammalian genome.
2020-07-06 | GSE153402 | GEO
Project description:Insulators play a critical role in spatiotemporal gene expression in metazoans by separating active and repressive chromatin domains and preventing inappropriate enhancer-promoter contacts. The evolutionarily conserved CCCTC-binding factor (CTCF) is required for insulator function in mammals, but not all of its binding sites act as insulators. Here, we explore the sequence requirements of CTCF-mediated transcriptional insulation with the use of a sensitive insulator reporter assay in mouse embryonic stem cells. We find that potent insulation is provided by multiple CTCF binding sites. Furthermore, CTCF-mediated insulation is dependent on DNA sequences adjacent to its core binding motifs, and CTCF binding sites from topologically associating domains (TAD) boundaries are more likely to function as insulators than those outside TAD boundaries independent of binding strength. Using chromosomal conformation capture assays and high resolution chromatin imaging techniques, we demonstrate that insulators reduce enhancer-promoter contacts by forming local chromatin domains. Taken together, our results provide strong genetic, molecular and imaging evidence connecting chromatin topology to action of insulators in the mammalian genome.
2020-07-06 | GSE153400 | GEO
Project description:3D genome architecture rewiring is known to influence spatiotemporal expression of lineage-specific genes and cell fate transition during multiple lineage progression and cell differentiation. However, it is yet unknown how nuclear architecture remodels and effects transcription changes during muscle stem cell (SC) development and ageing process. Here, we comprehensively map the 3D chromatin reorganization and integrate genome topology with transcriptional and epigenetic change during muscle SC lineage development and ageing process. Rewiring of compartmentalization is most pronounced when SC become activated, while striking loss in insulation of TAD borders and chromatin looping during early activation process. Meanwhile, super-enhancer containing TAD cluster reorganize in nuclear space and orchestrate stage-specific gene expression. In depth analysis identifies and verifies cis-regulatory elements at Pax7 locus controlling the local chromatin interactions and Pax7 expression. Geriatric cells display a more prominent gain in long-range contacts and loss insulation of TAD borders. Moreover, genome compartmentalization and chromatin loop has already altered for aged SC while geriatric SC display a more prominent loss in strength of TAD borders. Together, our results implicate 3D chromatin extensively reorganizes at multiple architectural levels and underpin the transcriptome remodeling and SC behaviors during SC lineage development and SC aging.
2023-02-03 | GSE189841 | GEO
Project description:3D genome architecture rewiring is known to influence spatiotemporal expression of lineage-specific genes and cell fate transition during multiple lineage progression and cell differentiation. However, it is yet unknown how nuclear architecture remodels and effects transcription changes during muscle stem cell (SC) development and ageing process. Here, we comprehensively map the 3D chromatin reorganization and integrate genome topology with transcriptional and epigenetic change during muscle SC lineage development and ageing process. Rewiring of compartmentalization is most pronounced when SC become activated, while striking loss in insulation of TAD borders and chromatin looping during early activation process. Meanwhile, super-enhancer containing TAD cluster reorganize in nuclear space and orchestrate stage-specific gene expression. In depth analysis identifies and verifies cis-regulatory elements at Pax7 locus controlling the local chromatin interactions and Pax7 expression. Geriatric cells display a more prominent gain in long-range contacts and loss insulation of TAD borders. Moreover, genome compartmentalization and chromatin loop has already altered for aged SC while geriatric SC display a more prominent loss in strength of TAD borders. Together, our results implicate 3D chromatin extensively reorganizes at multiple architectural levels and underpin the transcriptome remodeling and SC behaviors during SC lineage development and SC aging.
2023-02-03 | GSE189840 | GEO
Project description:3D genome architecture rewiring is known to influence spatiotemporal expression of lineage-specific genes and cell fate transition during multiple lineage progression and cell differentiation. However, it is yet unknown how nuclear architecture remodels and effects transcription changes during muscle stem cell (SC) development and ageing process. Here, we comprehensively map the 3D chromatin reorganization and integrate genome topology with transcriptional and epigenetic change during muscle SC lineage development and ageing process. Rewiring of compartmentalization is most pronounced when SC become activated, while striking loss in insulation of TAD borders and chromatin looping during early activation process. Meanwhile, super-enhancer containing TAD cluster reorganize in nuclear space and orchestrate stage-specific gene expression. In depth analysis identifies and verifies cis-regulatory elements at Pax7 locus controlling the local chromatin interactions and Pax7 expression. Geriatric cells display a more prominent gain in long-range contacts and loss insulation of TAD borders. Moreover, genome compartmentalization and chromatin loop has already altered for aged SC while geriatric SC display a more prominent loss in strength of TAD borders. Together, our results implicate 3D chromatin extensively reorganizes at multiple architectural levels and underpin the transcriptome remodeling and SC behaviors during SC lineage development and SC aging.
2023-02-03 | GSE223967 | GEO
Project description:3D genome architecture rewiring is known to influence spatiotemporal expression of lineage-specific genes and cell fate transition during multiple lineage progression and cell differentiation. However, it is yet unknown how nuclear architecture remodels and effects transcription changes during muscle stem cell (SC) development and ageing process. Here, we comprehensively map the 3D chromatin reorganization and integrate genome topology with transcriptional and epigenetic change during muscle SC lineage development and ageing process. Rewiring of compartmentalization is most pronounced when SC become activated, while striking loss in insulation of TAD borders and chromatin looping during early activation process. Meanwhile, super-enhancer containing TAD cluster reorganize in nuclear space and orchestrate stage-specific gene expression. In depth analysis identifies and verifies cis-regulatory elements at Pax7 locus controlling the local chromatin interactions and Pax7 expression. Geriatric cells display a more prominent gain in long-range contacts and loss insulation of TAD borders. Moreover, genome compartmentalization and chromatin loop has already altered for aged SC while geriatric SC display a more prominent loss in strength of TAD borders. Together, our results implicate 3D chromatin extensively reorganizes at multiple architectural levels and underpin the transcriptome remodeling and SC behaviors during SC lineage development and SC aging.
2023-02-03 | GSE223904 | GEO
Project description:3D genome architecture rewiring is known to influence spatiotemporal expression of lineage-specific genes and cell fate transition during multiple lineage progression and cell differentiation. However, it is yet unknown how nuclear architecture remodels and effects transcription changes during muscle stem cell (SC) development and ageing process. Here, we comprehensively map the 3D chromatin reorganization and integrate genome topology with transcriptional and epigenetic change during muscle SC lineage development and ageing process. Rewiring of compartmentalization is most pronounced when SC become activated, while striking loss in insulation of TAD borders and chromatin looping during early activation process. Meanwhile, super-enhancer containing TAD cluster reorganize in nuclear space and orchestrate stage-specific gene expression. In depth analysis identifies and verifies cis-regulatory elements at Pax7 locus controlling the local chromatin interactions and Pax7 expression. Geriatric cells display a more prominent gain in long-range contacts and loss insulation of TAD borders. Moreover, genome compartmentalization and chromatin loop has already altered for aged SC while geriatric SC display a more prominent loss in strength of TAD borders. Together, our results implicate 3D chromatin extensively reorganizes at multiple architectural levels and underpin the transcriptome remodeling and SC behaviors during SC lineage development and SC aging.
2023-02-03 | GSE223903 | GEO