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Capture of TAD reorganization endows variant patterns of gene transcription (Hi-C)

ABSTRACT: Capture of TAD reorganization endows variant patterns of gene transcription (Hi-C)

PROVIDER: PRJNA962583 | ENA |

REPOSITORIES: ENA

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Capture of TAD reorganization endows variant patterns of gene transcription (Hi-C)

Project description:TAD (Topologically Associating Domain) reorganization occurs commonly in cell nucleus and contributes to gene activation and inhibition through separation or fusion of adjacent TADs. However, identification of functional genes impacted by TAD alteration and revealing of TAD-reorganization mechanism underlying gene transcription remain to be fully elucidated. Here, we firstly developed a novel approach termed Inter3D to specifically dig out genes regulated by TAD reorganization. By constructing the comprehensive TAD reorganization medicating epigenomic landscapes in tumor cells, we showed that TAD separation interrupted the intrachromosomal loop at MYL12B locus and abrogated its transcription, while TAD fusion generated the chromosomal interaction and triggered CYP27B1 activation. Our study provides a comprehensive insight into capture of TAD rearrangement-mediated gene loci and moves towards recognizing the functional role of TAD reorganization in gene transcription.

2024-04-29 | GSE230795 | GEO

Capture of TAD reorganization endows variant patterns of gene transcription

Project description:Capture of TAD reorganization endows variant patterns of gene transcription

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Capture of TAD reorganization endows variant patterns of gene transcription (RNA-Seq)

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Capture of TAD reorganization endows variant patterns of gene transcription (ATAC-Seq)

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Capture of TAD reorganization endows variant patterns of gene transcription (ATAC-Seq)

Project description:Capture of TAD reorganization endows variant patterns of gene transcription (ATAC-Seq)

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Capture of TAD reorganization endows variant patterns of gene transcription (RNA-Seq)

Project description:Capture of TAD reorganization endows variant patterns of gene transcription (RNA-Seq)

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Capture of TAD reorganization endows variant patterns of gene transcription

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

2024-04-29 | GSE230798 | GEO

HSFA1a controls plant heat stress response through its action on the 3D chromatin reorganization of enhancer-promoter interactions [Capture Hi-C]

Project description:We investigated the role of HSFA1a, a master regulator of heat stress response, in this reorganization through promotion of the formation of promoter/enhancer chromatin loops. To determine whether distal REs come into contact with promoters, instead of using a classical Hi-C, we further combined Hi-C with a capture enrichment step. We generated a biotinylated RNA bait library specifically targeting 212,735 promoter regions and performed a capture Hi-C after 0h, 1h and 6h after stress.

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Transcription-Associated Chromatin Reorganization During Cellular Rejuvenation (Hi-C)

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Transcription-Associated Chromatin Reorganization During Cellular Rejuvenation (Hi-C)

Project description:Aging is associated with a progressive decline in cellular function. To reset the aged cellular phenotype, various reprogramming approaches, including mechanical routes, have been proposed. However, the epigenetic mechanisms underlying cellular rejuvenation are poorly understood. We studied the transcriptional and genome-wide chromatin organization changes in young, aged and mechanically rejuvenated fibroblasts using RNA-seq and Hi-C experiments. The mechanically rejuvenated aged fibroblasts, that had reset their transcription to a younger cell state, showed a reorganization of the inter-chromosomal contacts and lamina-associated domains. Interestingly, the observed chromatin reorganization correlated with the transcriptional changes. Immunofluorescence experiments in the rejuvenated state confirmed increased contractility and reduced chromosome copy number variations, similar to younger fibroblasts. In addition, the rejuvenated contractile properties were maintained over multiple cell passages. Taken together, our results provide a multi-scale characterization of the chromatin reorganization that accompanies cellular aging and rejuvenation.

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