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

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

PROVIDER: PRJNA962581 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR24327310_1.fastq.gz	Fastqsanger.gz
	SRR24327310_2.fastq.gz	Fastqsanger.gz
	SRR24327311_1.fastq.gz	Fastqsanger.gz
	SRR24327311_2.fastq.gz	Fastqsanger.gz

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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 (Hi-C)

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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 (RNA-Seq)

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 | GSE230797 | GEO

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

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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

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

2024-04-29 | GSE230798 | GEO

M1BP cooperates with CP190 to activate transcription at TAD borders and promote chromatin insulator activity

Project description:Genome organization is driven by forces affecting transcriptional state, but the relationship between transcription and genome architecture remains unclear. Here, we identified the Drosophila transcription factor Motif 1 Binding Protein (M1BP) in physical association with the gypsy chromatin insulator core complex, including the universal insulator protein CP190. M1BP is required for enhancer-blocking and barrier activities of the gypsy insulator as well as its proper nuclear localization. Genome-wide, M1BP specifically colocalizes with CP190 at Motif 1-containing promoters, which are enriched at topologically associating domain (TAD) borders. M1BP facilitates CP190 chromatin binding at many shared sites and vice versa. Both factors promote Motif 1-dependent gene expression and transcription near TAD borders genome-wide. Finally, loss of M1BP reduces chromatin accessibility and increases both inter- and intra-TAD local genome compaction. Our results reveal physical and functional interaction between CP190 and M1BP to activate transcription at TAD borders and mediate chromatin insulator-dependent genome organization.

2021-06-07 | PXD026497 | Pride

Characterisation of the mouse alpha-globin sub-TAD 3' boundary in erythroid cells [NG Capture-C]

Project description:Mammalian genomes are subdivided into large (50-2000 kb) regions of chromatin referred to as Topologically Associating Domains (TADs or sub-TADs). Chromatin within an individual TAD contacts itself more frequently than with regions in surrounding TADs thereby directing enhancer-promoter interactions. In many cases, the borders of TADs are defined by convergently orientated boundary elements associated with CCCTC-binding factor (CTCF), which stabilises the cohesin complex on chromatin and prevents its translocation. This delimits chromatin loop extrusion which is thought to underlie the formation of TADs. However, not all CTCF-bound sites act as boundaries and, importantly, not all TADs are flanked by convergent CTCF sites. Here, we examined the CTCF binding sites within a ~70 kb sub-TAD containing the duplicated mouse α-like globin genes and their five enhancers (5’-R1-R2-R3-Rm-R4-α1-α2-3’). The 5’ border of this sub-TAD is defined by a pair of CTCF sites. Surprisingly, we show that deletion of the CTCF binding sites within and downstream of the α-globin locus leaves the sub-TAD largely intact. The predominant 3’ border of the sub-TAD is defined by a steep reduction in contacts: this corresponds to the transcribed α2-globin gene rather than the CTCF sites at the 3’-end of the sub-TAD. Of interest, the almost identical α1- and α2-globin genes interact differently with the enhancers, resulting in preferential expression of the proximal α1-globin gene which behaves as a partial boundary between the enhancers and the distal α2-globin gene. Together, these observations provide direct evidence that actively transcribed genes can behave as boundary elements.

2022-06-01 | GSE153208 | GEO

Manipulation of TAD reorganization by chemical-dependent genome linking.

Project description:Reorganization of topologically associated domain (TAD) is considered to be a novel mechanism for cell fate transitions. Here, we present a protocol to manipulate TAD via abscisic acid (ABA)-dependent genome linking. We use this protocol to merge two adjacent TADs and evaluate the influence on cell fate transitions. The advantages are that the manipulation does not change the genome and is reversible by withdrawing ABA. The major challenge is how to select linking loci for efficient TAD reorganization. For complete details on the use and execution of this protocol, please refer to Wang et al. (2021).

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