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3D Landscape of Regulatory Elements and Transcription Factors for Transcriptional Regulation in Arabidopsis

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE233528 | GEO | 2023/07/10

REPOSITORIES: GEO

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3D organization of regulatory elements for transcriptional regulation in Arabidopsis.

Project description:BackgroundAlthough spatial organization of compartments and topologically associating domains at large scale is relatively well studied, the spatial organization of regulatory elements at fine scale is poorly understood in plants.ResultsHere we perform high-resolution chromatin interaction analysis using paired-end tag sequencing approach. We map chromatin interactions tethered with RNA polymerase II and associated with heterochromatic, transcriptionally active, and Polycomb-repressive histone modifications in Arabidopsis. Analysis of the regulatory repertoire shows that distal active cis-regulatory elements are linked to their target genes through long-range chromatin interactions with increased expression of the target genes, while poised cis-regulatory elements are linked to their target genes through long-range chromatin interactions with depressed expression of the target genes. Furthermore, we demonstrate that transcription factor MYC2 is critical for chromatin spatial organization, and propose that MYC2 occupancy and MYC2-mediated chromatin interactions coordinately facilitate transcription within the framework of 3D chromatin architecture. Analysis of functionally related gene-defined chromatin connectivity networks reveals that genes implicated in flowering-time control are functionally compartmentalized into separate subdomains via their spatial activity in the leaf or shoot apical meristem, linking active mark- or Polycomb-repressive mark-associated chromatin conformation to coordinated gene expression.ConclusionThe results reveal that the regulation of gene transcription in Arabidopsis is not only by linear juxtaposition, but also by long-range chromatin interactions. Our study uncovers the fine scale genome organization of Arabidopsis and the potential roles of such organization in orchestrating transcription and development.

| S-EPMC10405511 | biostudies-literature

3D Landscape of Regulatory Elements and Transcription Factors for Transcriptional Regulation in Arabidopsis [ATAC-seq]

Project description:Analyses of the regulatory repertoire showed that distal active cis-regulatory elements (CREs) are linked to their target genes through long-range chromatin interactions with increased expression, and poised CREs are linked to their target genes through long-range chromatin interactions with depressed expression. Furthermore, we demonstrated that transcription factor MYC2 is critical for chromatin spatial organization, and proposed that MYC2 occupancy and MYC2-mediated chromatin interactions coordinately facilitate transcription within the framework of 3D chromatin architecture. An analysis of functionally related gene-defined chromatin connectivity networks revealed that genes implicated in flowering-time control are functionally compartmentalized into separate subdomains via their spatial activity in the leaf or shoot apical meristem, linking active mark- or H3K27me3-associated chromatin conformation to coordinated gene expression. The results showed that the guiding principle for modulating gene transcription in Arabidopsis includes not only the linear juxtaposition, but also the long-range chromatin interactions.

2023-07-10 | GSE233525 | GEO

3D Landscape of Regulatory Elements and Transcription Factors for Transcriptional Regulation in Arabidopsis [RNA-seq]

2023-07-10 | GSE233524 | GEO

3D Landscape of Regulatory Elements and Transcription Factors for Transcriptional Regulation in Arabidopsis [ChIA-PET]

2023-07-10 | GSE233527 | GEO

3D Landscape of Regulatory Elements and Transcription Factors for Transcriptional Regulation in Arabidopsis [ChIP-seq]

2023-07-10 | GSE233526 | GEO

3D Landscape of Regulatory Elements and Transcription Factors for Transcription in Arabidopsis

Project description:Whereas spatial genome organization at large scale of compartments and topologically associating domains (TADs) is relatively well studied, the spatial organization of regulatory elements at finer scales is poorly understood in plants. Here, using high-resolution chromatin interaction analysis by paired-end tag sequencing (ChIA-PET) approach, we mapped histone modification-marked DNA elements-associated and RNA polymerase II (RNAPII)-tethered chromatin interactions involving in transcriptionally active, inactive and Polycomb-repressed states in Arabidopsis. Analysis of the regulatory repertoire showed that both active proximal and distal cis-regulatory elements (CREs) promote the transcription of their nearest and long-range connecting genes; poised CREs act as transcriptional repressors to repress their interacting genes’ expression, indicating that the linear juxtaposition is not the only guiding principle modulating gene transcription. Chromatin connectivity networks revealed that genes implicating in flowering-time control are functionally compartmentalized into separate subnuclear domains, linking active mark- and H3K27me3-associated chromatin conformation to coordinated gene expression. Our study uncovers fine-scale Arabidopsis genome organization and their roles in orchestrating transcription and development.

2023-07-10 | GSE207010 | GEO

3D Landscape of Regulatory Elements and Transcription Factors for Transcriptional Regulation in Arabidopsis

Project description:3D Landscape of Regulatory Elements and Transcription Factors for Transcriptional Regulation in Arabidopsis

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3D Landscape of Regulatory Elements and Transcription Factors for Transcriptional Regulation in Arabidopsis [ATAC-seq]

Project description:3D Landscape of Regulatory Elements and Transcription Factors for Transcriptional Regulation in Arabidopsis [ATAC-seq]

| PRJNA976616 | ENA

3D Landscape of Regulatory Elements and Transcription Factors for Transcriptional Regulation in Arabidopsis [RNA-seq]

Project description:3D Landscape of Regulatory Elements and Transcription Factors for Transcriptional Regulation in Arabidopsis [RNA-seq]

| PRJNA976615 | ENA

3D Landscape of Regulatory Elements and Transcription Factors for Transcriptional Regulation in Arabidopsis [ChIA-PET]

Project description:3D Landscape of Regulatory Elements and Transcription Factors for Transcriptional Regulation in Arabidopsis [ChIA-PET]