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

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. 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.