3D organization of regulatory elements for transcriptional regulation in Arabidopsis

Deng，Li1; Zhou，Qiangwei1,2; Zhou，Jie1; Zhang，Qing1; Jia，Zhibo1; Zhu，Guangfeng1; Cheng，Sheng1,2; Cheng，Lulu1; Yin，Caijun1; Yang，Chao1; Shen，Jinxiong1; Nie，Junwei3; Zhu，Jian Kang4,5; Li，Guoliang1,2; Zhao，Lun1

2023-12-01

10.1186/s13059-023-03018-4

Genome Biology   Impact Factor & Quartile

1474-7596

1474-760X

Background: Although 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. Results: Here 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. Conclusion: The 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.

Arabidopsis ChIA-PET Chromatin architecture Transcriptional regulation

SCI

English

Corresponding

Fundamental Research Funds for the Central Universities[2662021PY005];National Natural Science Foundation of China[31930032];National Natural Science Foundation of China[32188102];National Natural Science Foundation of China[32222063];

Biotechnology & Applied Microbiology ; Genetics & Heredity

Biotechnology & Applied Microbiology ; Genetics & Heredity

WOS:001044278200001

BMC

MOLECULAR BIOLOGY & GENETICS

2-s2.0-85166783787

Scopus

1.National Key Laboratory of Crop Genetic Improvement,Hubei Hongshan Laboratory,Huazhong Agricultural University,Wuhan,430070,China
2.Agricultural Bioinformatics Key Laboratory of Hubei Province and Hubei Engineering Technology Research Center of Agricultural Big Data,3D Genomics Research Center,Huazhong Agricultural University,Wuhan,430070,China
3.Vazyme Biotech Co.,Ltd.,Nanjing,210000,China
4.Institute of Advanced Biotechnology and School of Life Sciences,Southern University of Science and Technology,Shenzhen,518055,China
5.Center for Advanced Bioindustry Technologies,Chinese Academy of Agricultural Sciences,Beijing,100081,China

Deng，Li,Zhou，Qiangwei,Zhou，Jie,et al. 3D organization of regulatory elements for transcriptional regulation in Arabidopsis[J]. Genome Biology,2023,24(1).

Deng，Li.,Zhou，Qiangwei.,Zhou，Jie.,Zhang，Qing.,Jia，Zhibo.,...&Zhao，Lun.(2023).3D organization of regulatory elements for transcriptional regulation in Arabidopsis.Genome Biology,24(1).

Deng，Li,et al."3D organization of regulatory elements for transcriptional regulation in Arabidopsis".Genome Biology 24.1(2023).