Global Profiling of RNA-chromatin Interactions Reveals Co-regulatory Gene Expression Networks in Arabidopsis

Overview

Journal Nat Plants

Specialties Biology
Genetics

Date 2021 Oct 15

PMID 34650265

Citations 8

Authors

Lanxia Li

Haofei Luo

Do-Hwan Lim

Lu Han

Yan Li

Xiang-Dong Fu

Yijun Qi

Affiliations

Soon will be listed here.

Abstract

It is increasingly evident that various RNAs can bind chromatin to regulate gene expression and genome organization. Here we adapted a sequencing-based technique to profile RNA-chromatin interactions at a genome-wide scale in Arabidopsis seedlings. We identified more than 10,000 RNA-chromatin interactions mediated by protein-coding RNAs and non-coding RNAs. Cis and intra-chromosomal interactions are mainly mediated by protein-coding RNAs, whereas inter-chromosomal interactions are primarily mediated by non-coding RNAs. Many RNA-chromatin interactions tend to positively correlate with DNA-DNA interactions, suggesting their mutual influence and reinforcement. We further show that some RNA-chromatin interactions undergo alterations in response to biotic and abiotic stresses and that altered RNA-chromatin interactions form co-regulatory networks. Our study provides a global view on RNA-chromatin interactions in Arabidopsis and a rich resource for future investigations of regulatory roles of RNAs in gene expression and genome organization.

Citing Articles

Comprehensive analysis of RNA-chromatin, RNA-, and DNA-protein interactions.

Khlebnikov D, Nikolskaya A, Zharikova A, Mironov A NAR Genom Bioinform. 2025; 7(1):lqaf010.

PMID: 40007725 PMC: 11850300. DOI: 10.1093/nargab/lqaf010.

Simultaneous profiling of chromatin-associated RNA at targeted DNA loci and RNA-RNA Interactions through TaDRIM-seq.

Ding C, Chen G, Luan S, Gao R, Fan Y, Zhang Y Nat Commun. 2025; 16(1):1500.

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Epigenetics in the modern era of crop improvements.

Xue Y, Cao X, Chen X, Deng X, Deng X, Ding Y Sci China Life Sci. 2025; .

PMID: 39808224 DOI: 10.1007/s11427-024-2784-3.

A fine-scale Arabidopsis chromatin landscape reveals chromatin conformation-associated transcriptional dynamics.

Zhang Y, Dong Q, Wang Z, Liu Q, Yu H, Sun W Nat Commun. 2024; 15(1):3253.

PMID: 38627396 PMC: 11021422. DOI: 10.1038/s41467-024-47678-7.

Interplay between coding and non-coding regulation drives the Arabidopsis seed-to-seedling transition.

Tremblay B, Santini C, Cheng Y, Zhang X, Rosa S, Questa J Nat Commun. 2024; 15(1):1724.

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