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Plant RNA Biology

Guest editors: Yiliang Ding and Z. Jeffrey Chen

RNA regulation has dramatic impacts on a wide range of biological processes in plants, from gene regulation, to growth, development, and stress response. Technological advances that allow genome-wide analysis of RNA modifications at a single nucleotide resolution, explore the RNA secondary structure, decipher small RNA involved epigenetic regulation, edit RNA sequences, and characterize novel classes of RNAs, have the potential to reveal the functional significance of RNA regulation in plants, and provide exciting new insights into plant RNA biology. Genome Biology will highlight the latest important advances in our understanding of the mechanisms and functions of plant RNA biology.

  1. RNA-DNA hybrid (R-loop)-associated long noncoding RNAs (lncRNAs), including the Arabidopsis lncRNA AUXIN-REGULATED PROMOTER LOOP (APOLO), are emerging as important regulators of three-dimensional chromatin confor...

    Authors: Camille Fonouni-Farde, Aurélie Christ, Thomas Blein, María Florencia Legascue, Lucía Ferrero, Michaël Moison, Leandro Lucero, Juan Sebastián Ramírez-Prado, David Latrasse, Daniel Gonzalez, Moussa Benhamed, Leandro Quadrana, Martin Crespi and Federico Ariel
    Citation: Genome Biology 2022 23:181
  2. Accurate and comprehensive annotation of transcript sequences is essential for transcript quantification and differential gene and transcript expression analysis. Single-molecule long-read sequencing technolog...

    Authors: Runxuan Zhang, Richard Kuo, Max Coulter, Cristiane P. G. Calixto, Juan Carlos Entizne, Wenbin Guo, Yamile Marquez, Linda Milne, Stefan Riegler, Akihiro Matsui, Maho Tanaka, Sarah Harvey, Yubang Gao, Theresa Wießner-Kroh, Alejandro Paniagua, Martin Crespi…
    Citation: Genome Biology 2022 23:149
  3. The precise spatiotemporal gene expression is orchestrated by enhancers that lack general sequence features and thus are difficult to be computationally identified. By nascent RNA sequencing combined with epig...

    Authors: Yilin Xie, Yan Chen, Zijuan Li, Jiafu Zhu, Min Liu, Yijing Zhang and Zhicheng Dong
    Citation: Genome Biology 2022 23:109
  4. Genome-wide association studies (GWAS) aim to correlate phenotypic changes with genotypic variation. Upon transcription, single nucleotide variants (SNVs) may alter mRNA structure, with potential impacts on tr...

    Authors: Ángel Ferrero-Serrano, Megan M. Sylvia, Peter C. Forstmeier, Andrew J. Olson, Doreen Ware, Philip C. Bevilacqua and Sarah M. Assmann
    Citation: Genome Biology 2022 23:101
  5. Hybridization and backcrossing are commonly used in animal and plant breeding to induce heritable variation including epigenetic changes such as paramutation. However, the molecular basis for hybrid-induced ep...

    Authors: Shuai Cao, Longfei Wang, Tongwen Han, Wenxue Ye, Yang Liu, Yi Sun, Stephen P. Moose, Qingxin Song and Z. Jeffrey Chen
    Citation: Genome Biology 2022 23:53
  6. N6-methyladenosine (m6A) mRNA modification is essential for mammalian and plant viability. The U6 m6A methyltransferases in other species regulate S-adenosylmethionine (SAM) homeostasis through installing m6A in ...

    Authors: Chunling Wang, Junbo Yang, Peizhe Song, Wei Zhang, Qiang Lu, Qiong Yu and Guifang Jia
    Citation: Genome Biology 2022 23:40
  7. Plants have the remarkable ability to generate callus, a pluripotent cell mass that acquires competence for subsequent tissue regeneration. Global chromatin remodeling is required for this cell fate transition...

    Authors: Yu-Chan Zhang, Yan-Fei Zhou, Yu Cheng, Jia-Hui Huang, Jian-Ping Lian, Lu Yang, Rui-Rui He, Meng-Qi Lei, Yu-Wei Liu, Chao Yuan, Wen-Long Zhao, Shi Xiao and Yue-Qin Chen
    Citation: Genome Biology 2022 23:28
  8. Models developed using Nanopore direct RNA sequencing data from in vitro synthetic RNA with all adenosine replaced by N6-methyladenosine (m6A) are likely distorted due to superimposed signals from saturated m6A r...

    Authors: Hang Qin, Liang Ou, Jian Gao, Longxian Chen, Jia-Wei Wang, Pei Hao and Xuan Li
    Citation: Genome Biology 2022 23:25
  9. Polyploidy, especially allopolyploidy, which entails merging divergent genomes via hybridization and whole-genome duplication (WGD), is a major route to speciation in plants. The duplication among the parental...

    Authors: Xiaofei Yang, Haopeng Yu, Wenqing Sun, Ling Ding, Ji Li, Jitender Cheema, Ricardo Ramirez-Gonzalez, Xuebo Zhao, Azahara C. Martín, Fei Lu, Bao Liu, Cristobal Uauy, Yiliang Ding and Huakun Zhang
    Citation: Genome Biology 2021 22:326
  10. The dynamic process of transcription termination produces transient RNA intermediates that are difficult to distinguish from each other via short-read sequencing methods.

    Authors: Weipeng Mo, Bo Liu, Hong Zhang, Xianhao Jin, Dongdong Lu, Yiming Yu, Yuelin Liu, Jinbu Jia, Yanping Long, Xian Deng, Xiaofeng Cao, Hongwei Guo and Jixian Zhai
    Citation: Genome Biology 2021 22:322
  11. Plant secondary growth depends on the activity of the vascular cambium, which produces xylem and phloem. Wood derived from xylem is the most abundant form of biomass globally and has played key socio-economic ...

    Authors: Yang Chen, Shaofei Tong, Yuanzhong Jiang, Fandi Ai, Yanlin Feng, Junlin Zhang, Jue Gong, Jiajia Qin, Yuanyuan Zhang, Yingying Zhu, Jianquan Liu and Tao Ma
    Citation: Genome Biology 2021 22:319

    The Correspondence to this article has been published in Genome Biology 2024 25:85