Literature DB >> 31403819

Plant Noncoding RNAs: Hidden Players in Development and Stress Responses.

Yu Yu1, Yuchan Zhang2, Xuemei Chen3, Yueqin Chen2.   

Abstract

A large and significant portion of eukaryotic transcriptomes consists of noncoding RNAs (ncRNAs) that have minimal or no protein-coding capacity but are functional. Diverse ncRNAs, including both small RNAs and long ncRNAs (lncRNAs), play essential regulatory roles in almost all biological processes by modulating gene expression at the transcriptional and posttranscriptional levels. In this review, we summarize the current knowledge of plant small RNAs and lncRNAs, with a focus on their biogenesis, modes of action, local and systemic movement, and functions at the nexus of plant development and environmental responses. The complex connections among small RNAs, lncRNAs, and small peptides in plants are also discussed, along with the challenges of identifying and investigating new classes of ncRNAs.

Entities:  

Keywords:  circRNA; lncRNA; microRNA; plant development; siRNA; stress response

Mesh:

Substances:

Year:  2019        PMID: 31403819      PMCID: PMC8034839          DOI: 10.1146/annurev-cellbio-100818-125218

Source DB:  PubMed          Journal:  Annu Rev Cell Dev Biol        ISSN: 1081-0706            Impact factor:   13.827


  185 in total

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Authors:  Biao Ding; Asuka Itaya; Xuehua Zhong
Journal:  Curr Opin Plant Biol       Date:  2005-09-21       Impact factor: 7.834

2.  ELF18-INDUCED LONG-NONCODING RNA Associates with Mediator to Enhance Expression of Innate Immune Response Genes in Arabidopsis.

Authors:  Jun Sung Seo; Hai-Xi Sun; Bong Soo Park; Chung-Hao Huang; Shyi-Dong Yeh; Choonkyun Jung; Nam-Hai Chua
Journal:  Plant Cell       Date:  2017-04-11       Impact factor: 11.277

3.  An siRNA pathway prevents transgenerational retrotransposition in plants subjected to stress.

Authors:  Hidetaka Ito; Hervé Gaubert; Etienne Bucher; Marie Mirouze; Isabelle Vaillant; Jerzy Paszkowski
Journal:  Nature       Date:  2011-03-13       Impact factor: 49.962

4.  Rice germline-specific Argonaute MEL1 protein binds to phasiRNAs generated from more than 700 lincRNAs.

Authors:  Reina Komiya; Hajime Ohyanagi; Mitsuru Niihama; Toshiaki Watanabe; Mutsuko Nakano; Nori Kurata; Ken-Ichi Nonomura
Journal:  Plant J       Date:  2014-04-15       Impact factor: 6.417

5.  Arabidopsis ARGONAUTE1 is an RNA Slicer that selectively recruits microRNAs and short interfering RNAs.

Authors:  N Baumberger; D C Baulcombe
Journal:  Proc Natl Acad Sci U S A       Date:  2005-08-04       Impact factor: 11.205

Review 6.  The FLC Locus: A Platform for Discoveries in Epigenetics and Adaptation.

Authors:  Charles Whittaker; Caroline Dean
Journal:  Annu Rev Cell Dev Biol       Date:  2017-07-10       Impact factor: 13.827

7.  A systemic small RNA signaling system in plants.

Authors:  Byung-Chun Yoo; Friedrich Kragler; Erika Varkonyi-Gasic; Valerie Haywood; Sarah Archer-Evans; Young Moo Lee; Tony J Lough; William J Lucas
Journal:  Plant Cell       Date:  2004-07-16       Impact factor: 11.277

8.  Characterization of conserved circular RNA in polyploid Gossypium species and their ancestors.

Authors:  Ting Zhao; Luyao Wang; Sai Li; Min Xu; Xueying Guan; Baoliang Zhou
Journal:  FEBS Lett       Date:  2017-10-13       Impact factor: 4.124

9.  Active DNA demethylation in plant companion cells reinforces transposon methylation in gametes.

Authors:  Christian A Ibarra; Xiaoqi Feng; Vera K Schoft; Tzung-Fu Hsieh; Rie Uzawa; Jessica A Rodrigues; Assaf Zemach; Nina Chumak; Adriana Machlicova; Toshiro Nishimura; Denisse Rojas; Robert L Fischer; Hisashi Tamaru; Daniel Zilberman
Journal:  Science       Date:  2012-09-14       Impact factor: 47.728

10.  Transcriptional read-through of the long non-coding RNA SVALKA governs plant cold acclimation.

Authors:  Peter Kindgren; Ryan Ard; Maxim Ivanov; Sebastian Marquardt
Journal:  Nat Commun       Date:  2018-11-01       Impact factor: 14.919

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  64 in total

Review 1.  The genetic arms race between plant and Xanthomonas: lessons learned from TALE biology.

Authors:  Jiao Xue; Zhanhua Lu; Wei Liu; Shiguang Wang; Dongbai Lu; Xiaofei Wang; Xiuying He
Journal:  Sci China Life Sci       Date:  2020-07-10       Impact factor: 6.038

2.  Identification, characterization, and functional prediction of circular RNAs in maize.

Authors:  Yang Han; Xinxin Li; Yan Yan; Ming-Hua Duan; Jian-Hong Xu
Journal:  Mol Genet Genomics       Date:  2020-01-01       Impact factor: 3.291

Review 3.  Research progress on plant noncoding RNAs in response to low-temperature stress.

Authors:  Chenmin Huo; Baowen Zhang; Ruiju Wang
Journal:  Plant Signal Behav       Date:  2021-12-19

4.  Hormonal regulation of microRNA expression dynamics in the gut of the yellow fever mosquito Aedes aegypti.

Authors:  Xiufeng Zhang; Alexander S Raikhel
Journal:  RNA Biol       Date:  2020-12-23       Impact factor: 4.652

5.  Genome-Wide Analysis Identified a Set of Conserved lncRNAs Associated with Domestication-Related Traits in Rice.

Authors:  Huang He; Yan-Fei Zhou; Yu-Wei Yang; Zhi Zhang; Meng-Qi Lei; Yan-Zhao Feng; Yu-Chan Zhang; Yue-Qin Chen; Jian-Ping Lian; Yang Yu
Journal:  Int J Mol Sci       Date:  2021-04-29       Impact factor: 5.923

Review 6.  Interplay between miRNAs and lncRNAs: Mode of action and biological roles in plant development and stress adaptation.

Authors:  Xiangxiang Meng; Aixia Li; Bin Yu; Shengjun Li
Journal:  Comput Struct Biotechnol J       Date:  2021-04-27       Impact factor: 7.271

7.  Transcriptome landscape of early inflorescence developmental stages identifies key flowering time regulators in chickpea.

Authors:  Udita Basu; Venkatraman S Hegde; Anurag Daware; Uday Chand Jha; Swarup K Parida
Journal:  Plant Mol Biol       Date:  2022-02-01       Impact factor: 4.076

8.  Trans-Kingdom RNA Silencing in Plant-Fungal Disease Control.

Authors:  Tao Zhang; Fei Wang; Hui-Shan Guo; Yun Jin
Journal:  Methods Mol Biol       Date:  2022

9.  A vast pool of lineage-specific microproteins encoded by long non-coding RNAs in plants.

Authors:  Igor Fesenko; Svetlana A Shabalina; Anna Mamaeva; Andrey Knyazev; Anna Glushkevich; Irina Lyapina; Rustam Ziganshin; Sergey Kovalchuk; Daria Kharlampieva; Vassili Lazarev; Michael Taliansky; Eugene V Koonin
Journal:  Nucleic Acids Res       Date:  2021-10-11       Impact factor: 16.971

10.  Function identification of miR394 in tomato resistance to Phytophthora infestans.

Authors:  Yuan-Yuan Zhang; Yu-Hui Hong; Ya-Rong Liu; Jun Cui; Yu-Shi Luan
Journal:  Plant Cell Rep       Date:  2021-07-06       Impact factor: 4.570

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