Literature DB >> 26530390

The expanding world of small RNAs in plants.

Filipe Borges1, Robert A Martienssen1.   

Abstract

Plant genomes encode various small RNAs that function in distinct, yet overlapping, genetic and epigenetic silencing pathways. However, the abundance and diversity of small-RNA classes varies among plant species, suggesting coevolution between environmental adaptations and gene-silencing mechanisms. Biogenesis of small RNAs in plants is well understood, but we are just beginning to uncover their intricate regulation and activity. Here, we discuss the biogenesis of plant small RNAs, such as microRNAs, secondary siRNAs and heterochromatic siRNAs, and their diverse cellular and developmental functions, including in reproductive transitions, genomic imprinting and paramutation. We also discuss the diversification of small-RNA-directed silencing pathways through the expansion of RNA-dependent RNA polymerases, DICER proteins and ARGONAUTE proteins.

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Year:  2015        PMID: 26530390      PMCID: PMC4948178          DOI: 10.1038/nrm4085

Source DB:  PubMed          Journal:  Nat Rev Mol Cell Biol        ISSN: 1471-0072            Impact factor:   94.444


  177 in total

1.  A germ cell specific gene of the ARGONAUTE family is essential for the progression of premeiotic mitosis and meiosis during sporogenesis in rice.

Authors:  Ken-Ichi Nonomura; Akane Morohoshi; Mutsuko Nakano; Mitsugu Eiguchi; Akio Miyao; Hirohiko Hirochika; Nori Kurata
Journal:  Plant Cell       Date:  2007-08-03       Impact factor: 11.277

Review 2.  RNA-directed DNA methylation: an epigenetic pathway of increasing complexity.

Authors:  Marjori A Matzke; Rebecca A Mosher
Journal:  Nat Rev Genet       Date:  2014-05-08       Impact factor: 53.242

3.  Stalled spliceosomes are a signal for RNAi-mediated genome defense.

Authors:  Phillip A Dumesic; Prashanthi Natarajan; Changbin Chen; Ines A Drinnenberg; Benjamin J Schiller; James Thompson; James J Moresco; John R Yates; David P Bartel; Hiten D Madhani
Journal:  Cell       Date:  2013-02-14       Impact factor: 41.582

4.  Intron splicing suppresses RNA silencing in Arabidopsis.

Authors:  Michael Christie; Larry J Croft; Bernard J Carroll
Journal:  Plant J       Date:  2011-08-05       Impact factor: 6.417

5.  MicroRNA gene evolution in Arabidopsis lyrata and Arabidopsis thaliana.

Authors:  Noah Fahlgren; Sanjuro Jogdeo; Kristin D Kasschau; Christopher M Sullivan; Elisabeth J Chapman; Sascha Laubinger; Lisa M Smith; Mark Dasenko; Scott A Givan; Detlef Weigel; James C Carrington
Journal:  Plant Cell       Date:  2010-04-20       Impact factor: 11.277

6.  The mechanism selecting the guide strand from small RNA duplexes is different among argonaute proteins.

Authors:  Atsushi Takeda; Shintaro Iwasaki; Toshiaki Watanabe; Maki Utsumi; Yuichiro Watanabe
Journal:  Plant Cell Physiol       Date:  2008-03-14       Impact factor: 4.927

7.  Arabidopsis ARGONAUTE7 selects miR390 through multiple checkpoints during RISC assembly.

Authors:  Yayoi Endo; Hiro-oki Iwakawa; Yukihide Tomari
Journal:  EMBO Rep       Date:  2013-06-04       Impact factor: 8.807

Review 8.  Small RNAs break out: the molecular cell biology of mobile small RNAs.

Authors:  Peter Sarkies; Eric A Miska
Journal:  Nat Rev Mol Cell Biol       Date:  2014-08       Impact factor: 94.444

9.  Gene expression and stress response mediated by the epigenetic regulation of a transposable element small RNA.

Authors:  Andrea D McCue; Saivageethi Nuthikattu; Sarah H Reeder; R Keith Slotkin
Journal:  PLoS Genet       Date:  2012-02-09       Impact factor: 5.917

10.  Genome-wide identification, organization and phylogenetic analysis of Dicer-like, Argonaute and RNA-dependent RNA Polymerase gene families and their expression analysis during reproductive development and stress in rice.

Authors:  Meenu Kapoor; Rita Arora; Tenisha Lama; Aashima Nijhawan; Jitendra P Khurana; Akhilesh K Tyagi; Sanjay Kapoor
Journal:  BMC Genomics       Date:  2008-10-01       Impact factor: 3.969

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  274 in total

1.  Insights into the function of the phasiRNA-triggering miR1514 in response to stress in legumes.

Authors:  Guadalupe Sosa-Valencia; Paulette S Romero-Pérez; V Miguel Palomar; Alejandra A Covarrubias; José L Reyes
Journal:  Plant Signal Behav       Date:  2017-03-04

2.  Identification of a New Host Factor Required for Antiviral RNAi and Amplification of Viral siRNAs.

Authors:  Zhongxin Guo; Xian-Bing Wang; Ying Wang; Wan-Xiang Li; Amit Gal-On; Shou-Wei Ding
Journal:  Plant Physiol       Date:  2017-11-28       Impact factor: 8.340

3.  Identification of alternatively spliced gene isoforms and novel noncoding RNAs by single-molecule long-read sequencing in Camellia.

Authors:  Zhikang Hu; Tao Lyu; Chao Yan; Yupeng Wang; Ning Ye; Zhengqi Fan; Xinlei Li; Jiyuan Li; Hengfu Yin
Journal:  RNA Biol       Date:  2020-03-19       Impact factor: 4.652

4.  Arabidopsis RNA Polymerase IV generates 21-22 nucleotide small RNAs that can participate in RNA-directed DNA methylation and may regulate genes.

Authors:  Kaushik Panda; Andrea D McCue; R Keith Slotkin
Journal:  Philos Trans R Soc Lond B Biol Sci       Date:  2020-02-10       Impact factor: 6.237

5.  Genetically Modified Organism-Free RNA Interference: Exogenous Application of RNA Molecules in Plants.

Authors:  Athanasios Dalakouras; Michael Wassenegger; Elena Dadami; Ioannis Ganopoulos; Maria L Pappas; Kalliope Papadopoulou
Journal:  Plant Physiol       Date:  2019-07-08       Impact factor: 8.340

6.  Dynamic regulation of chromatin topology and transcription by inverted repeat-derived small RNAs in sunflower.

Authors:  Delfina Gagliardi; Damian A Cambiagno; Agustin L Arce; Ariel H Tomassi; Jorge I Giacomelli; Federico D Ariel; Pablo A Manavella
Journal:  Proc Natl Acad Sci U S A       Date:  2019-08-13       Impact factor: 11.205

7.  Meiocyte-specific Small RNAs and Meiotic Recombination: Questions and Anthers.

Authors:  Jennifer Mach
Journal:  Plant Cell       Date:  2019-02-20       Impact factor: 11.277

8.  High-throughput sequencing of small RNAs revealed the diversified cold-responsive pathways during cold stress in the wild banana (Musa itinerans).

Authors:  Weihua Liu; Chunzhen Cheng; Fanglan Chen; Shanshan Ni; Yuling Lin; Zhongxiong Lai
Journal:  BMC Plant Biol       Date:  2018-11-29       Impact factor: 4.215

9.  Plant Extracellular Vesicles Contain Diverse Small RNA Species and Are Enriched in 10- to 17-Nucleotide "Tiny" RNAs.

Authors:  Patricia Baldrich; Brian D Rutter; Hana Zand Karimi; Ram Podicheti; Blake C Meyers; Roger W Innes
Journal:  Plant Cell       Date:  2019-01-31       Impact factor: 11.277

10.  Water-deficit stress-responsive microRNAs and their targets in four durum wheat genotypes.

Authors:  Haipei Liu; Amanda J Able; Jason A Able
Journal:  Funct Integr Genomics       Date:  2016-08-25       Impact factor: 3.410

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