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Literature DB >> 24632306

Seeing the forest for the trees: annotating small RNA producing genes in plants.

Ceyda Coruh¹, Saima Shahid¹, Michael J Axtell².

Abstract

A key goal in genomics is the complete annotation of the expressed regions of the genome. In plants, substantial portions of the genome make regulatory small RNAs produced by Dicer-Like (DCL) proteins and utilized by Argonaute (AGO) proteins. These include miRNAs and various types of endogenous siRNAs. Small RNA-seq, enabled by cheap and fast DNA sequencing, has produced an enormous volume of data on plant miRNA and siRNA expression in recent years. In this review, we discuss recent progress in using small RNA-seq data to produce stable and reliable annotations of miRNA and siRNA genes in plants. In addition, we highlight key goals for the future of small RNA gene annotation in plants.

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Year: 2014 PMID： 24632306 PMCID： PMC4001702 DOI： 10.1016/j.pbi.2014.02.008

Source DB: PubMed Journal: Curr Opin Plant Biol ISSN： 1369-5266 Impact factor: 7.834

60 in total

1. Two small regulatory RNAs establish opposing fates of a developmental axis.

Authors: Fabio T S Nogueira; Shahinez Madi; Daniel H Chitwood; Michelle T Juarez; Marja C P Timmermans
Journal: Genes Dev Date: 2007-04-01 Impact factor: 11.361

2. ncPRO-seq: a tool for annotation and profiling of ncRNAs in sRNA-seq data.

Authors: Chong-Jian Chen; Nicolas Servant; Joern Toedling; Alexis Sarazin; Antonin Marchais; Evelyne Duvernois-Berthet; Valérie Cognat; Vincent Colot; Olivier Voinnet; Edith Heard; Constance Ciaudo; Emmanuel Barillot
Journal: Bioinformatics Date: 2012-10-07 Impact factor: 6.937

3. Functional analysis of three Arabidopsis ARGONAUTES using slicer-defective mutants.

Authors: Alberto Carbonell; Noah Fahlgren; Hernan Garcia-Ruiz; Kerrigan B Gilbert; Taiowa A Montgomery; Tammy Nguyen; Josh T Cuperus; James C Carrington
Journal: Plant Cell Date: 2012-09-28 Impact factor: 11.277

4. Distinct extremely abundant siRNAs associated with cosuppression in petunia.

Authors: Emanuele De Paoli; Ana Dorantes-Acosta; Jixian Zhai; Monica Accerbi; Dong-Hoon Jeong; Sunhee Park; Blake C Meyers; Richard A Jorgensen; Pamela J Green
Journal: RNA Date: 2009-09-23 Impact factor: 4.942

5. PolIVb influences RNA-directed DNA methylation independently of its role in siRNA biogenesis.

Authors: Rebecca A Mosher; Frank Schwach; David Studholme; David C Baulcombe
Journal: Proc Natl Acad Sci U S A Date: 2008-02-19 Impact factor: 11.205

6. miR156 and miR390 regulate tasiRNA accumulation and developmental timing in Physcomitrella patens.

Authors: Sung Hyun Cho; Ceyda Coruh; Michael J Axtell
Journal: Plant Cell Date: 2012-12-21 Impact factor: 11.277

7. DTF1 is a core component of RNA-directed DNA methylation and may assist in the recruitment of Pol IV.

Authors: Heng Zhang; Ze-Yang Ma; Liang Zeng; Kaori Tanaka; Cui-Jun Zhang; Jun Ma; Ge Bai; Pengcheng Wang; Su-Wei Zhang; Zhang-Wei Liu; Tao Cai; Kai Tang; Renyi Liu; Xiaobing Shi; Xin-Jian He; Jian-Kang Zhu
Journal: Proc Natl Acad Sci U S A Date: 2013-05-01 Impact factor: 11.205

8. Methylation as a crucial step in plant microRNA biogenesis.

Authors: Bin Yu; Zhiyong Yang; Junjie Li; Svetlana Minakhina; Maocheng Yang; Richard W Padgett; Ruth Steward; Xuemei Chen
Journal: Science Date: 2005-02-11 Impact factor: 47.728

9. Epigenomic consequences of immortalized plant cell suspension culture.

Authors: Milos Tanurdzic; Matthew W Vaughn; Hongmei Jiang; Tae-Jin Lee; R Keith Slotkin; Bryon Sosinski; William F Thompson; R W Doerge; Robert A Martienssen
Journal: PLoS Biol Date: 2008-12-09 Impact factor: 8.029

10. AGO1 homeostasis involves differential production of 21-nt and 22-nt miR168 species by MIR168a and MIR168b.

Authors: Hervé Vaucheret
Journal: PLoS One Date: 2009-07-30 Impact factor: 3.240

13 in total

Review 1. Plant and Animal microRNAs (miRNAs) and Their Potential for Inter-kingdom Communication.

Authors: Yuhai Zhao; Lin Cong; Walter J Lukiw
Journal: Cell Mol Neurobiol Date: 2017-09-06 Impact factor: 5.046

2. Comprehensive Annotation of Physcomitrella patens Small RNA Loci Reveals That the Heterochromatic Short Interfering RNA Pathway Is Largely Conserved in Land Plants.

Authors: Ceyda Coruh; Sung Hyun Cho; Saima Shahid; Qikun Liu; Andrzej Wierzbicki; Michael J Axtell
Journal: Plant Cell Date: 2015-07-24 Impact factor: 11.277

3. Identification of AGO3-associated miRNAs and computational prediction of their targets in the green alga Chlamydomonas reinhardtii.

Authors: Adam Voshall; Eun-Jeong Kim; Xinrong Ma; Etsuko N Moriyama; Heriberto Cerutti
Journal: Genetics Date: 2015-03-13 Impact factor: 4.562

Seeing the forest for the trees: annotating small RNA producing genes in plants.

1. Two small regulatory RNAs establish opposing fates of a developmental axis.

2. ncPRO-seq: a tool for annotation and profiling of ncRNAs in sRNA-seq data.

3. Functional analysis of three Arabidopsis ARGONAUTES using slicer-defective mutants.

4. Distinct extremely abundant siRNAs associated with cosuppression in petunia.

5. PolIVb influences RNA-directed DNA methylation independently of its role in siRNA biogenesis.

6. miR156 and miR390 regulate tasiRNA accumulation and developmental timing in Physcomitrella patens.

7. DTF1 is a core component of RNA-directed DNA methylation and may assist in the recruitment of Pol IV.

8. Methylation as a crucial step in plant microRNA biogenesis.

9. Epigenomic consequences of immortalized plant cell suspension culture.

10. AGO1 homeostasis involves differential production of 21-nt and 22-nt miR168 species by MIR168a and MIR168b.

Review 1. Plant and Animal microRNAs (miRNAs) and Their Potential for Inter-kingdom Communication.

2. Comprehensive Annotation of Physcomitrella patens Small RNA Loci Reveals That the Heterochromatic Short Interfering RNA Pathway Is Largely Conserved in Land Plants.

3. Identification of AGO3-associated miRNAs and computational prediction of their targets in the green alga Chlamydomonas reinhardtii.

Review 4. microRNA biogenesis, degradation and activity in plants.

5. plantDARIO: web based quantitative and qualitative analysis of small RNA-seq data in plants.

6. Improved Placement of Multi-mapping Small RNAs.

7. Assessing the Gene Content of the Megagenome: Sugar Pine (Pinus lambertiana).

8. Towards annotating the plant epigenome: the Arabidopsis thaliana small RNA locus map.

9. Involvement of MEM1 in DNA demethylation in Arabidopsis.

10. The Role of UV-B light on Small RNA Activity During Grapevine Berry Development.