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

被引：24
作者：
Coruh, Ceyda [1 ,2 ,3 ]
Shahid, Saima [1 ,2 ,3 ]
Axtell, Michael J. [1 ,2 ,3 ]
机构：
[1] Penn State Univ, Dept Biol, University Pk, PA 16802 USA
[2] Penn State Univ, Plant Biol Intercoll PhD Program, University Pk, PA 16802 USA
[3] Penn State Univ, Huck Inst Life Sci, University Pk, PA 16802 USA
来源：
CURRENT OPINION IN PLANT BIOLOGY | 2014年 / 18卷
基金：
美国国家科学基金会;
关键词：
DIRECTED DNA-METHYLATION; GENOME-WIDE ANALYSIS; TRANSPOSABLE ELEMENTS; MICRORNA; SECONDARY; CLASSIFICATION; INTERFERENCE; BIOGENESIS; PATHWAY; SIRNAS;
D O I：
10.1016/j.pbi.2014.02.008
中图分类号：
Q94 [植物学];
学科分类号：
071001 ;
摘要：
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.
引用
收藏
页码：87 / 95
页数：9
相关论文
共 60 条
[1]   DICER-LIKE3 Activity in Physcomitrella patens DICER-LIKE4 Mutants Causes Severe Developmental Dysfunction and Sterility [J].
Arif, M. Asif ;
Fattash, Isam ;
Ma, Zhaorong ;
Cho, Sung Hyun ;
Beike, Anna K. ;
Reski, Ralf ;
Axtell, Michael J. ;
Frank, Wolfgang .
MOLECULAR PLANT, 2012, 5 (06) :1281-1294
[2]   Common functions for diverse small RNAs of land plants [J].
Axtell, Michael J. ;
Snyder, Jo Ann ;
Bartell, David P. .
PLANT CELL, 2007, 19 (06) :1750-1769
[3]   A two-hit trigger for siRNA biogenesis in plants [J].
Axtell, Michael J. ;
Jan, Calvin ;
Rajagopalan, Ramya ;
Bartel, David P. .
CELL, 2006, 127 (03) :565-577
[4]   ShortStack: Comprehensive annotation and quantification of small RNA genes [J].
Axtell, Michael J. .
RNA, 2013, 19 (06) :740-751
[5]   Classification and Comparison of Small RNAs from Plants [J].
Axtell, Michael J. .
ANNUAL REVIEW OF PLANT BIOLOGY, VOL 64, 2013, 64 :137-159
[6]   Update of ASRP:: The Arabidopsis small RNA project database [J].
Backman, Tyler W. H. ;
Sullivan, Christopher M. ;
Cumbie, Jason S. ;
Miller, Zachary A. ;
Chapman, Elisabeth J. ;
Fahlgren, Noah ;
Givan, Scott A. ;
Carrington, James C. ;
Kasschau, Kristin D. .
NUCLEIC ACIDS RESEARCH, 2008, 36 :D982-D985
[7]   Functional Analysis of Three Arabidopsis ARGONAUTES Using Slicer-Defective Mutants [J].
Carbonell, Alberto ;
Fahlgren, Noah ;
Garcia-Ruiz, Hernan ;
Gilbert, Kerrigan B. ;
Montgomery, Taiowa A. ;
Nguyen, Tammy ;
Cuperus, Josh T. ;
Carrington, James C. .
PLANT CELL, 2012, 24 (09) :3613-3629
[8]   ncPRO-seq: a tool for annotation and profiling of ncRNAs in sRNA-seq data [J].
Chen, Chong-Jian ;
Servant, Nicolas ;
Toedling, Joern ;
Sarazin, Alexis ;
Marchais, Antonin ;
Duvernois-Berthet, Evelyne ;
Cognat, Valerie ;
Colot, Vincent ;
Voinnet, Olivier ;
Heard, Edith ;
Ciaudo, Constance ;
Barillot, Emmanuel .
BIOINFORMATICS, 2012, 28 (23) :3147-3149
[9]   Bioinformatic prediction and experimental validation of a microRNA-directed tandem trans-acting siRNA cascade in Arabidopsis [J].
Chen, Ho-Ming ;
Li, Yi-Hang ;
Wu, Shu-Hsing .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2007, 104 (09) :3318-3323
[10]   miR156 and miR390 Regulate tasiRNA Accumulation and Developmental Timing in Physcomitrella patens [J].
Cho, Sung Hyun ;
Coruh, Ceyda ;
Axtell, Michael J. .
PLANT CELL, 2012, 24 (12) :4837-4849
123456