TY - JOUR
T1 - Seeing the forest for the trees
T2 - Annotating small RNA producing genes in plants
AU - Coruh, Ceyda
AU - Shahid, Saima
AU - Axtell, Michael J.
PY - 2014/4
Y1 - 2014/4
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=84896033622&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=84896033622&partnerID=8YFLogxK
U2 - 10.1016/j.pbi.2014.02.008
DO - 10.1016/j.pbi.2014.02.008
M3 - Review article
C2 - 24632306
AN - SCOPUS:84896033622
SN - 1369-5266
VL - 18
SP - 87
EP - 95
JO - Current Opinion in Plant Biology
JF - Current Opinion in Plant Biology
IS - 1
ER -