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

Curr Opin Plant Biol. 2014 Apr:18:87-95. doi: 10.1016/j.pbi.2014.02.008. Epub 2014 Mar 15.

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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, U.S. Gov't, Non-P.H.S.
  • Review

MeSH terms

  • Genes, Plant*
  • Heterochromatin / metabolism
  • MicroRNAs / genetics*
  • Molecular Sequence Annotation*
  • Plants / genetics*
  • RNA, Plant / genetics*

Substances

  • Heterochromatin
  • MicroRNAs
  • RNA, Plant