Identification of small ORFs in vertebrates using ribosome footprinting and evolutionary conservation

EMBO J. 2014 May 2;33(9):981-93. doi: 10.1002/embj.201488411. Epub 2014 Apr 4.


Identification of the coding elements in the genome is a fundamental step to understanding the building blocks of living systems. Short peptides (< 100 aa) have emerged as important regulators of development and physiology, but their identification has been limited by their size. We have leveraged the periodicity of ribosome movement on the mRNA to define actively translated ORFs by ribosome footprinting. This approach identifies several hundred translated small ORFs in zebrafish and human. Computational prediction of small ORFs from codon conservation patterns corroborates and extends these findings and identifies conserved sequences in zebrafish and human, suggesting functional peptide products (micropeptides). These results identify micropeptide-encoding genes in vertebrates, providing an entry point to define their function in vivo.

Publication types

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

MeSH terms

  • Animals
  • Base Sequence
  • Computational Biology
  • Conserved Sequence*
  • Evolution, Molecular*
  • Gene Expression Profiling
  • Humans
  • Molecular Sequence Data
  • Nuclease Protection Assays
  • Oligopeptides / genetics
  • Open Reading Frames / genetics*
  • RNA, Messenger / genetics*
  • RNA, Messenger / metabolism
  • Ribosomes / metabolism*
  • Sequence Analysis, RNA / methods
  • Zebrafish / embryology
  • Zebrafish / genetics*


  • Oligopeptides
  • RNA, Messenger

Associated data

  • GENBANK/GSE53693