ZFIN ID: ZDB-PUB-140513-192
Identification of small ORFs in vertebrates using ribosome footprinting and evolutionary conservation
Bazzini, A.A., Johnstone, T.G., Christiano, R., Mackowiak, S.D., Obermayer, B., Fleming, E.S., Vejnar, C.E., Lee, M.T., Rajewsky, N., Walther, T.C., Giraldez, A.J.
Date: 2014
Source: The EMBO journal   33: 981-93 (Journal)
Registered Authors: Giraldez, Antonio, Lee, Miler
Keywords: none
Microarrays: GEO:GSE53693
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*
PubMed: 24705786 Full text @ EMBO J.
ABSTRACT
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.
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