PUBLICATION

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

Authors
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.
ID
ZDB-PUB-140513-192
Date
2014
Source
The EMBO journal   33: 981-93 (Journal)
Registered Authors
Giraldez, Antonio, Lee, Miler
Keywords
none
Datasets
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.
Genes / Markers
Figures
Expression
Phenotype
Mutations / Transgenics
Human Disease / Model
Sequence Targeting Reagents
Fish
Antibodies
Orthology
Engineered Foreign Genes
Mapping