E-GEOD-53693 - Identification of small ORFs in vertebrates using ribosome footprinting and evolutionary conservation

Status
Released on 4 April 2014, last updated on 6 May 2014
Organism
Danio rerio
Samples (30)
Protocols (3)
Description
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. Ribosome profiling experiments at five timepoints across zebrafish development in WT embryos
Experiment types
RNA-seq of coding RNA, RNA-seq of non coding RNA 
Contacts
Antonio J. Giraldez <antonio.giraldez@yale.edu>, Antonio J Giraldez, Ariel A Bazzini, Benedikt Obermayer, Charles E Vejnar, Elizabeth S Fleming, Miler T Lee, Nikolaus Rajewsky, Romain Christiano, Sebastian D Mackowiak, Timothy G Johnstone, Tobias C Walther
Citation
Identification of small ORFs in vertebrates using ribosome footprinting and evolutionary conservation. Bazzini AA, Johnstone TG, Christiano R, Mackowiak SD, Obermayer B, Fleming ES, Vejnar CE, Lee MT, Rajewsky N, Walther TC, Giraldez AJ. , Europe PMC 24705786
MINSEQE
Exp. designProtocolsFactorsProcessedSeq. reads
Files
Investigation descriptionE-GEOD-53693.idf.txt
Sample and data relationshipE-GEOD-53693.sdrf.txt
Links