Transcriptomics

Dataset Information

116

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


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. Ribosome profiling experiments at five timepoints across zebrafish development in WT embryos

ORGANISM(S): Danio rerio  

SUBMITTER: Nikolaus Rajewsky  Romain Christiano   Miler T Lee   Tobias C Walther   Benedikt Obermayer   Elizabeth S Fleming   Timothy G Johnstone   Antonio J. Giraldez   Ariel A Bazzini   Sebastian D Mackowiak   Antonio J Giraldez   Charles E Vejnar    

PROVIDER: E-GEOD-53693 | ArrayExpress| 2014-05-06

SECONDARY ACCESSION(S): SRP034750GSE53693PRJNA232649

REPOSITORIES: GEO, ArrayExpress, ENA

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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. Comp  ...[more]

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