Unknown,Transcriptomics,Genomics,Proteomics

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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 micropeptideM-bM-^@M-^Pencoding 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: Antonio Giraldez

PROVIDER: E-GEOD-53693 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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

Bazzini Ariel A AA Johnstone Timothy G TG Christiano Romain R Mackowiak Sebastian D SD Obermayer Benedikt B Fleming Elizabeth S ES Vejnar Charles E CE Lee Miler T MT Rajewsky Nikolaus N Walther Tobias C TC Giraldez Antonio J AJ

The EMBO journal 20140404 9

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]

PMID: 24705786

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Dataset Information

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

Publications

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

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