|
| Status |
Public on Apr 04, 2014 |
| Title |
Identification of small ORFs in vertebrates using ribosome footprinting and evolutionary conservation |
| Organism |
Danio rerio |
| Experiment type |
Expression profiling by high throughput sequencing
Non-coding RNA profiling by high throughput sequencing
|
| Summary |
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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| |
|
| Overall design |
Ribosome profiling experiments at five timepoints across zebrafish development in WT embryos
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| |
|
| Contributor(s) |
Bazzini AA, Johnstone TG, Christiano R, Mackowiak SD, Obermayer B, Fleming ES, Vejnar CE, Lee MT, Rajewsky N, Walther TC, Giraldez AJ |
| Citation(s) |
24705786, 26896445 |
| Submission date |
Dec 27, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Antonio J. Giraldez |
| E-mail(s) |
antonio.giraldez@yale.edu
|
| Phone |
203 785 5423
|
| Organization name |
Yale University
|
| Department |
Genetics
|
| Lab |
Giraldez Lab
|
| Street address |
333 Cedar Street
|
| City |
New Haven |
| State/province |
CT |
| ZIP/Postal code |
06510 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL14875 |
Illumina HiSeq 2000 (Danio rerio) |
|
| Samples (30)
|
|
| Relations |
| BioProject |
PRJNA232649 |
| SRA |
SRP034750 |
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