PUBLICATION
Conserved and highly expressed tRNA derived fragments in zebrafish
- Authors
- Soares, A.R., Fernandes, N., Reverendo, M., Araújo, H.R., Oliveira, J.L., Moura, G.M., Santos, M.A.
- ID
- ZDB-PUB-151224-9
- Date
- 2015
- Source
- BMC Molecular Biology 16: 22 (Journal)
- Registered Authors
- Santos, Manuel
- Keywords
- tRNA derived fragments, Zebrafish, Small non coding RNAs, tRNAs
- Datasets
- GEO:GSE66718
- MeSH Terms
-
- Animals
- Base Sequence/genetics*
- Cell Line
- Colorectal Neoplasms/genetics
- Conserved Sequence/genetics*
- Gene Expression Regulation/genetics
- High-Throughput Nucleotide Sequencing
- Humans
- Mice
- NIH 3T3 Cells
- RNA Interference
- RNA, Small Untranslated/genetics*
- RNA, Transfer/genetics*
- Regulatory Sequences, Ribonucleic Acid/genetics*
- Ribonuclease III/metabolism
- Sequence Analysis, RNA
- Zebrafish
- PubMed
- 26694924 Full text @ BMC Mol. Biol.
Citation
Soares, A.R., Fernandes, N., Reverendo, M., Araújo, H.R., Oliveira, J.L., Moura, G.M., Santos, M.A. (2015) Conserved and highly expressed tRNA derived fragments in zebrafish. BMC Molecular Biology. 16:22.
Abstract
Background Small non-coding RNAs (sncRNAs) are a class of transcripts implicated in several eukaryotic regulatory mechanisms, namely gene silencing and chromatin regulation. Despite significant progress in their identification by next generation sequencing (NGS) we are still far from understanding their full diversity and functional repertoire.
Results Here we report the identification of tRNA derived fragments (tRFs) by NGS of the sncRNA fraction of zebrafish. The tRFs identified are 18-30 nt long, are derived from specific 5' and 3' processing of mature tRNAs and are differentially expressed during development and in differentiated tissues, suggesting that they are likely produced by specific processing rather than random degradation of tRNAs. We further show that a highly expressed tRF (5'tRF-Pro(CGG)) is cleaved in vitro by Dicer and has silencing ability, indicating that it can enter the RNAi pathway. A computational analysis of zebrafish tRFs shows that they are conserved among vertebrates and mining of publicly available datasets reveals that some 5'tRFs are differentially expressed in disease conditions, namely during infection and colorectal cancer.
Conclusions tRFs constitute a class of conserved regulatory RNAs in vertebrates and may be involved in mechanisms of genome regulation and in some diseases.
Genes / Markers
Expression
Phenotype
Mutations / Transgenics
Human Disease / Model
Sequence Targeting Reagents
Fish
Orthology
Engineered Foreign Genes
Mapping