A microRNA catalog of the developing chicken embryo identified by a deep sequencing approach

Glazov, Evgeny A., Cottee, Pauline A., Barris, Wesley C., Moore, Robert J., Dalrymple, Brian P. and Tizard, Mark L. (2008) A microRNA catalog of the developing chicken embryo identified by a deep sequencing approach. Genome Research, 18 6: 957-964. doi:10.1101/gr.074740.107

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Author Glazov, Evgeny A.
Cottee, Pauline A.
Barris, Wesley C.
Moore, Robert J.
Dalrymple, Brian P.
Tizard, Mark L.
Title A microRNA catalog of the developing chicken embryo identified by a deep sequencing approach
Journal name Genome Research   Check publisher's open access policy
ISSN 1088-9051
1549-5469
Publication date 2008-06-01
Sub-type Article (original research)
DOI 10.1101/gr.074740.107
Open Access Status File (Publisher version)
Volume 18
Issue 6
Start page 957
End page 964
Total pages 8
Place of publication Cold Spring Harbor, NY, United States
Publisher Cold Spring Harbor Laboratory Press
Language eng
Formatted abstract
MicroRNA (miRNA) and other types of small regulatory RNAs play a crucial role in the regulation of gene expression in eukaryotes. Several distinct classes of small regulatory RNAs have been discovered in recent years. To extend the repertoire of small regulatory RNAs characterized in chickens we used a deep sequencing approach developed by Solexa (now Illumina Inc.). We sequenced three small RNA libraries prepared from different developmental stages of the chicken embryo (days five, seven, and nine) to produce over 9.5 million short sequence reads. We developed a bioinformatics pipeline to distinguish authentic mature miRNA sequences from other classes of small RNAs and short RNA fragments represented in the sequencing data. Using this approach we detected almost all of the previously known chicken miRNAs and their respective miRNA* sequences. In addition we discovered 449 new chicken miRNAs including 88 miRNA candidates. Of these, 430 miRNAs appear to be specific to the avian lineage. Another six new miRNAs had evidence of evolutionary conservation in at least one vertebrate species outside of the bird lineage. The remaining 13 putative miRNAs appear to represent chicken orthologs of known vertebrate miRNAs. We discovered 39 additional putative miRNA candidates originating from miRNA generating intronic sequences known as mirtrons.
©2008 by Cold Spring Harbor Laboratory Press
Keyword MicroRNA
Bioinformatics
Chicken
Embryo development
Gene library
Gene sequence
Genetic conservation
Intron
Nucleotide sequence
RNA sequence
Sequence analysis
Embryonic development
MicroRNAs
Sequence analysis
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status Non-UQ
Additional Notes Supplemental material is available online at http://www.genome.org/ The raw sequence data from this study have been submitted to Gene Expression Omnibus under accession no. GSE10686.

Document type: Journal Article
Sub-type: Article (original research)
Collections: Excellence in Research Australia (ERA) - Collection
UQ Diamantina Institute Publications
 
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