原创力文档a comparative genome-wide study of ncrnas in trypanosomatids比较基因组研究ncrnas trypanosomatids.pdfVIP
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a comparative genome-wide study of ncrnas in trypanosomatids比较基因组研究ncrnas trypanosomatids
Doniger et al. BMC Genomics 2010, 11:615
/1471-2164/11/615
RESEARCH ARTICLE Open Access
A comparative genome-wide study of ncRNAs
in trypanosomatids
1 1,2 1,2 1,2 1*
Tirza Doniger , Rodolfo Katz , Chaim Wachtel , Shulamit Michaeli , Ron Unger
Abstract
Background: Recent studies have provided extensive evidence for multitudes of non-coding RNA (ncRNA)
transcripts in a wide range of eukaryotic genomes. ncRNAs are emerging as key players in multiple layers of
cellular regulation. With the availability of many whole genome sequences, comparative analysis has become a
powerful tool to identify ncRNA molecules. In this study, we performed a systematic genome-wide in silico screen
to search for novel small ncRNAs in the genome of Trypanosoma brucei using techniques of comparative
genomics.
Results: In this study, we identified by comparative genomics, and validated by experimental analysis several novel
ncRNAs that are conserved across multiple trypanosomatid genomes. When tested on known ncRNAs, our
procedure was capable of finding almost half of the known repertoire through homology over six genomes, and
about two-thirds of the known sequences were found in at least four genomes. After filtering, 72 conserved
unannotated sequences in at least four genomes were found, 29 of which, ranging in size from 30 to 392 nts,
were conserved in all six genomes. Fifty of the 72 candidates in the final set were chosen for experimental
validation. Eighteen of the 50 (36%) were shown to be expressed, and for 11 of them a distinct expression product
was detected, suggesting that they are short ncRNAs. Using functional experimental assays, five of the candidates
were shown to be novel H/ACA and C/D snoRNAs; these included three
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