Prediction of non-coding RNA and their targets in Spirulina platensis genome

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Author list: Srisuk T., Pornputtapong N., Cheevadhanarak S., Thammarongtham C.

Publisher: Springer Verlag (Germany): Computer Proceedings

Publication year: 2010

Volume number: 115 CCIS

Start page: 106

End page: 117

Number of pages: 12

ISBN: 3642167497; 9783642167492

ISSN: 1865-0929

URL: https://www.scopus.com/inward/record.uri?eid=2-s2.0-78649515630&doi=10.1007%2f978-3-642-16750-8_10&partnerID=40&md5=8d752b92620375ea198e6416665900e9

Languages: English-Great Britain (EN-GB)

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Abstract

Non-coding RNAs (ncRNAs), transcripts that have function without being translated to protein, have a number of roles in the cell including important regulatory roles. Efforts to identify the whole set of ncRNAs and then to elucidate their functions would gain better biological understanding. Although ncRNA is another type of genome constituent, most of the genes for ncRNA are overlooked by standard genome annotation of genome sequencing projects. This also happens in Spirulina platensis genome sequencing project. It is because gene finding tools generally are able to identify only protein-coding genes but not non-protein-coding ones. In this study, S. platensis ncRNAs were detected by comparative genomics approach using computational tools, together with RNA secondary structure prediction. It was found that more than 100 predicted ncRNA loci matched with known ncRNAs for example cobalamin riboswitch, RNaseP, Signal Recognition Particle RNA, Group II intron RNA and Yfr1. It has been reported that Yfr1 has been found in most cyanobacterial genomes sequenced. The result showed that more than 70 putative loci were similar to Group II intron RNAs. In addition, approximately 100 predicted ncRNA loci were not matched with any known ncRNAs. The predicted targets for some putative ncRNAs are also proposed. ฉ 2010 Springer-Verlag Berlin Heidelberg.

Keywords

non-coding RNA prediction, non-coding RNA target prediction