Filtering of deep sequencing data reveals the existence of abundant Dicer-dependent small RNAs derived from tRNAs

Cole, C; Sobala, A; Lu, C; Thatcher, SR; Bowman, A; Brown, JWS; Green, PJ; Barton, GJ; Hutvagner, G

Filtering of deep sequencing data reveals the existence of abundant Dicer-dependent small RNAs derived from tRNAs

Cole, C Sobala, A Lu, C Thatcher, SR Bowman, A Brown, JWS Green, PJ Barton, GJ Hutvagner, G

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Publication Type:: Journal Article
Citation:: RNA, 2009, 15 (12), pp. 2147 - 2160
Issue Date:: 2009-12-01

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Field	Value	Language
dc.contributor.author	Cole, C	en_US
dc.contributor.author	Sobala, A	en_US
dc.contributor.author	Lu, C	en_US
dc.contributor.author	Thatcher, SR	en_US
dc.contributor.author	Bowman, A	en_US
dc.contributor.author	Brown, JWS	en_US
dc.contributor.author	Green, PJ	en_US
dc.contributor.author	Barton, GJ	en_US
dc.contributor.author	Hutvagner, G https://orcid.org/0000-0002-7231-9446	en_US
dc.date.issued	2009-12-01	en_US
dc.identifier.citation	RNA, 2009, 15 (12), pp. 2147 - 2160	en_US
dc.identifier.issn	1355-8382	en_US
dc.identifier.uri	http://hdl.handle.net/10453/15245
dc.description.abstract	Deep sequencing technologies such as Illumina, SOLiD, and 454 platforms have become very powerful tools in discovering and quantifying small RNAs in diverse organisms. Sequencing small RNA fractions always identifies RNAs derived from abundant RNA species such as rRNAs, tRNAs, snRNA, and snoRNA, and they are widely considered to be random degradation products. We carried out bioinformatic analysis of deep sequenced HeLa RNA and after quality filtering, identified highly abundant small RNA fragments, derived from mature tRNAs that are likely produced by specific processing rather than from random degradation. Moreover, we showed that the processing of small RNAs derived from tRNA Gln is dependent on Dicer in vivo and that Dicer cleaves the tRNA in vitro. Published by Cold Spring Harbor Laboratory Press. Copyright © 2009 RNA Society.	en_US
dc.relation.ispartof	RNA	en_US
dc.relation.isbasedon	10.1261/rna.1738409	en_US
dc.subject.classification	Developmental Biology	en_US
dc.subject.mesh	Hela Cells	en_US
dc.subject.mesh	Humans	en_US
dc.subject.mesh	Ribonuclease III	en_US
dc.subject.mesh	MicroRNAs	en_US
dc.subject.mesh	RNA, Small Interfering	en_US
dc.subject.mesh	RNA, Transfer	en_US
dc.subject.mesh	Computational Biology	en_US
dc.subject.mesh	RNA Splicing	en_US
dc.subject.mesh	Base Sequence	en_US
dc.subject.mesh	Nucleic Acid Conformation	en_US
dc.subject.mesh	Molecular Sequence Data	en_US
dc.subject.mesh	HeLa Cells	en_US
dc.title	Filtering of deep sequencing data reveals the existence of abundant Dicer-dependent small RNAs derived from tRNAs	en_US
dc.type	Journal Article
utslib.citation.volume	12	en_US
utslib.citation.volume	15	en_US
utslib.for	0903 Biomedical Engineering	en_US
utslib.for	0601 Biochemistry and Cell Biology	en_US
dc.location.activity	ISI:000272169000007	en_US
pubs.embargo.period	Not known	en_US
pubs.organisational-group	/University of Technology Sydney
pubs.organisational-group	/University of Technology Sydney/Faculty of Engineering and Information Technology
pubs.organisational-group	/University of Technology Sydney/Faculty of Engineering and Information Technology/School of Biomedical Engineering
pubs.organisational-group	/University of Technology Sydney/Strength - CHT - Health Technologies
utslib.copyright.status	closed_access
pubs.issue	12	en_US
pubs.publication-status	Published	en_US
pubs.volume	15	en_US

Abstract:

Deep sequencing technologies such as Illumina, SOLiD, and 454 platforms have become very powerful tools in discovering and quantifying small RNAs in diverse organisms. Sequencing small RNA fractions always identifies RNAs derived from abundant RNA species such as rRNAs, tRNAs, snRNA, and snoRNA, and they are widely considered to be random degradation products. We carried out bioinformatic analysis of deep sequenced HeLa RNA and after quality filtering, identified highly abundant small RNA fragments, derived from mature tRNAs that are likely produced by specific processing rather than from random degradation. Moreover, we showed that the processing of small RNAs derived from tRNA Gln is dependent on Dicer in vivo and that Dicer cleaves the tRNA in vitro. Published by Cold Spring Harbor Laboratory Press. Copyright © 2009 RNA Society.

Please use this identifier to cite or link to this item:

http://hdl.handle.net/10453/15245