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

Christian Cole; Andrew Sobala; Cheng Lu; Shawn R. Thatcher; A. Bowman; John W. S. Brown; Pamela J. Green; Geoffrey J. Barton; Gyorgy Hutvagner

doi:10.1261/rna.1738409

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

Christian Cole, Andrew Sobala, Cheng Lu, Shawn R. Thatcher, A. Bowman, John W. S. Brown, Pamela J. Green, Geoffrey J. Barton (Lead / Corresponding author), Gyorgy Hutvagner (Lead / Corresponding author)

Research output: Contribution to journal › Article › peer-review

508 Citations (Scopus)

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.

Original language	English
Pages (from-to)	2147-2160
Number of pages	14
Journal	RNA: a Publication of the RNA Society
Volume	15
Issue number	12
DOIs	https://doi.org/10.1261/rna.1738409
Publication status	Published - Dec 2009

Keywords

small RNA
miRNA
deep sequencing
Dicer
tRNA
SMALL INTERFERING RNAS
SMALL SILENCING RNAS
ENDOGENOUS SIRNAS
ALIGNMENT EDITOR
SOMATIC-CELLS
MOUSE OOCYTES
DROSOPHILA
PATHWAY
EXPRESSION
GENES

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

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.",

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author = "Christian Cole and Andrew Sobala and Cheng Lu and Thatcher, {Shawn R.} and A. Bowman and Brown, {John W. S.} and Green, {Pamela J.} and Barton, {Geoffrey J.} and Gyorgy Hutvagner",

year = "2009",

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AU - Cole, Christian

AU - Sobala, Andrew

AU - Lu, Cheng

AU - Thatcher, Shawn R.

AU - Bowman, A.

AU - Brown, John W. S.

AU - Green, Pamela J.

AU - Barton, Geoffrey J.

AU - Hutvagner, Gyorgy

PY - 2009/12

Y1 - 2009/12

N2 - 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.

AB - 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.

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KW - miRNA

KW - deep sequencing

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KW - SMALL INTERFERING RNAS

KW - SMALL SILENCING RNAS

KW - ENDOGENOUS SIRNAS

KW - ALIGNMENT EDITOR

KW - SOMATIC-CELLS

KW - MOUSE OOCYTES

KW - DROSOPHILA

KW - PATHWAY

KW - EXPRESSION

KW - GENES

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DO - 10.1261/rna.1738409

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SN - 1355-8382

VL - 15

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EP - 2160

JO - RNA: a Publication of the RNA Society

JF - RNA: a Publication of the RNA Society

IS - 12

ER -

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

Abstract

Keywords

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