Identifying RNA editing sites using RNA sequencing data alone

Gokul Ramaswami; Rui Zhang; Robert Piskol; Liam P Keegan; Patricia Deng; Mary A O'Connell; Jin Billy Li

doi:10.1038/nmeth.2330

Identifying RNA editing sites using RNA sequencing data alone

Gokul Ramaswami, Rui Zhang, Robert Piskol, Liam P Keegan, Patricia Deng, Mary A O'Connell, Jin Billy Li

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

Abstract

We show that RNA editing sites can be called with high confidence using RNA sequencing data from multiple samples across either individuals or species, without the need for matched genomic DNA sequence. We identified many previously unidentified editing sites in both humans and Drosophila; our results nearly double the known number of human protein recoding events. We also found that human genes harboring conserved editing sites within Alu repeats are enriched for neuronal functions.

Original language	English
Pages (from-to)	128-32
Number of pages	5
Journal	Nature Methods
Volume	10
Issue number	2
DOIs	https://doi.org/10.1038/nmeth.2330
Publication status	Published - Feb 2013

Keywords

Adenosine
Alu Elements
Animals
Computational Biology
Drosophila melanogaster
Humans
Inosine
RNA Editing
Sequence Analysis, RNA

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10.1038/nmeth.2330

Identifying RNA editing sites using RNA sequencing data alone
Published in final edited form as: Nat Methods. 2013 February; 10(2): 128–132. Published online 2013 January 6. doi: 10.1038/nmeth.2330
Accepted author manuscript, 1.24 MB

http://www.nature.com/nmeth/journal/v10/n2/full/nmeth.2330.html

Cite this

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title = "Identifying RNA editing sites using RNA sequencing data alone",

abstract = "We show that RNA editing sites can be called with high confidence using RNA sequencing data from multiple samples across either individuals or species, without the need for matched genomic DNA sequence. We identified many previously unidentified editing sites in both humans and Drosophila; our results nearly double the known number of human protein recoding events. We also found that human genes harboring conserved editing sites within Alu repeats are enriched for neuronal functions.",

keywords = "Adenosine, Alu Elements, Animals, Computational Biology, Drosophila melanogaster, Humans, Inosine, RNA Editing, Sequence Analysis, RNA",

author = "Gokul Ramaswami and Rui Zhang and Robert Piskol and Keegan, {Liam P} and Patricia Deng and O'Connell, {Mary A} and Li, {Jin Billy}",

note = "Medical Research Council funding to Mary O'Connell.",

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AU - Zhang, Rui

AU - Piskol, Robert

AU - Keegan, Liam P

AU - Deng, Patricia

AU - O'Connell, Mary A

AU - Li, Jin Billy

N1 - Medical Research Council funding to Mary O'Connell.

PY - 2013/2

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AB - We show that RNA editing sites can be called with high confidence using RNA sequencing data from multiple samples across either individuals or species, without the need for matched genomic DNA sequence. We identified many previously unidentified editing sites in both humans and Drosophila; our results nearly double the known number of human protein recoding events. We also found that human genes harboring conserved editing sites within Alu repeats are enriched for neuronal functions.

KW - Adenosine

KW - Alu Elements

KW - Animals

KW - Computational Biology

KW - Drosophila melanogaster

KW - Humans

KW - Inosine

KW - RNA Editing

KW - Sequence Analysis, RNA

U2 - 10.1038/nmeth.2330

DO - 10.1038/nmeth.2330

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VL - 10

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JO - Nature Methods

JF - Nature Methods

SN - 1548-7091

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Identifying RNA editing sites using RNA sequencing data alone

Abstract

Keywords

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