Genome sequence-independent identification of RNA editing sites

Nature Methods
Qing Zhang, Xinshu Xiao

Abstract

RNA editing generates post-transcriptional sequence changes that can be deduced from RNA-seq data, but detection typically requires matched genomic sequence or multiple related expression data sets. We developed the GIREMI tool (genome-independent identification of RNA editing by mutual information; https://www.ibp.ucla.edu/research/xiao/GIREMI.html) to predict adenosine-to-inosine editing accurately and sensitively from a single RNA-seq data set of modest sequencing depth. Using GIREMI on existing data, we observed tissue-specific and evolutionary patterns in editing sites in the human population.

References

Apr 5, 2002·Genome Research·W James Kent
Jun 5, 2002·Annual Review of Biochemistry·Brenda L Bass
Jan 1, 2009·Genome Research·Jeremy R SanfordYunlong Liu
Mar 6, 2009·Genome Biology·Ben LangmeadSteven L Salzberg
Feb 4, 2010·PLoS Genetics·Michael James ClarkStanley F Nelson
Mar 3, 2010·Annual Review of Biochemistry·Kazuko Nishikura
Apr 17, 2010·Trends in Genetics : TIG·Sanaz Farajollahi, Stefan Maas
Jul 6, 2010·Nature Structural & Molecular Biology·Julian KönigJernej Ule
Nov 5, 2010·PLoS Biology·Zhen WangJernej Ule
Nov 9, 2010·Nature Methods·Yarden KatzChristopher B Burge
Mar 2, 2011·Nature Neuroscience·James R TollerveyJernej Ule
Nov 15, 2011·Nature Structural & Molecular Biology·Jessica I HoellThomas Tuschl
Nov 17, 2011·Nucleic Acids Research·Timothy R DreszerW James Kent
Mar 17, 2012·Science·Claudia L Kleinman, Jacek Majewski
Mar 17, 2012·Science·Joseph K PickrellJonathan K Pritchard
Apr 10, 2012·Nature Methods·Gokul RamaswamiJin Billy Li
Jul 17, 2012·Nature Structural & Molecular Biology·Sara MaciasJavier F Cáceres
Sep 8, 2012·Nature·Sarah DjebaliThomas R Gingeras
Sep 11, 2012·Molecular Cell·Melissa L WilbertGene W Yeo
Nov 7, 2012·Nature·UNKNOWN 1000 Genomes Project ConsortiumGil A McVean
Jan 8, 2013·Nature Methods·Gokul RamaswamiJin Billy Li
May 30, 2013·Nature Genetics·UNKNOWN GTEx Consortium
Jul 3, 2013·Proceedings of the National Academy of Sciences of the United States of America·Liang Chen
Apr 12, 2014·PLoS Genetics·Jia-Yu ChenChuan-Yun Li
May 16, 2014·Nucleic Acids Research·Lily BazakEli Eisenberg

❮ Previous
Next ❯

Citations

Jan 16, 2016·BMC Genomics·Melanie A HuntleyRobert Gentleman
Dec 17, 2015·Mass Spectrometry Reviews·Gerben Menschaert, David Fenyö
Sep 2, 2015·Bioinformatics·Jaegyoon Ahn, Xinshu Xiao
Nov 28, 2015·Scientific Reports·Zhongshan ChengKwok-Yung Yuen
Oct 10, 2015·Scientific Reports·Ernesto PicardiGraziano Pesole
May 22, 2016·Methods : a Companion to Methods in Enzymology·Gokul Ramaswami, Jin Billy Li
Aug 16, 2016·Human Mutation·Dario VenezianoCarlo M Croce
Oct 4, 2016·Briefings in Bioinformatics·David JohnShizuka Uchida
Feb 2, 2017·International Journal of Molecular Sciences·Rick KampsAndrea Romano
Oct 17, 2017·Bioinformatics·Feng ZhangWeidong Tian
Oct 20, 2017·Molecular Biology and Evolution·Yuange DuanJian Lu
Oct 3, 2017·Briefings in Bioinformatics·Li YaoYicheng Zhao
Jan 3, 2018·Genome Biology and Evolution·Li-Yuan HungTrees-Juen Chuang
Apr 12, 2018·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Shuangyang WuSongnian Hu
Jul 28, 2016·Molecular BioSystems·Ahmet F CoskunSaiful Islam
May 5, 2018·Genome Research·Yun-Hua Esther HsiaoXinshu Xiao
Oct 13, 2018·Briefings in Functional Genomics·Yan GuoYing-Yong Zhao
Oct 13, 2017·Nature·Meng How TanJin Billy Li
Oct 19, 2017·Briefings in Bioinformatics·Maria Angela DiromaErnesto Picardi
Oct 23, 2019·Nature Methods·Shalom Hillel RothEli Eisenberg
Sep 25, 2019·Journal of Translational Medicine·Theodoulakis Christofi, Apostolos Zaravinos
Jul 7, 2017·Nature Communications·Sayed Mohammad Ebrahim SahraeianHugo Y K Lam
Aug 15, 2018·Scientific Reports·Zhangyi OuyangWenjie Shu
Jan 18, 2019·Communications Biology·Giovanni Quinones-ValdezXinshu Xiao
Jan 31, 2020·Nature Protocols·Claudio Lo GiudiceErnesto Picardi
May 28, 2020·Journal of Clinical Medicine·Lilach SimchiHanoch Kaphzan
Apr 26, 2018·Nature Reviews. Genetics·Eli Eisenberg, Erez Y Levanon
Nov 3, 2017·Nature Communications·Anneke BrümmerXinshu Xiao
Jun 6, 2018·Frontiers in Physiology·Tyler WeirickShizuka Uchida
Mar 29, 2019·Journal of Animal Science and Biotechnology·Yuanyuan ZhangXuemei Deng
Dec 5, 2019·High-throughput·Tyler WeirickShizuka Uchida
Mar 3, 2019·Cold Spring Harbor Perspectives in Biology·Daniel P Reich, Brenda L Bass
Dec 19, 2020·Frontiers in Cell and Developmental Biology·Yunjin LiGeng Chen
Jan 12, 2020·Communications Biology·Giovanni Quinones-ValdezXinshu Xiao
May 1, 2021·Cancers·Gioacchino P MarcecaGiovanni Nigita

❮ Previous
Next ❯

Datasets Mentioned

BETA
GM12878

Methods Mentioned

BETA
RNA-Seq
RNASeq
CLIP-Seq
CLIP

Software Mentioned

GIREMI
Ensembl
Blat
GIREMI ( Identification of RNA Editing by Mutual )
R
Bowtie
Perl
dbGAP
UCSC browser

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.

Related Papers

Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme
S Yamanaka, H Iwao
Frontiers of Hormone Research
K A HollandN Navaratnam
Postepy biochemii
C Zekanowski
© 2022 Meta ULC. All rights reserved