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Analysis of intronic and exonic reads in RNA-seq data characterizes transcriptional and post-transcriptional regulation
被引:194
作者:

Gaidatzis, Dimos
论文数: 0 引用数: 0
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机构:
Friedrich Miescher Inst Biomed Res, Basel, Switzerland
Swiss Inst Bioinformat, Basel, Switzerland Friedrich Miescher Inst Biomed Res, Basel, Switzerland

Burger, Lukas
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h-index: 0
机构:
Friedrich Miescher Inst Biomed Res, Basel, Switzerland
Swiss Inst Bioinformat, Basel, Switzerland Friedrich Miescher Inst Biomed Res, Basel, Switzerland

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Stadler, Michael B.
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机构:
Friedrich Miescher Inst Biomed Res, Basel, Switzerland
Swiss Inst Bioinformat, Basel, Switzerland Friedrich Miescher Inst Biomed Res, Basel, Switzerland
机构:
[1] Friedrich Miescher Inst Biomed Res, Basel, Switzerland
[2] Swiss Inst Bioinformat, Basel, Switzerland
[3] Univ Basel, Basel, Switzerland
关键词:
DIFFERENTIAL EXPRESSION ANALYSIS;
PRE-MESSENGER-RNA;
GENE-EXPRESSION;
MAMMALIAN MICRORNAS;
REVEALS;
RECONSTRUCTION;
LANDSCAPE;
PRECISION;
DYNAMICS;
BINDING;
D O I:
10.1038/nbt.3269
中图分类号:
Q81 [生物工程学(生物技术)];
Q93 [微生物学];
学科分类号:
071005 ;
0836 ;
090102 ;
100705 ;
摘要:
RNA-seq experiments generate reads derived not only from mature RNA transcripts but also from pre-mRNA. Here we present a computational approach called exon-intron split analysis (EISA) that measures changes in mature RNA and pre-mRNA reads across different experimental conditions to quantify transcriptional and post-transcriptional regulation of gene expression. We apply EISA to 17 diverse data sets to show that most intronic reads arise from nuclear RNA and changes in intronic read counts accurately predict changes in transcriptional activity. Furthermore, changes in post-transcriptional regulation can be predicted from differences between exonic and intronic changes. EISA reveals both transcriptional and post-transcriptional contributions to expression changes, increasing the amount of information that can be gained from RNA-seq data sets.
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页码:722 / 729
页数:8
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[1]
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[4]
Differentiation of mouse embryonic stem cells into a defined neuronal lineage
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Bibel, M
;
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;
Schrenk, K
;
Tucker, KL
;
Staiger, V
;
Korte, M
;
Goetz, M
;
Barde, YA
.
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Goetz, M
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[J].
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;
Nielsen, Cydney B.
;
Qian, Jenny Q.
;
Varhol, Richard
;
Stazyk, Greg
;
Morin, Ryan D.
;
Zhao, Yongjun
;
Hirst, Martin
;
Schein, Jacqueline E.
;
Horsman, Doug E.
;
Connors, Joseph M.
;
Gascoyne, Randy D.
;
Marra, Marco A.
;
Jones, Steven J. M.
.
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:2872-2877

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Genome Sci Ctr, Vancouver, BC V5Z 4S6, Canada Genome Sci Ctr, Vancouver, BC V5Z 4S6, Canada
[6]
Regulatory element detection using correlation with expression
[J].
Bussemaker, HJ
;
Li, H
;
Siggia, ED
.
NATURE GENETICS,
2001, 27 (02)
:167-171

Bussemaker, HJ
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h-index: 0
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Rockefeller Univ, Ctr Studies Phys & Biol, New York, NY 10021 USA Rockefeller Univ, Ctr Studies Phys & Biol, New York, NY 10021 USA

Li, H
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h-index: 0
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[7]
Modeling the relative relationship of transcription factor binding and histone modifications to gene expression levels in mouse embryonic stem cells
[J].
Cheng, Chao
;
Gerstein, Mark
.
NUCLEIC ACIDS RESEARCH,
2012, 40 (02)
:553-568

Cheng, Chao
论文数: 0 引用数: 0
h-index: 0
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Yale Univ, Dept Mol Biophys & Biochem, New Haven, CT 06520 USA
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论文数: 引用数:
h-index:
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[8]
Nascent RNA Sequencing Reveals Widespread Pausing and Divergent Initiation at Human Promoters
[J].
Core, Leighton J.
;
Waterfall, Joshua J.
;
Lis, John T.
.
SCIENCE,
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:1845-1848

Core, Leighton J.
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h-index: 0
机构:
Cornell Univ, Dept Mol Biol & Genet, Ithaca, NY 14853 USA Cornell Univ, Dept Mol Biol & Genet, Ithaca, NY 14853 USA

Waterfall, Joshua J.
论文数: 0 引用数: 0
h-index: 0
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Lis, John T.
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h-index: 0
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[9]
A comparison between ribo-minus RNA-sequencing and polyA-selected RNA-sequencing
[J].
Cui, Peng
;
Lin, Qiang
;
Ding, Feng
;
Xin, Chengqi
;
Gong, Wei
;
Zhang, Lingfang
;
Geng, Jianing
;
Zhang, Bing
;
Yu, Xiaomin
;
Yang, Jin
;
Hu, Songnian
;
Yu, Jun
.
GENOMICS,
2010, 96 (05)
:259-265

Cui, Peng
论文数: 0 引用数: 0
h-index: 0
机构:
Chinese Acad Sci, Beijing Inst Genom, CAS Key Lab Genome Sci & Informat, Beijing 100029, Peoples R China Chinese Acad Sci, Beijing Inst Genom, CAS Key Lab Genome Sci & Informat, Beijing 100029, Peoples R China

Lin, Qiang
论文数: 0 引用数: 0
h-index: 0
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Chinese Acad Sci, Beijing Inst Genom, CAS Key Lab Genome Sci & Informat, Beijing 100029, Peoples R China
Chinese Acad Sci, Grad Sch, Beijing 100029, Peoples R China Chinese Acad Sci, Beijing Inst Genom, CAS Key Lab Genome Sci & Informat, Beijing 100029, Peoples R China

Ding, Feng
论文数: 0 引用数: 0
h-index: 0
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Chinese Acad Sci, Beijing Inst Genom, CAS Key Lab Genome Sci & Informat, Beijing 100029, Peoples R China Chinese Acad Sci, Beijing Inst Genom, CAS Key Lab Genome Sci & Informat, Beijing 100029, Peoples R China

Xin, Chengqi
论文数: 0 引用数: 0
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Chinese Acad Sci, Beijing Inst Genom, CAS Key Lab Genome Sci & Informat, Beijing 100029, Peoples R China
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h-index: 0
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Chinese Acad Sci, Beijing Inst Genom, CAS Key Lab Genome Sci & Informat, Beijing 100029, Peoples R China
Chinese Acad Sci, Grad Sch, Beijing 100029, Peoples R China Chinese Acad Sci, Beijing Inst Genom, CAS Key Lab Genome Sci & Informat, Beijing 100029, Peoples R China

Zhang, Lingfang
论文数: 0 引用数: 0
h-index: 0
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Chinese Acad Sci, Beijing Inst Genom, CAS Key Lab Genome Sci & Informat, Beijing 100029, Peoples R China
Chinese Acad Sci, Grad Sch, Beijing 100029, Peoples R China Chinese Acad Sci, Beijing Inst Genom, CAS Key Lab Genome Sci & Informat, Beijing 100029, Peoples R China

Geng, Jianing
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h-index: 0
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Chinese Acad Sci, Beijing Inst Genom, CAS Key Lab Genome Sci & Informat, Beijing 100029, Peoples R China Chinese Acad Sci, Beijing Inst Genom, CAS Key Lab Genome Sci & Informat, Beijing 100029, Peoples R China

Zhang, Bing
论文数: 0 引用数: 0
h-index: 0
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Chinese Acad Sci, Beijing Inst Genom, CAS Key Lab Genome Sci & Informat, Beijing 100029, Peoples R China Chinese Acad Sci, Beijing Inst Genom, CAS Key Lab Genome Sci & Informat, Beijing 100029, Peoples R China

Yu, Xiaomin
论文数: 0 引用数: 0
h-index: 0
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Chinese Acad Sci, Beijing Inst Genom, CAS Key Lab Genome Sci & Informat, Beijing 100029, Peoples R China Chinese Acad Sci, Beijing Inst Genom, CAS Key Lab Genome Sci & Informat, Beijing 100029, Peoples R China

Yang, Jin
论文数: 0 引用数: 0
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Chinese Acad Sci, Beijing Inst Genom, CAS Key Lab Genome Sci & Informat, Beijing 100029, Peoples R China Chinese Acad Sci, Beijing Inst Genom, CAS Key Lab Genome Sci & Informat, Beijing 100029, Peoples R China

Hu, Songnian
论文数: 0 引用数: 0
h-index: 0
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Chinese Acad Sci, Beijing Inst Genom, CAS Key Lab Genome Sci & Informat, Beijing 100029, Peoples R China Chinese Acad Sci, Beijing Inst Genom, CAS Key Lab Genome Sci & Informat, Beijing 100029, Peoples R China

Yu, Jun
论文数: 0 引用数: 0
h-index: 0
机构:
Chinese Acad Sci, Beijing Inst Genom, CAS Key Lab Genome Sci & Informat, Beijing 100029, Peoples R China Chinese Acad Sci, Beijing Inst Genom, CAS Key Lab Genome Sci & Informat, Beijing 100029, Peoples R China
[10]
RNA-SeQC: RNA-seq metrics for quality control and process optimization
[J].
DeLuca, David S.
;
Levin, Joshua Z.
;
Sivachenko, Andrey
;
Fennell, Timothy
;
Nazaire, Marc-Danie
;
Williams, Chris
;
Reich, Michael
;
Winckler, Wendy
;
Getz, Gad
.
BIOINFORMATICS,
2012, 28 (11)
:1530-1532

DeLuca, David S.
论文数: 0 引用数: 0
h-index: 0
机构:
Broad Inst MIT & Harvard, Cambridge, MA USA Broad Inst MIT & Harvard, Cambridge, MA USA

Levin, Joshua Z.
论文数: 0 引用数: 0
h-index: 0
机构:
Broad Inst MIT & Harvard, Cambridge, MA USA Broad Inst MIT & Harvard, Cambridge, MA USA

Sivachenko, Andrey
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h-index: 0
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Broad Inst MIT & Harvard, Cambridge, MA USA Broad Inst MIT & Harvard, Cambridge, MA USA

Fennell, Timothy
论文数: 0 引用数: 0
h-index: 0
机构:
Broad Inst MIT & Harvard, Cambridge, MA USA Broad Inst MIT & Harvard, Cambridge, MA USA

Nazaire, Marc-Danie
论文数: 0 引用数: 0
h-index: 0
机构:
Broad Inst MIT & Harvard, Cambridge, MA USA Broad Inst MIT & Harvard, Cambridge, MA USA

Williams, Chris
论文数: 0 引用数: 0
h-index: 0
机构:
Broad Inst MIT & Harvard, Cambridge, MA USA Broad Inst MIT & Harvard, Cambridge, MA USA

Reich, Michael
论文数: 0 引用数: 0
h-index: 0
机构:
Broad Inst MIT & Harvard, Cambridge, MA USA Broad Inst MIT & Harvard, Cambridge, MA USA

Winckler, Wendy
论文数: 0 引用数: 0
h-index: 0
机构:
Broad Inst MIT & Harvard, Cambridge, MA USA Broad Inst MIT & Harvard, Cambridge, MA USA

Getz, Gad
论文数: 0 引用数: 0
h-index: 0
机构:
Broad Inst MIT & Harvard, Cambridge, MA USA Broad Inst MIT & Harvard, Cambridge, MA USA