Large-scale mapping of branchpoints in human pre-mRNA transcripts in vivo

被引：89

作者：

Taggart, Allison J. ^{[1
,2
]}

DeSimone, Alec M. ^{[1
]}

Shih, Janice S. ^{[3
]}

Filloux, Madeleine E. ^{[1
]}

Fairbrother, William G. ^{[1
,2
,3
,4
]}

机构：

[1] Brown Univ, Mol Med Lab, Dept Mol Biol Cell Biol & Biochem, Providence, RI 02912 USA

[2] Brown Univ, Ctr Biomed Engn, Providence, RI 02912 USA

[3] Brown Univ, Mol Med Lab, Dept Mol Microbiol & Immunol, Providence, RI 02912 USA

[4] Brown Univ, Ctr Computat Mol Biol, Providence, RI 02912 USA

来源：

NATURE STRUCTURAL & MOLECULAR BIOLOGY | 2012年 / 19卷 / 07期

基金：

美国国家科学基金会;

关键词：

3; SPLICE-SITE; MAMMALIAN INTRONS; SELECTION; REVEALS; GENOME; AG; SEQUENCES; ALIGNMENT; UPDATE; DNA;

D O I：

10.1038/nsmb.2327

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

We present the first large-scale identification of lariats-the transient branched introns that are released as a byproduct of pre-mRNA splicing. The locations of the branchpoints in these introns provide insight into the early steps of splicing. From this data set, we have developed a comprehensive model of 3' splice-site selection, identified new mechanisms of alternative splicing and mapped the distribution of splicing factors around branchpoints.

引用

页码：719 / +

页数：5

共 21 条

[1] Evidence for a linear search in bimolecular 3′ splice site AG selection [J].

Chen, SY ;

Anderson, K ;

Moore, MJ .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2000, 97 (02) :593-598

[2] Multiple sequence alignment with the Clustal series of programs [J].

Chenna, R ;

Sugawara, H ;

Koike, T ;

Lopez, R ;

Gibson, TJ ;

Higgins, DG ;

Thompson, JD .

NUCLEIC ACIDS RESEARCH, 2003, 31 (13) :3497-3500

[3] An upstream AG determines whether a downstream AG is selected during catalytic step II of splicing [J].

Chua, K ;

Reed, R .

MOLECULAR AND CELLULAR BIOLOGY, 2001, 21 (05) :1509-1514

[4] WebLogo: A sequence logo generator [J].

Crooks, GE ;

Hon, G ;

Chandonia, JM ;

Brenner, SE .

GENOME RESEARCH, 2004, 14 (06) :1188-1190

[5] Sfold web server for statistical folding and rational design of nucleic acids [J].

Ding, Y ;

Chan, CY ;

Lawrence, CE .

NUCLEIC ACIDS RESEARCH, 2004, 32 :W135-W141

[6] A class of human exons with predicted distant branch points revealed by analysis of AG dinucleotide exclusion zones [J].

Gooding, C ;

Clark, F ;

Wollerton, MC ;

Grellscheid, SN ;

Groom, H ;

Smith, CWJ .

GENOME BIOLOGY, 2006, 7 (01)

[7] Identifying DNA and protein patterns with statistically significant alignments of multiple sequences [J].

Hertz, GZ ;

Stormo, GD .

BIOINFORMATICS, 1999, 15 (7-8) :563-577

[8] Integrative Genome-wide Analysis Reveals Cooperative Regulation of Alternative Splicing by hnRNP Proteins [J].

Huelga, Stephanie C. ;

Vu, Anthony Q. ;

Arnold, Justin D. ;

Liang, Tiffany Y. ;

Liu, Patrick P. ;

Yan, Bernice Y. ;

Donohue, John Paul ;

Shiue, Lily ;

Hoon, Shawn ;

Brenner, Sydney ;

Ares, Manuel, Jr. ;

Yeo, Gene W. .

CELL REPORTS, 2012, 1 (02) :167-178

[9] iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution [J].

Koenig, Julian ;

Zarnack, Kathi ;

Rot, Gregor ;

Curk, Tomaz ;

Kayikci, Melis ;

Zupan, Blaz ;

Turner, Daniel J. ;

Luscombe, Nicholas M. ;

Ule, Jernej .

NATURE STRUCTURAL & MOLECULAR BIOLOGY, 2010, 17 (07) :909-U166

[10] Ultrafast and memory-efficient alignment of short DNA sequences to the human genome [J].

Langmead, Ben ;

Trapnell, Cole ;

Pop, Mihai ;

Salzberg, Steven L. .

GENOME BIOLOGY, 2009, 10 (03)

← 1 2 3 →