Identification of N6-methyladenosine reader proteins

被引：5

作者：

Zhou, Katherine I. ^{[1
]}

Liu, Nian ^{[2
,4
]}

Pan, Tao ^{[3
]}

机构：

[1] Univ Chicago, Med Scientist Training Program, Chicago, IL 60637 USA

[2] Univ Chicago, Dept Chem, 5735 S Ellis Ave, Chicago, IL 60637 USA

[3] Univ Chicago, Dept Biochem & Mol Biol, 920 E 58Th St, Chicago, IL 60637 USA

[4] Stanford Univ, Stanford Sch Med, Dept Chem & Syst Biol, Stanford, CA 94305 USA

来源：

METHODS | 2017年 / 126卷

基金：

美国国家卫生研究院;

关键词：

N-6-Methyladenosine (m(6)A); RNA binding proteins; m(6)A reader proteins; RNA pull-down; Photoactivatable-ribonucleoside-enhanced crosslinking and immunoprecipitation (PAR-CLIP); m(6)A-specific methylated RNA immunoprecipitation (MeRIP); SINGLE-NUCLEOTIDE-RESOLUTION; M(6)A RNA METHYLOMES; MESSENGER-RNA; NUCLEAR-RNA; N6-METHYLADENOSINE; RECOGNITION; COMPLEX; BINDING;

D O I：

10.1016/j.ymeth.2017.04.019

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

The reversible N-6-methyladenosine (m(6)A) modification of eukaryotic messenger RNAs (mRNAs) is a widespread regulatory mechanism that impacts every step in the mRNA life cycle. The effect of m(6)A on mRNA fate depends on the binding of "m(6)A reader" proteins - RNA binding proteins that specifically bind to RNA5 containing m(6)A. Here, we describe an RNA pull-down method that can be used to identify novel m(6)A reader proteins starting from a known m(6)A-modified site in cellular or viral RNA. We further describe how a combination of immunoprecipitation-based sequencing methods can be used to identify m(6)A-modified sites bound by an m(6)A reader protein on a transcriptome-wide level. The discovery of new m(6)A reader proteins and their m(6)A-modified targets would provide further insight into the mechanisms and functions of m(6)A in the cell. (C) 2017 Elsevier Inc. All rights reserved.

引用

页码：105 / 111

页数：7

共 45 条

[1] HNRNPA2B1 Is a Mediator of m6A-Dependent Nuclear RNA Processing Events [J].

Alarcon, Claudio R. ;

Goodarzi, Hani ;

Lee, Hyeseung ;

Liu, Xuhang ;

Tavazoie, Saeed ;

Tavazoie, Sohail F. .

CELL, 2015, 162 (06) :1299-1308

[2] N6-methyladenosine marks primary microRNAs for processing [J].

Alarcon, Claudio R. ;

Lee, Hyeseung ;

Goodarzi, Hani ;

Halberg, Nils ;

Tavazoie, Sohail F. .

NATURE, 2015, 519 (7544) :482-+

[3] Identification of RNA-protein interaction networks using PAR-CLIP [J].

Ascano, Manuel ;

Hafner, Markus ;

Cekan, Pavol ;

Gerstberger, Stefanie ;

Tuschl, Thomas .

WILEY INTERDISCIPLINARY REVIEWS-RNA, 2012, 3 (02) :159-177

[4] m6A RNA Modification Controls Cell Fate Transition in Mammalian Embryonic Stem Cells [J].

Batista, Pedro J. ;

Molinie, Benoit ;

Wang, Jinkai ;

Qu, Kun ;

Zhang, Jiajing ;

Li, Lingjie ;

Bouley, Donna M. ;

Lujan, Ernesto ;

Haddad, Bahareh ;

Daneshvar, Kaveh ;

Carter, Ava C. ;

Flynn, Ryan A. ;

Zhou, Chan ;

Lim, Kok-Seong ;

Dedon, Peter ;

Wernig, Marius ;

Mullen, Alan C. ;

Xing, Yi ;

Giallourakis, Cosmas C. ;

Chang, Howard Y. .

CELL STEM CELL, 2014, 15 (06) :707-719

[5] PARalyzer: definition of RNA binding sites from PAR-CLIP short-read sequence data [J].

Corcoran, David L. ;

Georgiev, Stoyan ;

Mukherjee, Neelanjan ;

Gottwein, Eva ;

Skalsky, Rebecca L. ;

Keene, Jack D. ;

Ohler, Uwe .

GENOME BIOLOGY, 2011, 12 (08)

[6] Identification of recognition residues for ligation-based detection and quantitation of pseudouridine and N6-methyladenosine [J].

Dai, Qing ;

Fong, Robert ;

Saikia, Mridusmita ;

Stephenson, David ;

Yu, Yi-Tao ;

Pan, Tao ;

Piccirilli, Joseph A. .

NUCLEIC ACIDS RESEARCH, 2007, 35 (18) :6322-6329

[7] Transcriptome-wide mapping of N6-methyladenosine by m6A-seq based on immunocapturing and massively parallel sequencing [J].

Dominissini, Dan ;

Moshitch-Moshkovitz, Sharon ;

Salmon-Divon, Mali ;

Amariglio, Ninette ;

Rechavi, Gideon .

NATURE PROTOCOLS, 2013, 8 (01) :176-189

[8] Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq [J].

Dominissini, Dan ;

Moshitch-Moshkovitz, Sharon ;

Schwartz, Schraga ;

Salmon-Divon, Mali ;

Ungar, Lior ;

Osenberg, Sivan ;

Cesarkas, Karen ;

Jacob-Hirsch, Jasmine ;

Amariglio, Ninette ;

Kupiec, Martin ;

Sorek, Rotem ;

Rechavi, Gideon .

NATURE, 2012, 485 (7397) :201-U84

[9] PROBING THE STRUCTURE OF RNAS IN SOLUTION [J].

EHRESMANN, C ;

BAUDIN, F ;

MOUGEL, M ;

ROMBY, P ;

EBEL, JP ;

EHRESMANN, B .

NUCLEIC ACIDS RESEARCH, 1987, 15 (22) :9109-9128

[10] Applications of isothermal titration calorimetry in RNA biochemistry and biophysics [J].

Feig, Andrew L. .

BIOPOLYMERS, 2007, 87 (5-6) :293-301

← 1 2 3 4 5 →