Nm-seq maps 2′-O-methytation sites in human mRNA with base precision

被引：207

作者：

Dai, Qing ^{[1
,2
]}

Moshitch-Moshkovitz, Sharon ^{[3
,4
]}

Han, Dali ^{[1
,2
]}

Kol, Nitzan ^{[3
]}

Amariglio, Ninette ^{[3
,4
,5
]}

Rechavi, Gideon ^{[3
,4
,6
]}

Dominissini, Dan ^{[3
,4
,6
]}

He, Chuan ^{[1
,2
,7
,8
]}

机构：

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

[2] Univ Chicago, Howard Hughes Med Inst, 5841 S Maryland Ave, Chicago, IL 60637 USA

[3] Chaim Sheba Med Ctr, Canc Res Ctr, Tel Hashomer, Israel

[4] Chaim Sheba Med Ctr, Wohl Ctr Translat Med, Tel Hashomer, Israel

[5] Bar Ilan Univ, Mina & Everard Goodman Fac Life Sci, Ramat Gan, Israel

[6] Tel Aviv Univ, Sackler Sch Med, Tel Aviv, Israel

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

[8] Univ Chicago, Inst Biophys Dynam, Chicago, IL 60637 USA

来源：

NATURE METHODS | 2017年 / 14卷 / 07期

基金：

美国国家卫生研究院;

关键词：

RIBOSOMAL-RNA; METHYLATION; CAP; THERMODYNAMICS; TRANSLATION; ELIMINATION; BIOGENESIS; COMPLEXES; PROTEINS; SEQUENCE;

D O I：

10.1038/nmeth.4294

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

The ribose of RNA nucleotides can be 2'-O-methylated (Nm). Despite advances in high-throughput detection, the inert chemical nature of Nm still limits sensitivity and precludes mapping in mRNA. We leveraged the differential reactivity of 2'-O-methylated and 2'-hydroxylated nucleosides to periodate oxidation to develop Nm-seq, a sensitive method for transcriptome-wide mapping of Nm with base precision. Nm-seq uncovered thousands of Nm sites in human mRNA with features suggesting functional roles.

引用

页码：695 / +

页数：6

共 37 条

[1] HTSeq-a Python']Python framework to work with high-throughput sequencing data
Anders, Simon
Pyl, Paul Theodor
Huber, Wolfgang
[J]. BIOINFORMATICS, 2015, 31 (02) : 166 - 169
[2] [Anonymous], 2015, ANGEW CHEM INT EDIT, DOI DOI 10.1002/ANGE.201408362
[3] A comprehensive database of high-throughput sequencing-based RNA secondary structure probing data (Structure Surfer)
Berkowitz, Nathan D.
Silverman, Ian M.
Childress, Daniel M.
Kazan, Hilal
Wang, Li-San
Gregory, Brian D.
[J]. BMC BIOINFORMATICS, 2016, 17
[4] RNA methyltransferases involved in 5′ cap biosynthesis
Byszewska, Magdalena
Smietanski, Miroslaw
Purta, Elzbieta
Bujnicki, Janusz M.
[J]. RNA BIOLOGY, 2014, 11 (12) : 1597 - 1607
[5] 2′-O methylation of the viral mRNA cap evades host restriction by IFIT family members
Daffis, Stephane
Szretter, Kristy J.
Schriewer, Jill
Li, Jianqing
Youn, Soonjeon
Errett, John
Lin, Tsai-Yu
Schneller, Stewart
Zust, Roland
Dong, Hongping
Thiel, Volker
Sen, Ganes C.
Fensterl, Volker
Klimstra, William B.
Pierson, Theodore C.
Buller, R. Mark
Gale, Michael, Jr.
Shi, Pei-Yong
Diamond, Michael S.
[J]. NATURE, 2010, 468 (7322) : 452 - 456
[6] Dai Q., 2017, PROTOCOL EXCHANGE
[7] Post-transcriptional modification of spliceosomal RNAs is normal in SMN-deficient cells
Deryusheva, Svetlana
Choleza, Maria
Barbarossa, Adrien
Gall, Joseph G.
Bordonne, Remy
[J]. RNA, 2012, 18 (01) : 31 - 36
[8] The dynamic N1-methyladenosine methylome in eukaryotic messenger RNA
Dominissini, Dan
Nachtergaele, Sigrid
Moshitch-Moshkovitz, Sharon
Peer, Eyal
Kol, Nitzan
Ben-Haim, Moshe Shay
Dai, Qing
Di Segni, Ayelet
Salmon-Divon, Mali
Clark, Wesley C.
Zheng, Guanqun
Pan, Tao
Solomon, Oz
Eyal, Eran
Hershkovitz, Vera
Han, Dali
Dore, Louis C.
Amariglio, Ninette
Rechavi, Gideon
He, Chuan
[J]. NATURE, 2016, 530 (7591) : 441 - +
[9] High-throughput identification of C/D box snoRNA targets with CLIP and RiboMeth-seq
Gumienny, Rafal
Jedlinski, Dominik J.
Schmidt, Alexander
Gypas, Foivos
Martin, Georges
Vina-Vilaseca, Arnau
Zavolan, Mihaela
[J]. NUCLEIC ACIDS RESEARCH, 2017, 45 (05) : 2341 - 2353
[10] Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities
Heinz, Sven
Benner, Christopher
Spann, Nathanael
Bertolino, Eric
Lin, Yin C.
Laslo, Peter
Cheng, Jason X.
Murre, Cornelis
Singh, Harinder
Glass, Christopher K.
[J]. MOLECULAR CELL, 2010, 38 (04) : 576 - 589

← 1 2 3 4 →