A conserved abundant cytoplasmic long noncoding RNA modulates repression by Pumilio proteins in human cells

被引：172

作者：

Tichon, Ailone ^{[1
]}

Gil, Noa ^{[1
]}

Lubelsky, Yoav ^{[1
]}

Solomon, Tal Havkin ^{[2
]}

Lemze, Doron ^{[3
]}

Itzkovitz, Shalev ^{[3
]}

Stern-Ginossar, Noam ^{[2
]}

Ulitsky, Igor ^{[1
]}

机构：

[1] Weizmann Inst Sci, Dept Regulat Biol, IL-76100 Rehovot, Israel

[2] Weizmann Inst Sci, Dept Mol Genet, IL-76100 Rehovot, Israel

[3] Weizmann Inst Sci, Dept Mol Cell Biol, IL-76100 Rehovot, Israel

来源：

NATURE COMMUNICATIONS | 2016年 / 7卷

基金：

欧洲研究理事会;

关键词：

EMBRYONIC STEM-CELLS; MAMMALIAN MICRORNAS; BINDING-PROTEIN; MESSENGER-RNAS; CIRCULAR RNAS; PUF FAMILY; PAR-CLIP; TRANSLATION; IDENTIFICATION; EVOLUTION;

D O I：

10.1038/ncomms12209

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

Thousands of long noncoding RNA (lncRNA) genes are encoded in the human genome, and hundreds of them are evolutionarily conserved, but their functions and modes of action remain largely obscure. Particularly enigmatic lncRNAs are those that are exported to the cytoplasm, including NORAD-an abundant and highly conserved cytoplasmic lncRNA. Here we show that most of the sequence of NORAD is comprised of repetitive units that together contain at least 17 functional binding sites for the two mammalian Pumilio homologues. Through binding to PUM1 and PUM2, NORAD modulates the mRNA levels of their targets, which are enriched for genes involved in chromosome segregation during cell division. Our results suggest that some cytoplasmic lncRNAs function by modulating the activities of RNA-binding proteins, an activity which positions them at key junctions of cellular signalling pathways.

引用

页数：10

共 50 条

[1] HTSeq-a Python']Python framework to work with high-throughput sequencing data [J].

Anders, Simon ;

Pyl, Paul Theodor ;

Huber, Wolfgang .

BIOINFORMATICS, 2015, 31 (02) :166-169

[2] Long non-coding antisense RNA controls Uchl1 translation through an embedded SINEB2 repeat [J].

Carrieri, Claudia ;

Cimatti, Laura ;

Biagioli, Marta ;

Beugnet, Anne ;

Zucchelli, Silvia ;

Fedele, Stefania ;

Pesce, Elisa ;

Ferrer, Isidre ;

Collavin, Licio ;

Santoro, Claudio ;

Forrest, Alistair R. R. ;

Carninci, Piero ;

Biffo, Stefano ;

Stupka, Elia ;

Gustincich, Stefano .

NATURE, 2012, 491 (7424) :454-+

[3] 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)

[4] A quantitative atlas of polyadenylation in five mammals [J].

Derti, Adnan ;

Garrett-Engele, Philip ;

MacIsaac, Kenzie D. ;

Stevens, Richard C. ;

Sriram, Shreedharan ;

Chen, Ronghua ;

Rohl, Carol A. ;

Johnson, Jason M. ;

Babak, Tomas .

GENOME RESEARCH, 2012, 22 (06) :1173-1183

[5] STAR: ultrafast universal RNA-seq aligner [J].

Dobin, Alexander ;

Davis, Carrie A. ;

Schlesinger, Felix ;

Drenkow, Jorg ;

Zaleski, Chris ;

Jha, Sonali ;

Batut, Philippe ;

Chaisson, Mark ;

Gingeras, Thomas R. .

BIOINFORMATICS, 2013, 29 (01) :15-21

[6] High-level and high-throughput recombinant protein production by transient transfection of suspension-growing human 293-EBNA1 cells [J].

Durocher, Y ;

Perret, S ;

Kamen, A .

NUCLEIC ACIDS RESEARCH, 2002, 30 (02) :E9

[7] mRNA Destabilization Is the Dominant Effect of Mammalian MicroRNAs by the Time Substantial Repression Ensues [J].

Eichhorn, Stephen W. ;

Guo, Huili ;

McGeary, Sean E. ;

Rodriguez-Mias, Ricard A. ;

Shin, Chanseok ;

Baek, Daehyun ;

Hsu, Shu-hao ;

Ghoshal, Kalpana ;

Villen, Judit ;

Bartel, David P. .

MOLECULAR CELL, 2014, 56 (01) :104-115

[8] A promoter-level mammalian expression atlas [J].

Forrest, Alistair R. R. ;

Kawaji, Hideya ;

Rehli, Michael ;

Baillie, J. Kenneth ;

de Hoon, Michiel J. L. ;

Haberle, Vanja ;

Lassmann, Timo ;

Kulakovskiy, Ivan V. ;

Lizio, Marina ;

Itoh, Masayoshi ;

Andersson, Robin ;

Mungall, Christopher J. ;

Meehan, Terrence F. ;

Schmeier, Sebastian ;

Bertin, Nicolas ;

Jorgensen, Mette ;

Dimont, Emmanuel ;

Arner, Erik ;

Schmidl, Christian ;

Schaefer, Ulf ;

Medvedeva, Yulia A. ;

Plessy, Charles ;

Vitezic, Morana ;

Severin, Jessica ;

Semple, Colin A. ;

Ishizu, Yuri ;

Young, Robert S. ;

Francescatto, Margherita ;

Alam, Intikhab ;

Albanese, Davide ;

Altschuler, Gabriel M. ;

Arakawa, Takahiro ;

Archer, John A. C. ;

Arner, Peter ;

Babina, Magda ;

Rennie, Sarah ;

Balwierz, Piotr J. ;

Beckhouse, Anthony G. ;

Pradhan-Bhatt, Swati ;

Blake, Judith A. ;

Blumenthal, Antje ;

Bodega, Beatrice ;

Bonetti, Alessandro ;

Briggs, James ;

Brombacher, Frank ;

Burroughs, A. Maxwell ;

Califano, Andrea ;

Cannistraci, Carlo V. ;

Carbajo, Daniel ;

Chen, Yun .

NATURE, 2014, 507 (7493) :462-+

[9] Analysis of intronic and exonic reads in RNA-seq data characterizes transcriptional and post-transcriptional regulation [J].

Gaidatzis, Dimos ;

Burger, Lukas ;

Florescu, Maria ;

Stadler, Michael B. .

NATURE BIOTECHNOLOGY, 2015, 33 (07) :722-729

[10] Comparative Analysis of mRNA Targets for Human PUF Family Proteins Suggests Extensive Interaction with the miRNA Regulatory System [J].

Galgano, Alessia ;

Forrer, Michael ;

Jaskiewicz, Lukasz ;

Kanitz, Alexander ;

Zavolan, Mihaela ;

Gerber, Andre P. .

PLOS ONE, 2008, 3 (09)

← 1 2 3 4 5 →