Understanding Long Noncoding RNA and Chromatin Interactions: What We Know So Far

被引：79

作者：

Mishra, Kankadeb ^{[1
,2
]}

Kanduri, Chandrasekhar ^{[1
]}

机构：

[1] Univ Gothenburg, Inst Biomed, Dept Med Biochem & Cell Biol, S-40530 Gothenburg, Sweden

[2] Mem Sloan Kettering Canc Ctr, Dept Cell Biol, Rockefeller Res Lab, 430 East 67th St,RRL 445, New York, NY 10065 USA

来源：

NON-CODING RNA | 2019年 / 5卷 / 04期

基金：

瑞典研究理事会;

关键词：

lncrna; chromatin; chromatin RNA; long noncoding RNA; gene regulation; RNA-chromatin interactions; REPEAT-CONTAINING RNA; R-LOOP FORMATION; ANTISENSE TRANSCRIPTION; WIDE IDENTIFICATION; ACTIVE CHROMATIN; BINDING PROTEIN; ENHANCER RNAS; CIRCULAR RNAS; X-CHROMOSOME; MAPS REVEAL;

D O I：

10.3390/ncrna5040054

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：

With the evolution of technologies that deal with global detection of RNAs to probing of lncRNA-chromatin interactions and lncRNA-chromatin structure regulation, we have been updated with a comprehensive repertoire of chromatin interacting lncRNAs, their genome-wide chromatin binding regions and mode of action. Evidence from these new technologies emphasize that chromatin targeting of lncRNAs is a prominent mechanism and that these chromatin targeted lncRNAs exert their functionality by fine tuning chromatin architecture resulting in an altered transcriptional readout. Currently, there are no unifying principles that define chromatin association of lncRNAs, however, evidence from a few chromatin-associated lncRNAs show presence of a short common sequence for chromatin targeting. In this article, we review how technological advancements contributed in characterizing chromatin associated lncRNAs, and discuss the potential mechanisms by which chromatin associated lncRNAs execute their functions.

引用

页数：28

共 164 条

[21] 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-+

[22] Identification of RNA-binding domains of RNA-binding proteins in cultured cells on a system-wide scale with RBDmap [J].

Castello, Alfredo ;

Frese, Christian K. ;

Fischer, Bernd ;

Jarvelin, Aino I. ;

Horos, Rastislav ;

Alleaume, Anne-Marie ;

Foehr, Sophia ;

Curk, Tomaz ;

Krijgsveld, Jeroen ;

Hentze, Matthias W. .

NATURE PROTOCOLS, 2017, 12 (12) :2447-2464

[23] Insights into RNA Biology from an Atlas of Mammalian mRNA-Binding Proteins [J].

Castello, Alfredo ;

Fischer, Bernd ;

Eichelbaum, Katrin ;

Horos, Rastislav ;

Beckmann, Benedikt M. ;

Strein, Claudia ;

Davey, Norman E. ;

Humphreys, David T. ;

Preiss, Thomas ;

Steinmetz, Lars M. ;

Krijgsveld, Jeroen ;

Hentze, Matthias W. .

CELL, 2012, 149 (06) :1393-1406

[24] A Long Noncoding RNA Controls Muscle Differentiation by Functioning as a Competing Endogenous RNA [J].

Cesana, Marcella ;

Cacchiarelli, Davide ;

Legnini, Ivano ;

Santini, Tiziana ;

Sthandier, Olga ;

Chinappi, Mauro ;

Tramontano, Anna ;

Bozzoni, Irene .

CELL, 2011, 147 (02) :358-369

[25] Isolation and genome-wide characterization of cellular DNA:RNA triplex structures [J].

Cetin, Nevcin Sentuerk ;

Kuo, Chao-Chung ;

Ribarska, Teodora ;

Li, Ronghui ;

Costa, Ivan G. ;

Grummt, Ingrid .

NUCLEIC ACIDS RESEARCH, 2019, 47 (05) :2306-2321

[26] Xist recruits the X chromosome to the nuclear lamina to enable chromosome-wide silencing [J].

Chen, Chun-Kan ;

Blanco, Mario ;

Jackson, Constanza ;

Aznauryan, Erik ;

Ollikainen, Noah ;

Surka, Christine ;

Chow, Amy ;

Cerase, Andrea ;

McDonel, Patrick ;

Guttman, Mitchell .

SCIENCE, 2016, 354 (6311) :468-472

[27] The Augmented R-Loop Is a Unifying Mechanism for Myelodysplastic Syndromes Induced by High-Risk Splicing Factor Mutations [J].

Chen, Liang ;

Chen, Jia-Yu ;

Huang, Yi-Jou ;

Gu, Ying ;

Qiu, Jinsong ;

Qian, Hao ;

Shao, Changwei ;

Zhang, Xuan ;

Hu, Jing ;

Li, Hairi ;

He, Shunmin ;

Zhou, Yu ;

Abdel-Wahab, Omar ;

Zhang, Dong-Er ;

Fu, Xiang-Dong .

MOLECULAR CELL, 2018, 69 (03) :412-+

[28] R-ChIP Using Inactive RNase H Reveals Dynamic Coupling of R-loops with Transcriptional Pausing at Gene Promoters [J].

Chen, Liang ;

Chen, Jia-Yu ;

Zhang, Xuan ;

Gu, Ying ;

Xiao, Rui ;

Shao, Changwei ;

Tang, Peng ;

Qian, Hao ;

Luo, Daji ;

Li, Hairi ;

Zhou, Yu ;

Zhang, Dong-Er ;

Fu, Xiang-Dong .

MOLECULAR CELL, 2017, 68 (04) :745-+

[29] The KCNQ1OT1 imprinting control region and non-coding RNA: new properties derived from the study of Beckwith-Wiedemann syndrome and Silver-Russell syndrome cases [J].

Chiesa, Nicoletta ;

De Crescenzo, Agostina ;

Mishra, Kankadeb ;

Perone, Lucia ;

Carella, Massimo ;

Palumbo, Orazio ;

Mussa, Alessandro ;

Sparago, Angela ;

Cerrato, Flavia ;

Russo, Silvia ;

Lapi, Elisabetta ;

Cubellis, Maria Vittoria ;

Kanduri, Chandrasekhar ;

Silengo, Margherita Cirillo ;

Riccio, Andrea ;

Ferrero, Giovanni Battista .

HUMAN MOLECULAR GENETICS, 2012, 21 (01) :10-25

[30] Systematic Discovery of Xist RNA Binding Proteins [J].

Chu, Ci ;

Zhang, Qiangfeng Cliff ;

da Rocha, Simao Teixeira ;

Flynn, Ryan A. ;

Bharadwaj, Maheetha ;

Calabrese, J. Mauro ;

Magnuson, Terry ;

Heard, Edith ;

Chang, Howard Y. .

CELL, 2015, 161 (02) :404-416

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