Literature DB >> 28193769

Long Noncoding RNAs: At the Intersection of Cancer and Chromatin Biology.

Adam M Schmitt1, Howard Y Chang2.   

Abstract

Although only 2% of the genome encodes protein, RNA is transcribed from the majority of the genetic sequence, suggesting a massive degree of cellular functionality is programmed in the noncoding genome. The mammalian genome contains tens of thousands of long noncoding RNAs (lncRNAs), many of which occur at disease-associated loci or are specifically expressed in cancer. Although the vast majority of lncRNAs have no known function, recurring molecular mechanisms for lncRNAs are now being observed in chromatin regulation and cancer pathways and emerging technologies are now providing tools to interrogate lncRNA molecular interactions and determine function of these abundant cellular macromolecules.
Copyright © 2017 Cold Spring Harbor Laboratory Press; all rights reserved.

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Year:  2017        PMID: 28193769      PMCID: PMC5495049          DOI: 10.1101/cshperspect.a026492

Source DB:  PubMed          Journal:  Cold Spring Harb Perspect Med        ISSN: 2157-1422            Impact factor:   6.915


  146 in total

1.  m(6)A RNA modification controls cell fate transition in mammalian embryonic stem cells.

Authors:  Pedro J Batista; Benoit Molinie; Jinkai Wang; Kun Qu; Jiajing Zhang; Lingjie Li; Donna M Bouley; Ernesto Lujan; Bahareh Haddad; Kaveh Daneshvar; Ava C Carter; Ryan A Flynn; Chan Zhou; Kok-Seong Lim; Peter Dedon; Marius Wernig; Alan C Mullen; Yi Xing; Cosmas C Giallourakis; Howard Y Chang
Journal:  Cell Stem Cell       Date:  2014-10-16       Impact factor: 24.633

Review 2.  X-inactivation, imprinting, and long noncoding RNAs in health and disease.

Authors:  Jeannie T Lee; Marisa S Bartolomei
Journal:  Cell       Date:  2013-03-14       Impact factor: 41.582

3.  lncRNA directs cooperative epigenetic regulation downstream of chemokine signals.

Authors:  Zhen Xing; Aifu Lin; Chunlai Li; Ke Liang; Shouyu Wang; Yang Liu; Peter K Park; Li Qin; Yongkun Wei; David H Hawke; Mien-Chie Hung; Chunru Lin; Liuqing Yang
Journal:  Cell       Date:  2014-11-13       Impact factor: 41.582

Review 4.  The multilayered complexity of ceRNA crosstalk and competition.

Authors:  Yvonne Tay; John Rinn; Pier Paolo Pandolfi
Journal:  Nature       Date:  2014-01-16       Impact factor: 49.962

5.  Recurrent somatic mutations in regulatory regions of human cancer genomes.

Authors:  Collin Melton; Jason A Reuter; Damek V Spacek; Michael Snyder
Journal:  Nat Genet       Date:  2015-06-08       Impact factor: 38.330

6.  Pint lincRNA connects the p53 pathway with epigenetic silencing by the Polycomb repressive complex 2.

Authors:  Oskar Marín-Béjar; Francesco P Marchese; Alejandro Athie; Yolanda Sánchez; Jovanna González; Victor Segura; Lulu Huang; Isabel Moreno; Alfons Navarro; Mariano Monzó; Jesús García-Foncillas; John L Rinn; Shuling Guo; Maite Huarte
Journal:  Genome Biol       Date:  2013       Impact factor: 13.583

7.  A virus-encoded telomerase RNA promotes malignant T cell lymphomagenesis.

Authors:  Sascha Trapp; Mark S Parcells; Jeremy P Kamil; Daniel Schumacher; B Karsten Tischer; Pankaj M Kumar; Venugopal K Nair; Nikolaus Osterrieder
Journal:  J Exp Med       Date:  2006-05-01       Impact factor: 14.307

8.  Gene expression signature of fibroblast serum response predicts human cancer progression: similarities between tumors and wounds.

Authors:  Howard Y Chang; Julie B Sneddon; Ash A Alizadeh; Ruchira Sood; Rob B West; Kelli Montgomery; Jen-Tsan Chi; Matt van de Rijn; David Botstein; Patrick O Brown
Journal:  PLoS Biol       Date:  2004-01-13       Impact factor: 8.029

9.  Integrative analysis of 111 reference human epigenomes.

Authors:  Anshul Kundaje; Wouter Meuleman; Jason Ernst; Misha Bilenky; Angela Yen; Alireza Heravi-Moussavi; Pouya Kheradpour; Zhizhuo Zhang; Jianrong Wang; Michael J Ziller; Viren Amin; John W Whitaker; Matthew D Schultz; Lucas D Ward; Abhishek Sarkar; Gerald Quon; Richard S Sandstrom; Matthew L Eaton; Yi-Chieh Wu; Andreas R Pfenning; Xinchen Wang; Melina Claussnitzer; Yaping Liu; Cristian Coarfa; R Alan Harris; Noam Shoresh; Charles B Epstein; Elizabeta Gjoneska; Danny Leung; Wei Xie; R David Hawkins; Ryan Lister; Chibo Hong; Philippe Gascard; Andrew J Mungall; Richard Moore; Eric Chuah; Angela Tam; Theresa K Canfield; R Scott Hansen; Rajinder Kaul; Peter J Sabo; Mukul S Bansal; Annaick Carles; Jesse R Dixon; Kai-How Farh; Soheil Feizi; Rosa Karlic; Ah-Ram Kim; Ashwinikumar Kulkarni; Daofeng Li; Rebecca Lowdon; GiNell Elliott; Tim R Mercer; Shane J Neph; Vitor Onuchic; Paz Polak; Nisha Rajagopal; Pradipta Ray; Richard C Sallari; Kyle T Siebenthall; Nicholas A Sinnott-Armstrong; Michael Stevens; Robert E Thurman; Jie Wu; Bo Zhang; Xin Zhou; Arthur E Beaudet; Laurie A Boyer; Philip L De Jager; Peggy J Farnham; Susan J Fisher; David Haussler; Steven J M Jones; Wei Li; Marco A Marra; Michael T McManus; Shamil Sunyaev; James A Thomson; Thea D Tlsty; Li-Huei Tsai; Wei Wang; Robert A Waterland; Michael Q Zhang; Lisa H Chadwick; Bradley E Bernstein; Joseph F Costello; Joseph R Ecker; Martin Hirst; Alexander Meissner; Aleksandar Milosavljevic; Bing Ren; John A Stamatoyannopoulos; Ting Wang; Manolis Kellis
Journal:  Nature       Date:  2015-02-19       Impact factor: 69.504

10.  Landscape and variation of RNA secondary structure across the human transcriptome.

Authors:  Yue Wan; Kun Qu; Qiangfeng Cliff Zhang; Ryan A Flynn; Ohad Manor; Zhengqing Ouyang; Jiajing Zhang; Robert C Spitale; Michael P Snyder; Eran Segal; Howard Y Chang
Journal:  Nature       Date:  2014-01-30       Impact factor: 49.962

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  34 in total

1.  Phylogenetic Analysis with Improved Parameters Reveals Conservation in lncRNA Structures.

Authors:  Rafael C A Tavares; Anna Marie Pyle; Srinivas Somarowthu
Journal:  J Mol Biol       Date:  2019-03-16       Impact factor: 5.469

Review 2.  Rules are made to be broken: a "simple" model organism reveals the complexity of gene regulation.

Authors:  Andrea L Higdon; Gloria A Brar
Journal:  Curr Genet       Date:  2020-11-01       Impact factor: 3.886

3.  Chromatin-enriched lncRNAs: a novel class of enhancer RNAs.

Authors:  Srimonta Gayen; Sundeep Kalantry
Journal:  Nat Struct Mol Biol       Date:  2017-07-06       Impact factor: 15.369

4.  Miat and interacting protein Metadherin maintain a stem-like niche to promote medulloblastoma tumorigenesis and treatment resistance.

Authors:  Kai-Lin Peng; Harish N Vasudevan; Dennis T Lockney; Rachel Baum; Ronald C Hendrickson; David R Raleigh; Adam M Schmitt
Journal:  Proc Natl Acad Sci U S A       Date:  2022-09-06       Impact factor: 12.779

5.  LncRNA CASC9 promotes cell proliferation and invasion in osteosarcoma through targeting miR-874-3p/SOX12 axis.

Authors:  Haiyan Qiu; Di Yang; Xiaolin Li; Fabo Feng
Journal:  J Orthop Surg Res       Date:  2022-10-20       Impact factor: 2.677

Review 6.  Nuclear Long Noncoding RNAs: Key Regulators of Gene Expression.

Authors:  Qinyu Sun; Qinyu Hao; Kannanganattu V Prasanth
Journal:  Trends Genet       Date:  2018-02-07       Impact factor: 11.639

7.  Paraspeckles are constructed as block copolymer micelles.

Authors:  Tomohiro Yamazaki; Tetsuya Yamamoto; Hyura Yoshino; Sylvie Souquere; Shinichi Nakagawa; Gerard Pierron; Tetsuro Hirose
Journal:  EMBO J       Date:  2021-04-22       Impact factor: 14.012

8.  Epigenome comparisons reveal linkage between gene expression and postnatal remodeling of chromatin domain topology.

Authors:  Bruce H Howard; Tazuko H Hirai; Valya R Russanova
Journal:  PLoS One       Date:  2018-02-21       Impact factor: 3.240

9.  Long Non-coding MIR205HG Depletes Hsa-miR-590-3p Leading to Unrestrained Proliferation in Head and Neck Squamous Cell Carcinoma.

Authors:  Silvia Di Agostino; Fabio Valenti; Andrea Sacconi; Giulia Fontemaggi; Matteo Pallocca; Claudio Pulito; Federica Ganci; Paola Muti; Sabrina Strano; Giovanni Blandino
Journal:  Theranostics       Date:  2018-02-12       Impact factor: 11.556

10.  Individualized lncRNA differential expression profile reveals heterogeneity of breast cancer.

Authors:  Zhangxiang Zhao; YingYing Guo; Yaoyao Liu; Lichun Sun; Bo Chen; Chengyu Wang; Tingting Chen; Yuquan Wang; Yawei Li; Qi Dong; Liqiang Ai; Ran Wang; Yunyan Gu; Xia Li
Journal:  Oncogene       Date:  2021-06-15       Impact factor: 9.867

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