Literature DB >> 27447984

RNA Matchmaking: Finding Cellular Pairing Partners.

Brenton R Graveley1.   

Abstract

RNA structure is intimately related to function, yet methods to identify base-paired RNA strands in a transcriptome-wide manner in cells have remained elusive. One recent paper in Cell and two in Molecular Cell describe related methods to identify RNA sequences that interact in living cells, setting the stage for breakthroughs in our understanding of RNA structure and function.
Copyright © 2016. Published by Elsevier Inc.

Entities:  

Mesh：

Substances：

Year:  2016        PMID： 27447984      PMCID： PMC4973470          DOI： 10.1016/j.molcel.2016.07.001

Source DB:  PubMed          Journal:  Mol Cell        ISSN： 1097-2765            Impact factor:   17.970


  14 in total

1.  Multiplexed RNA structure characterization with selective 2'-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq).

Authors:  Julius B Lucks; Stefanie A Mortimer; Cole Trapnell; Shujun Luo; Sharon Aviran; Gary P Schroth; Lior Pachter; Jennifer A Doudna; Adam P Arkin
Journal:  Proc Natl Acad Sci U S A       Date:  2011-06-03       Impact factor: 11.205

2.  In Vivo Mapping of Eukaryotic RNA Interactomes Reveals Principles of Higher-Order Organization and Regulation.

Authors:  Jong Ghut Ashley Aw; Yang Shen; Andreas Wilm; Miao Sun; Xin Ni Lim; Kum-Loong Boon; Sidika Tapsin; Yun-Shen Chan; Cheng-Peow Tan; Adelene Y L Sim; Tong Zhang; Teodorus Theo Susanto; Zhiyan Fu; Niranjan Nagarajan; Yue Wan
Journal:  Mol Cell       Date:  2016-05-12       Impact factor: 17.970

Review 3.  Understanding the transcriptome through RNA structure.

Authors:  Yue Wan; Michael Kertesz; Robert C Spitale; Eran Segal; Howard Y Chang
Journal:  Nat Rev Genet       Date:  2011-08-18       Impact factor: 53.242

4.  RNA Duplex Map in Living Cells Reveals Higher-Order Transcriptome Structure.

Authors:  Zhipeng Lu; Qiangfeng Cliff Zhang; Byron Lee; Ryan A Flynn; Martin A Smith; James T Robinson; Chen Davidovich; Anne R Gooding; Karen J Goodrich; John S Mattick; Jill P Mesirov; Thomas R Cech; Howard Y Chang
Journal:  Cell       Date:  2016-05-12       Impact factor: 41.582

5.  Resources for the Comprehensive Discovery of Functional RNA Elements.

Authors:  Balaji Sundararaman; Lijun Zhan; Steven M Blue; Rebecca Stanton; Keri Elkins; Sara Olson; Xintao Wei; Eric L Van Nostrand; Gabriel A Pratt; Stephanie C Huelga; Brendan M Smalec; Xiaofeng Wang; Eurie L Hong; Jean M Davidson; Eric Lécuyer; Brenton R Graveley; Gene W Yeo
Journal:  Mol Cell       Date:  2016-03-17       Impact factor: 17.970

6.  Detection of RNA-Protein Interactions in Living Cells with SHAPE.

Authors:  Matthew J Smola; J Mauro Calabrese; Kevin M Weeks
Journal:  Biochemistry       Date:  2015-11-11       Impact factor: 3.162

7.  FragSeq: transcriptome-wide RNA structure probing using high-throughput sequencing.

Authors:  Jason G Underwood; Andrew V Uzilov; Sol Katzman; Courtney S Onodera; Jacob E Mainzer; David H Mathews; Todd M Lowe; Sofie R Salama; David Haussler
Journal:  Nat Methods       Date:  2010-11-07       Impact factor: 28.547

8.  Genome-wide probing of RNA structure reveals active unfolding of mRNA structures in vivo.

Authors:  Silvi Rouskin; Meghan Zubradt; Stefan Washietl; Manolis Kellis; Jonathan S Weissman
Journal:  Nature       Date:  2013-12-15       Impact factor: 49.962

9.  Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP).

Authors:  Eric L Van Nostrand; Gabriel A Pratt; Alexander A Shishkin; Chelsea Gelboin-Burkhart; Mark Y Fang; Balaji Sundararaman; Steven M Blue; Thai B Nguyen; Christine Surka; Keri Elkins; Rebecca Stanton; Frank Rigo; Mitchell Guttman; Gene W Yeo
Journal:  Nat Methods       Date:  2016-03-28       Impact factor: 28.547

10.  Mod-seq: high-throughput sequencing for chemical probing of RNA structure.

Authors:  Jason Talkish; Gemma May; Yizhu Lin; John L Woolford; C Joel McManus
Journal:  RNA       Date:  2014-03-24       Impact factor: 4.942
View more
  9 in total

1.  RNA base-pairing complexity in living cells visualized by correlated chemical probing.

Authors:  Anthony M Mustoe; Nicole N Lama; Patrick S Irving; Samuel W Olson; Kevin M Weeks
Journal:  Proc Natl Acad Sci U S A       Date:  2019-11-19       Impact factor: 11.205

2.  DNA Tiling Enables Precise Acylation-Based Labeling and Control of mRNA.

Authors:  Lu Xiao; Yong Woong Jun; Eric T Kool
Journal:  Angew Chem Int Ed Engl       Date:  2021-11-16       Impact factor: 15.336

3.  Site-Selective RNA Functionalization via DNA-Induced Structure.

Authors:  Lu Xiao; Maryam Habibian; Eric T Kool
Journal:  J Am Chem Soc       Date:  2020-09-14       Impact factor: 15.419

Review 4.  RNA matchmaking in chromatin regulation.

Authors:  Stephen K Wu; Justin T Roberts; Maggie M Balas; Aaron M Johnson
Journal:  Biochem Soc Trans       Date:  2020-12-18       Impact factor: 5.407

5.  Direct Mapping of Higher-Order RNA Interactions by SHAPE-JuMP.

Authors:  Thomas W Christy; Catherine A Giannetti; Gillian Houlihan; Matthew J Smola; Greggory M Rice; Jian Wang; Nikolay V Dokholyan; Alain Laederach; Philipp Holliger; Kevin M Weeks
Journal:  Biochemistry       Date:  2021-06-14       Impact factor: 3.321

Review 6.  Does mRNA structure contain genetic information for regulating co-translational protein folding?

Authors:  Jian-Rong Yang
Journal:  Zool Res       Date:  2017-01-18

7.  Coordinate regulation of alternative pre-mRNA splicing events by the human RNA chaperone proteins hnRNPA1 and DDX5.

Authors:  Yeon J Lee; Qingqing Wang; Donald C Rio
Journal:  Genes Dev       Date:  2018-07-24       Impact factor: 11.361

8.  Establishing RNA-RNA interactions remodels lncRNA structure and promotes PRC2 activity.

Authors:  Maggie M Balas; Erik W Hartwick; Chloe Barrington; Justin T Roberts; Stephen K Wu; Ryan Bettcher; April M Griffin; Jeffrey S Kieft; Aaron M Johnson
Journal:  Sci Adv       Date:  2021-04-14       Impact factor: 14.136

9.  Specificity of mRNA Folding and Its Association with Evolutionarily Adaptive mRNA Secondary Structures.

Authors:  Gongwang Yu; Hanbing Zhu; Xiaoshu Chen; Jian-Rong Yang
Journal:  Genomics Proteomics Bioinformatics       Date:  2021-02-17       Impact factor: 6.409
  9 in total

北京卡尤迪生物科技股份有限公司 © 2022-2023.