Literature DB >> 36203019

Advances and opportunities in RNA structure experimental determination and computational modeling.

Jinsong Zhang1,2,3, Yuhan Fei1,2,3, Lei Sun4,5,6, Qiangfeng Cliff Zhang7,8,9.   

Abstract

Beyond transferring genetic information, RNAs are molecules with diverse functions that include catalyzing biochemical reactions and regulating gene expression. Most of these activities depend on RNAs' specific structures. Therefore, accurately determining RNA structure is integral to advancing our understanding of RNA functions. Here, we summarize the state-of-the-art experimental and computational technologies developed to evaluate RNA secondary and tertiary structures. We also highlight how the rapid increase of experimental data facilitates the integrative modeling approaches for better resolving RNA structures. Finally, we provide our thoughts on the latest advances and challenges in RNA structure determination methods, as well as on future directions for both experimental approaches and artificial intelligence-based computational tools to model RNA structure. Ultimately, we hope the technological advances will deepen our understanding of RNA biology and facilitate RNA structure-based biomedical research such as designing specific RNA structures for therapeutics and deploying RNA-targeting small-molecule drugs.
© 2022. Springer Nature America, Inc.

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Year:  2022        PMID: 36203019     DOI: 10.1038/s41592-022-01623-y

Source DB:  PubMed          Journal:  Nat Methods        ISSN: 1548-7091            Impact factor:   47.990


  110 in total

Review 1.  Genome regulation by long noncoding RNAs.

Authors:  John L Rinn; Howard Y Chang
Journal:  Annu Rev Biochem       Date:  2012       Impact factor: 23.643

2.  In vivo genome-wide profiling of RNA secondary structure reveals novel regulatory features.

Authors:  Yiliang Ding; Yin Tang; Chun Kit Kwok; Yu Zhang; Philip C Bevilacqua; Sarah M Assmann
Journal:  Nature       Date:  2013-11-24       Impact factor: 49.962

Review 3.  Ribozymes, riboswitches and beyond: regulation of gene expression without proteins.

Authors:  Alexander Serganov; Dinshaw J Patel
Journal:  Nat Rev Genet       Date:  2007-09-11       Impact factor: 53.242

Review 4.  The roles of structural dynamics in the cellular functions of RNAs.

Authors:  Laura R Ganser; Megan L Kelly; Daniel Herschlag; Hashim M Al-Hashimi
Journal:  Nat Rev Mol Cell Biol       Date:  2019-08       Impact factor: 94.444

5.  Genome-wide measurement of RNA secondary structure in yeast.

Authors:  Michael Kertesz; Yue Wan; Elad Mazor; John L Rinn; Robert C Nutter; Howard Y Chang; Eran Segal
Journal:  Nature       Date:  2010-09-02       Impact factor: 49.962

Review 6.  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

Review 7.  Ribozymes: a distinct class of metalloenzymes.

Authors:  A M Pyle
Journal:  Science       Date:  1993-08-06       Impact factor: 47.728

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

Review 9.  Cryo-EM advances in RNA structure determination.

Authors:  Haiyun Ma; Xinyu Jia; Kaiming Zhang; Zhaoming Su
Journal:  Signal Transduct Target Ther       Date:  2022-02-23

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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