Literature DB >> 35717434

Recent advances in RNA structurome.

Bingbing Xu1, Yanda Zhu1, Changchang Cao2, Hao Chen3, Qiongli Jin4, Guangnan Li5, Junfeng Ma6, Siwy Ling Yang7, Jieyu Zhao8, Jianghui Zhu9,10, Yiliang Ding11, Xianyang Fang12, Yongfeng Jin13, Chun Kit Kwok14,15, Aiming Ren16, Yue Wan17, Zhiye Wang18, Yuanchao Xue19,20, Huakun Zhang21, Qiangfeng Cliff Zhang22,23, Yu Zhou24.   

Abstract

RNA structures are essential to support RNA functions and regulation in various biological processes. Recently, a range of novel technologies have been developed to decode genome-wide RNA structures and novel modes of functionality across a wide range of species. In this review, we summarize key strategies for probing the RNA structurome and discuss the pros and cons of representative technologies. In particular, these new technologies have been applied to dissect the structural landscape of the SARS-CoV-2 RNA genome. We also summarize the functionalities of RNA structures discovered in different regulatory layers-including RNA processing, transport, localization, and mRNA translation-across viruses, bacteria, animals, and plants. We review many versatile RNA structural elements in the context of different physiological and pathological processes (e.g., cell differentiation, stress response, and viral replication). Finally, we discuss future prospects for RNA structural studies to map the RNA structurome at higher resolution and at the single-molecule and single-cell level, and to decipher novel modes of RNA structures and functions for innovative applications.
© 2022. Science China Press and Springer-Verlag GmbH Germany, part of Springer Nature.

Entities:  

Keywords:  3D structure; RNA secondary structure; RNA structurome; SARS-CoV-2; decoding; function; genome-wide; high-throughput techniques

Mesh:

Substances:

Year:  2022        PMID: 35717434      PMCID: PMC9206424          DOI: 10.1007/s11427-021-2116-2

Source DB:  PubMed          Journal:  Sci China Life Sci        ISSN: 1674-7305            Impact factor:   10.372


  330 in total

1.  Genome-wide profiling of in vivo RNA structure at single-nucleotide resolution using structure-seq.

Authors:  Yiliang Ding; Chun Kit Kwok; Yin Tang; Philip C Bevilacqua; Sarah M Assmann
Journal:  Nat Protoc       Date:  2015-06-18       Impact factor: 13.491

2.  Analysis of intron sequences reveals hallmarks of circular RNA biogenesis in animals.

Authors:  Andranik Ivanov; Sebastian Memczak; Emanuel Wyler; Francesca Torti; Hagit T Porath; Marta R Orejuela; Michael Piechotta; Erez Y Levanon; Markus Landthaler; Christoph Dieterich; Nikolaus Rajewsky
Journal:  Cell Rep       Date:  2014-12-31       Impact factor: 9.423

Review 3.  Biological small-angle neutron scattering: recent results and development.

Authors:  Emilie Mahieu; Frank Gabel
Journal:  Acta Crystallogr D Struct Biol       Date:  2018-07-17       Impact factor: 7.652

4.  Analyses of mRNA structure dynamics identify embryonic gene regulatory programs.

Authors:  Jean-Denis Beaudoin; Eva Maria Novoa; Charles E Vejnar; Valeria Yartseva; Carter M Takacs; Manolis Kellis; Antonio J Giraldez
Journal:  Nat Struct Mol Biol       Date:  2018-07-30       Impact factor: 15.369

5.  Noncoding RNA: from dark matter to bright star.

Authors:  Yuanchao Xue; Runsheng Chen; Lianghu Qu; Xiaofeng Cao
Journal:  Sci China Life Sci       Date:  2020-03-13       Impact factor: 6.038

6.  Thermodynamic and phylogenetic prediction of RNA secondary structures in the coding region of hepatitis C virus.

Authors:  Andrew Tuplin; Jonny Wood; David J Evans; Arvind H Patel; Peter Simmonds
Journal:  RNA       Date:  2002-06       Impact factor: 4.942

7.  HIV-1 can escape from RNA interference by evolving an alternative structure in its RNA genome.

Authors:  Ellen M Westerhout; Marcel Ooms; Monique Vink; Atze T Das; Ben Berkhout
Journal:  Nucleic Acids Res       Date:  2005-02-01       Impact factor: 16.971

8.  hiCLIP reveals the in vivo atlas of mRNA secondary structures recognized by Staufen 1.

Authors:  Yoichiro Sugimoto; Alessandra Vigilante; Elodie Darbo; Alexandra Zirra; Cristina Militti; Andrea D'Ambrogio; Nicholas M Luscombe; Jernej Ule
Journal:  Nature       Date:  2015-03-18       Impact factor: 49.962

Review 9.  Evolving SAXS versatility: solution X-ray scattering for macromolecular architecture, functional landscapes, and integrative structural biology.

Authors:  Chris A Brosey; John A Tainer
Journal:  Curr Opin Struct Biol       Date:  2019-06-13       Impact factor: 6.809

10.  Automated and optimally FRET-assisted structural modeling.

Authors:  Mykola Dimura; Thomas-Otavio Peulen; Hugo Sanabria; Dmitro Rodnin; Katherina Hemmen; Christian A Hanke; Claus A M Seidel; Holger Gohlke
Journal:  Nat Commun       Date:  2020-10-26       Impact factor: 14.919

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