Literature DB >> 35524112

Direct Sequencing of RNA and RNA Modification Identification Using Nanopore.

Thidathip Wongsurawat1, Piroon Jenjaroenpun2, Intawat Nookaew3.   

Abstract

Direct RNA sequencing (dRNA-seq) simultaneously enables the detection of RNA modifications and characterization of full-length transcripts. In principle, full-length native RNA molecule is translocated through the nanopore by a motor protein while a sensor measures ionic current shifts. Then, the current shifts are interpreted by an algorithm that turn out to RNA sequence. Currently, the standard protocol of dRNA-seq provided by Oxford Nanopore Technologies (ONT) allows to directly ligate and sequence only polyadenylated RNA (poly(A) RNA). Here, we describe a method of dRNA-seq that can be applied for both poly(A) RNA and non-poly(A) tailed-RNA.
© 2022. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.

Entities:  

Keywords:  Direct RNA sequencing; Epitranscriptome; Long-read; Methylation; Modification; Nanopore; Native; RNA; Sequencing Technology; Transcriptome

Mesh：

Substances：

Year:  2022        PMID： 35524112     DOI： 10.1007/978-1-0716-2257-5_5

Source DB:  PubMed          Journal:  Methods Mol Biol        ISSN： 1064-3745


  14 in total

1.  Highly parallel direct RNA sequencing on an array of nanopores.

Authors:  Daniel R Garalde; Elizabeth A Snell; Daniel Jachimowicz; Botond Sipos; Joseph H Lloyd; Mark Bruce; Nadia Pantic; Tigist Admassu; Phillip James; Anthony Warland; Michael Jordan; Jonah Ciccone; Sabrina Serra; Jemma Keenan; Samuel Martin; Luke McNeill; E Jayne Wallace; Lakmal Jayasinghe; Chris Wright; Javier Blasco; Stephen Young; Denise Brocklebank; Sissel Juul; James Clarke; Andrew J Heron; Daniel J Turner
Journal:  Nat Methods       Date:  2018-01-15       Impact factor: 28.547

2.  Rapid Sequencing of Multiple RNA Viruses in Their Native Form.

Authors:  Thidathip Wongsurawat; Piroon Jenjaroenpun; Mariah K Taylor; Jasper Lee; Aline Lavado Tolardo; Jyothi Parvathareddy; Sangam Kandel; Taylor D Wadley; Bualan Kaewnapan; Niracha Athipanyasilp; Andrew Skidmore; Donghoon Chung; Chutikarn Chaimayo; Michael Whitt; Wannee Kantakamalakul; Ruengpung Sutthent; Navin Horthongkham; David W Ussery; Colleen B Jonsson; Intawat Nookaew
Journal:  Front Microbiol       Date:  2019-02-25       Impact factor: 5.640

3.  Nanopore direct RNA sequencing maps the complexity of Arabidopsis mRNA processing and m6A modification.

Authors:  Matthew T Parker; Katarzyna Knop; Anna V Sherwood; Nicholas J Schurch; Katarzyna Mackinnon; Peter D Gould; Anthony Jw Hall; Geoffrey J Barton; Gordon G Simpson
Journal:  Elife       Date:  2020-01-14       Impact factor: 8.140

4.  Profiling of circular RNA N6 -methyladenosine in moso bamboo (Phyllostachys edulis) using nanopore-based direct RNA sequencing.

Authors:  Yongsheng Wang; Huihui Wang; Feihu Xi; Huiyuan Wang; Ximei Han; Wentao Wei; Hangxiao Zhang; Qianyue Zhang; Yushan Zheng; Qiang Zhu; Markus V Kohnen; Anireddy S N Reddy; Lianfeng Gu
Journal:  J Integr Plant Biol       Date:  2020-08-31       Impact factor: 7.061

Review 5.  Analysis of Transcriptome and Epitranscriptome in Plants Using PacBio Iso-Seq and Nanopore-Based Direct RNA Sequencing.

Authors:  Liangzhen Zhao; Hangxiao Zhang; Markus V Kohnen; Kasavajhala V S K Prasad; Lianfeng Gu; Anireddy S N Reddy
Journal:  Front Genet       Date:  2019-03-21       Impact factor: 4.599

Review 6.  Recent advances in the detection of base modifications using the Nanopore sequencer.

Authors:  Liu Xu; Masahide Seki
Journal:  J Hum Genet       Date:  2019-10-11       Impact factor: 3.172

7.  Amplicon-Based, Next-Generation Sequencing Approaches to Characterize Single Nucleotide Polymorphisms of Orthohantavirus Species.

Authors:  Mariah K Taylor; Evan P Williams; Thidathip Wongsurawat; Piroon Jenjaroenpun; Intawat Nookaew; Colleen B Jonsson
Journal:  Front Cell Infect Microbiol       Date:  2020-10-14       Impact factor: 5.293

8.  Decoding the epitranscriptional landscape from native RNA sequences.

Authors:  Piroon Jenjaroenpun; Thidathip Wongsurawat; Taylor D Wadley; Trudy M Wassenaar; Jun Liu; Qing Dai; Visanu Wanchai; Nisreen S Akel; Azemat Jamshidi-Parsian; Aime T Franco; Gunnar Boysen; Michael L Jennings; David W Ussery; Chuan He; Intawat Nookaew
Journal:  Nucleic Acids Res       Date:  2020-07-25       Impact factor: 16.971

9.  Nanopore native RNA sequencing of a human poly(A) transcriptome.

Authors:  Rachael E Workman; Alison D Tang; Paul S Tang; Miten Jain; John R Tyson; Roham Razaghi; Philip C Zuzarte; Timothy Gilpatrick; Alexander Payne; Joshua Quick; Norah Sadowski; Nadine Holmes; Jaqueline Goes de Jesus; Karen L Jones; Cameron M Soulette; Terrance P Snutch; Nicholas Loman; Benedict Paten; Matthew Loose; Jared T Simpson; Hugh E Olsen; Angela N Brooks; Mark Akeson; Winston Timp
Journal:  Nat Methods       Date:  2019-11-18       Impact factor: 28.547

10.  Complete genomic and transcriptional landscape analysis using third-generation sequencing: a case study of Saccharomyces cerevisiae CEN.PK113-7D.

Authors:  Piroon Jenjaroenpun; Thidathip Wongsurawat; Rui Pereira; Preecha Patumcharoenpol; David W Ussery; Jens Nielsen; Intawat Nookaew
Journal:  Nucleic Acids Res       Date:  2018-04-20       Impact factor: 16.971
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