Literature DB >> 28488699

Charting the unknown epitranscriptome.

Eva Maria Novoa1,2, Christopher E Mason3, John S Mattick1,2.   

Abstract

RNA modifications can alter RNA structure-function relationships and various cellular processes. However, the genomic distribution and biological roles of most RNA modifications remain uncharacterized. Here, we propose using phage display antibody technology and direct sequencing through nanopores to facilitate systematic interrogation of the distribution, location and dynamics of RNA modifications.

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Year:  2017        PMID： 28488699     DOI： 10.1038/nrm.2017.49

Source DB:  PubMed          Journal:  Nat Rev Mol Cell Biol        ISSN： 1471-0072            Impact factor:   94.444


  7 in total

1.  Selection of human antibody fragments by phage display.

Authors:  Carol M Y Lee; Niccolo Iorno; Frederic Sierro; Daniel Christ
Journal:  Nat Protoc       Date:  2007       Impact factor: 13.491

2.  Detecting DNA cytosine methylation using nanopore sequencing.

Authors:  Jared T Simpson; Rachael E Workman; P C Zuzarte; Matei David; L J Dursi; Winston Timp
Journal:  Nat Methods       Date:  2017-02-20       Impact factor: 28.547

3.  Comprehensive analysis of mRNA methylation reveals enrichment in 3' UTRs and near stop codons.

Authors:  Kate D Meyer; Yogesh Saletore; Paul Zumbo; Olivier Elemento; Christopher E Mason; Samie R Jaffrey
Journal:  Cell       Date:  2012-05-17       Impact factor: 41.582

4.  N6-methyladenosine in nuclear RNA is a major substrate of the obesity-associated FTO.

Authors:  Guifang Jia; Ye Fu; Xu Zhao; Qing Dai; Guanqun Zheng; Ying Yang; Chengqi Yi; Tomas Lindahl; Tao Pan; Yun-Gui Yang; Chuan He
Journal:  Nat Chem Biol       Date:  2011-10-16       Impact factor: 15.040

5.  The birth of the Epitranscriptome: deciphering the function of RNA modifications.

Authors:  Yogesh Saletore; Kate Meyer; Jonas Korlach; Igor D Vilfan; Samie Jaffrey; Christopher E Mason
Journal:  Genome Biol       Date:  2012-10-31       Impact factor: 13.583

6.  The reverse transcription signature of N-1-methyladenosine in RNA-Seq is sequence dependent.

Authors:  Ralf Hauenschild; Lyudmil Tserovski; Katharina Schmid; Kathrin Thüring; Marie-Luise Winz; Sunny Sharma; Karl-Dieter Entian; Ludivine Wacheul; Denis L J Lafontaine; James Anderson; Juan Alfonzo; Andreas Hildebrandt; Andres Jäschke; Yuri Motorin; Mark Helm
Journal:  Nucleic Acids Res       Date:  2015-09-13       Impact factor: 16.971

7.  Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq.

Authors:  Dan Dominissini; Sharon Moshitch-Moshkovitz; Schraga Schwartz; Mali Salmon-Divon; Lior Ungar; Sivan Osenberg; Karen Cesarkas; Jasmine Jacob-Hirsch; Ninette Amariglio; Martin Kupiec; Rotem Sorek; Gideon Rechavi
Journal:  Nature       Date:  2012-04-29       Impact factor: 49.962
  7 in total
  13 in total

Review 1.  A-to-I RNA editing - immune protector and transcriptome diversifier.

Authors:  Eli Eisenberg; Erez Y Levanon
Journal:  Nat Rev Genet       Date:  2018-08       Impact factor: 53.242

Review 2.  Loop-Mediated Isothermal Amplification Detection of SARS-CoV-2 and Myriad Other Applications.

Authors:  Keith J M Moore; Jeremy Cahill; Guy Aidelberg; Rachel Aronoff; Ali Bektaş; Daniela Bezdan; Daniel J Butler; Sridar V Chittur; Martin Codyre; Fernan Federici; Nathan A Tanner; Scott W Tighe; Randy True; Sarah B Ware; Anne L Wyllie; Evan E Afshin; Andres Bendesky; Connie B Chang; Richard Dela Rosa; Eran Elhaik; David Erickson; Andrew S Goldsborough; George Grills; Kathrin Hadasch; Andrew Hayden; Seong-Young Her; Julie A Karl; Chang Hee Kim; Alison J Kriegel; Thomas Kunstman; Zeph Landau; Kevin Land; Bradley W Langhorst; Ariel B Lindner; Benjamin E Mayer; Lee A McLaughlin; Matthew T McLaughlin; Jenny Molloy; Christopher Mozsary; Jerry L Nadler; Melinee D'Silva; David Ng; David H O'Connor; Jerry E Ongerth; Olayinka Osuolale; Ana Pinharanda; Dennis Plenker; Ravi Ranjan; Michael Rosbash; Assaf Rotem; Jacob Segarra; Stephan Schürer; Scott Sherrill-Mix; Helena Solo-Gabriele; Shaina To; Merly C Vogt; Albert D Yu; Christopher E Mason
Journal:  J Biomol Tech       Date:  2021-09

3.  Quantitative profiling of pseudouridylation dynamics in native RNAs with nanopore sequencing.

Authors:  Oguzhan Begik; Morghan C Lucas; Leszek P Pryszcz; Jose Miguel Ramirez; Rebeca Medina; Ivan Milenkovic; Sonia Cruciani; Huanle Liu; Helaine Graziele Santos Vieira; Aldema Sas-Chen; John S Mattick; Schraga Schwartz; Eva Maria Novoa
Journal:  Nat Biotechnol       Date:  2021-05-13       Impact factor: 54.908

Review 4.  Deciphering RNA modifications at base resolution: from chemistry to biology.

Authors:  Turja K Debnath; Blerta Xhemalçe
Journal:  Brief Funct Genomics       Date:  2021-03-27       Impact factor: 4.241

5.  Subcellular relocalization and nuclear redistribution of the RNA methyltransferases TRMT1 and TRMT1L upon neuronal activation.

Authors:  Nicky Jonkhout; Sonia Cruciani; Helaine Graziele Santos Vieira; Julia Tran; Huanle Liu; Ganqiang Liu; Russell Pickford; Dominik Kaczorowski; Gloria R Franco; Franz Vauti; Noelia Camacho; Seyedeh Sedigheh Abedini; Hossein Najmabadi; Lluís Ribas de Pouplana; Daniel Christ; Nicole Schonrock; John S Mattick; Eva Maria Novoa
Journal:  RNA Biol       Date:  2021-02-15       Impact factor: 4.652

Review 6.  The RNA modification landscape in human disease.

Authors:  Nicky Jonkhout; Julia Tran; Martin A Smith; Nicole Schonrock; John S Mattick; Eva Maria Novoa
Journal:  RNA       Date:  2017-08-30       Impact factor: 4.942

7.  China's most typical nonferrous organic-metal facilities own specific microbial communities.

Authors:  Jian-Li Liu; Jun Yao; Fei Wang; Wen Ni; Xing-Yu Liu; Geoffrey Sunahara; Robert Duran; Gyozo Jordan; Karen A Hudson-Edwards; Lena Alakangas; Tatjana Solevic-Knudsen; Xiao-Zhe Zhu; Yi-Yue Zhang; Zi-Fu Li
Journal:  Sci Rep       Date:  2018-08-22       Impact factor: 4.379

8.  m6Acomet: large-scale functional prediction of individual m6A RNA methylation sites from an RNA co-methylation network.

Authors:  Xiangyu Wu; Zhen Wei; Kunqi Chen; Qing Zhang; Jionglong Su; Hui Liu; Lin Zhang; Jia Meng
Journal:  BMC Bioinformatics       Date:  2019-05-02       Impact factor: 3.169

Review 9.  Methodologies for Transcript Profiling Using Long-Read Technologies.

Authors:  Spyros Oikonomopoulos; Anthony Bayega; Somayyeh Fahiminiya; Haig Djambazian; Pierre Berube; Jiannis Ragoussis
Journal:  Front Genet       Date:  2020-07-07       Impact factor: 4.599

10.  The State of Long Non-Coding RNA Biology.

Authors:  John S Mattick
Journal:  Noncoding RNA       Date:  2018-08-10
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