Literature DB >> 27208508

Identification of human RNA editing sites: A historical perspective.

Gokul Ramaswami1, Jin Billy Li2.   

Abstract

A-to-I RNA editing is an essential gene regulatory mechanism. Once thought to be a rare phenomenon only occurring in a few transcripts, the emergence of high-throughput RNA sequencing has facilitated the identification of over 2 million RNA editing sites in the human transcriptome. In this review, we survey the current RNA-seq based methods as well as historical methods used to identify RNA editing sites.
Copyright © 2016 Elsevier Inc. All rights reserved.

Entities:  

Keywords:  Post-transcriptional gene regulation; RNA editing; RNA sequencing

Mesh：

Year:  2016        PMID： 27208508      PMCID： PMC5014717          DOI： 10.1016/j.ymeth.2016.05.011

Source DB:  PubMed          Journal:  Methods        ISSN： 1046-2023            Impact factor:   3.608


  60 in total

1.  BLAT--the BLAST-like alignment tool.

Authors:  W James Kent
Journal:  Genome Res       Date:  2002-04       Impact factor: 9.043

2.  Altered editing of serotonin 2C receptor pre-mRNA in the prefrontal cortex of depressed suicide victims.

Authors:  Ilona Gurevich; Hadassah Tamir; Victoria Arango; Andrew J Dwork; J John Mann; Claudia Schmauss
Journal:  Neuron       Date:  2002-04-25       Impact factor: 17.173

3.  Recoding RNA editing of AZIN1 predisposes to hepatocellular carcinoma.

Authors:  Leilei Chen; Yan Li; Chi Ho Lin; Tim Hon Man Chan; Raymond Kwok Kei Chow; Yangyang Song; Ming Liu; Yun-Fei Yuan; Li Fu; Kar Lok Kong; Lihua Qi; Yan Li; Na Zhang; Amy Hin Yan Tong; Dora Lai-Wan Kwong; Kwan Man; Chung Mau Lo; Si Lok; Daniel G Tenen; Xin-Yuan Guan
Journal:  Nat Med       Date:  2013-01-06       Impact factor: 53.440

Review 4.  Functions and regulation of RNA editing by ADAR deaminases.

Authors:  Kazuko Nishikura
Journal:  Annu Rev Biochem       Date:  2010       Impact factor: 23.643

Review 5.  Genome sequence of the nematode C. elegans: a platform for investigating biology.

Authors: 
Journal:  Science       Date:  1998-12-11       Impact factor: 47.728

6.  Identification of widespread ultra-edited human RNAs.

Authors:  Shai Carmi; Itamar Borukhov; Erez Y Levanon
Journal:  PLoS Genet       Date:  2011-10-20       Impact factor: 5.917

7.  Very few RNA and DNA sequence differences in the human transcriptome.

Authors:  Daniel R Schrider; Jean-Francois Gout; Matthew W Hahn
Journal:  PLoS One       Date:  2011-10-12       Impact factor: 3.240

8.  A genome-wide map of hyper-edited RNA reveals numerous new sites.

Authors:  Hagit T Porath; Shai Carmi; Erez Y Levanon
Journal:  Nat Commun       Date:  2014-08-27       Impact factor: 14.919

9.  Prediction of constitutive A-to-I editing sites from human transcriptomes in the absence of genomic sequences.

Authors:  Shanshan Zhu; Jian-Feng Xiang; Tian Chen; Ling-Ling Chen; Li Yang
Journal:  BMC Genomics       Date:  2013-03-27       Impact factor: 3.969

10.  Darned in 2013: inclusion of model organisms and linking with Wikipedia.

Authors:  Anmol M Kiran; John J O'Mahony; Komal Sanjeev; Pavel V Baranov
Journal:  Nucleic Acids Res       Date:  2012-10-15       Impact factor: 16.971
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  31 in total

Review 1.  Adenosine deaminase acting on RNA (ADAR1), a suppressor of double-stranded RNA-triggered innate immune responses.

Authors:  Charles E Samuel
Journal:  J Biol Chem       Date:  2019-02-01       Impact factor: 5.157

Review 2.  Identifying and characterizing functional 3' nucleotide addition in the miRNA pathway.

Authors:  A Maxwell Burroughs; Yoshinari Ando
Journal:  Methods       Date:  2018-08-20       Impact factor: 3.608

Review 3.  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

4.  Hyper-Editing of Cell-Cycle Regulatory and Tumor Suppressor RNA Promotes Malignant Progenitor Propagation.

Authors:  Qingfei Jiang; Jane Isquith; Maria Anna Zipeto; Raymond H Diep; Jessica Pham; Nathan Delos Santos; Eduardo Reynoso; Julisia Chau; Heather Leu; Elisa Lazzari; Etienne Melese; Wenxue Ma; Rongxin Fang; Mark Minden; Sheldon Morris; Bing Ren; Gabriel Pineda; Frida Holm; Catriona Jamieson
Journal:  Cancer Cell       Date:  2019-01-03       Impact factor: 31.743

Review 5.  What sequencing technologies can teach us about innate immunity.

Authors:  Mays Mohammed Salih; Susan Carpenter
Journal:  Immunol Rev       Date:  2021-11-07       Impact factor: 12.988

6.  RNA editing underlies genetic risk of common inflammatory diseases.

Authors:  Stephen B Montgomery; Jin Billy Li; Qin Li; Michael J Gloudemans; Jonathan M Geisinger; Boming Fan; François Aguet; Tao Sun; Gokul Ramaswami; Yang I Li; Jin-Biao Ma; Jonathan K Pritchard
Journal:  Nature       Date:  2022-08-03       Impact factor: 69.504

7.  Dynamic landscape and regulation of RNA editing in mammals.

Authors:  Meng How Tan; Qin Li; Raghuvaran Shanmugam; Robert Piskol; Jennefer Kohler; Amy N Young; Kaiwen Ivy Liu; Rui Zhang; Gokul Ramaswami; Kentaro Ariyoshi; Ankita Gupte; Liam P Keegan; Cyril X George; Avinash Ramu; Ni Huang; Elizabeth A Pollina; Dena S Leeman; Alessandra Rustighi; Y P Sharon Goh; Ajay Chawla; Giannino Del Sal; Gary Peltz; Anne Brunet; Donald F Conrad; Charles E Samuel; Mary A O'Connell; Carl R Walkley; Kazuko Nishikura; Jin Billy Li
Journal:  Nature       Date:  2017-10-11       Impact factor: 49.962

Review 8.  Epitranscriptomic Modifications Modulate Normal and Pathological Functions in CNS.

Authors:  Anil K Chokkalla; Suresh L Mehta; Raghu Vemuganti
Journal:  Transl Stroke Res       Date:  2021-07-05       Impact factor: 6.829

9.  A-to-I RNA editing in the rat brain is age-dependent, region-specific and sensitive to environmental stress across generations.

Authors:  Hiba Zaidan; Gokul Ramaswami; Yaela N Golumbic; Noa Sher; Assaf Malik; Michal Barak; Dalia Galiani; Nava Dekel; Jin B Li; Inna Gaisler-Salomon
Journal:  BMC Genomics       Date:  2018-01-08       Impact factor: 3.969

Review 10.  Rewriting the transcriptome: adenosine-to-inosine RNA editing by ADARs.

Authors:  Carl R Walkley; Jin Billy Li
Journal:  Genome Biol       Date:  2017-10-30       Impact factor: 13.583
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