Literature DB >> 25565026

Discovery and annotation of long noncoding RNAs.

John S Mattick1, John L Rinn2.   

Abstract

Recent advances in RNA-sequencing technologies have led to the discovery of thousands of previously unannotated noncoding transcripts, including many long noncoding RNAs (lncRNAs) whose functions remain largely unknown. Here we discuss considerations and best practices in lncRNA identification and annotation, which we hope will foster functional and mechanistic exploration.

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Year:  2015        PMID： 25565026     DOI： 10.1038/nsmb.2942

Source DB:  PubMed          Journal:  Nat Struct Mol Biol        ISSN： 1545-9985            Impact factor:   15.369


  25 in total

1.  Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses.

Authors:  Moran N Cabili; Cole Trapnell; Loyal Goff; Magdalena Koziol; Barbara Tazon-Vega; Aviv Regev; John L Rinn
Journal:  Genes Dev       Date:  2011-09-02       Impact factor: 11.361

2.  RNA Function. RNA and dynamic nuclear organization.

Authors:  John Rinn; Mitchell Guttman
Journal:  Science       Date:  2014-09-12       Impact factor: 47.728

3.  Targeted sequencing for gene discovery and quantification using RNA CaptureSeq.

Authors:  Tim R Mercer; Michael B Clark; Joanna Crawford; Marion E Brunck; Daniel J Gerhardt; Ryan J Taft; Lars K Nielsen; Marcel E Dinger; John S Mattick
Journal:  Nat Protoc       Date:  2014-04-03       Impact factor: 13.491

Review 4.  Modular regulatory principles of large non-coding RNAs.

Authors:  Mitchell Guttman; John L Rinn
Journal:  Nature       Date:  2012-02-15       Impact factor: 49.962

5.  Ribosome profiling provides evidence that large noncoding RNAs do not encode proteins.

Authors:  Mitchell Guttman; Pamela Russell; Nicholas T Ingolia; Jonathan S Weissman; Eric S Lander
Journal:  Cell       Date:  2013-06-27       Impact factor: 41.582

6.  Peptidomic discovery of short open reading frame-encoded peptides in human cells.

Authors:  Sarah A Slavoff; Andrew J Mitchell; Adam G Schwaid; Moran N Cabili; Jiao Ma; Joshua Z Levin; Amir D Karger; Bogdan A Budnik; John L Rinn; Alan Saghatelian
Journal:  Nat Chem Biol       Date:  2012-11-18       Impact factor: 15.040

7.  The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression.

Authors:  Thomas Derrien; Rory Johnson; Giovanni Bussotti; Andrea Tanzer; Sarah Djebali; Hagen Tilgner; Gregory Guernec; David Martin; Angelika Merkel; David G Knowles; Julien Lagarde; Lavanya Veeravalli; Xiaoan Ruan; Yijun Ruan; Timo Lassmann; Piero Carninci; James B Brown; Leonard Lipovich; Jose M Gonzalez; Mark Thomas; Carrie A Davis; Ramin Shiekhattar; Thomas R Gingeras; Tim J Hubbard; Cedric Notredame; Jennifer Harrow; Roderic Guigó
Journal:  Genome Res       Date:  2012-09       Impact factor: 9.043

8.  lncRNAdb v2.0: expanding the reference database for functional long noncoding RNAs.

Authors:  Xiu Cheng Quek; Daniel W Thomson; Jesper L V Maag; Nenad Bartonicek; Bethany Signal; Michael B Clark; Brian S Gloss; Marcel E Dinger
Journal:  Nucleic Acids Res       Date:  2014-10-20       Impact factor: 16.971

9.  CPAT: Coding-Potential Assessment Tool using an alignment-free logistic regression model.

Authors:  Liguo Wang; Hyun Jung Park; Surendra Dasari; Shengqin Wang; Jean-Pierre Kocher; Wei Li
Journal:  Nucleic Acids Res       Date:  2013-01-17       Impact factor: 16.971

10.  Landscape of transcription in human cells.

Authors:  Sarah Djebali; Carrie A Davis; Angelika Merkel; Alex Dobin; Timo Lassmann; Ali Mortazavi; Andrea Tanzer; Julien Lagarde; Wei Lin; Felix Schlesinger; Chenghai Xue; Georgi K Marinov; Jainab Khatun; Brian A Williams; Chris Zaleski; Joel Rozowsky; Maik Röder; Felix Kokocinski; Rehab F Abdelhamid; Tyler Alioto; Igor Antoshechkin; Michael T Baer; Nadav S Bar; Philippe Batut; Kimberly Bell; Ian Bell; Sudipto Chakrabortty; Xian Chen; Jacqueline Chrast; Joao Curado; Thomas Derrien; Jorg Drenkow; Erica Dumais; Jacqueline Dumais; Radha Duttagupta; Emilie Falconnet; Meagan Fastuca; Kata Fejes-Toth; Pedro Ferreira; Sylvain Foissac; Melissa J Fullwood; Hui Gao; David Gonzalez; Assaf Gordon; Harsha Gunawardena; Cedric Howald; Sonali Jha; Rory Johnson; Philipp Kapranov; Brandon King; Colin Kingswood; Oscar J Luo; Eddie Park; Kimberly Persaud; Jonathan B Preall; Paolo Ribeca; Brian Risk; Daniel Robyr; Michael Sammeth; Lorian Schaffer; Lei-Hoon See; Atif Shahab; Jorgen Skancke; Ana Maria Suzuki; Hazuki Takahashi; Hagen Tilgner; Diane Trout; Nathalie Walters; Huaien Wang; John Wrobel; Yanbao Yu; Xiaoan Ruan; Yoshihide Hayashizaki; Jennifer Harrow; Mark Gerstein; Tim Hubbard; Alexandre Reymond; Stylianos E Antonarakis; Gregory Hannon; Morgan C Giddings; Yijun Ruan; Barbara Wold; Piero Carninci; Roderic Guigó; Thomas R Gingeras
Journal:  Nature       Date:  2012-09-06       Impact factor: 49.962
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  242 in total

Review 1.  A Uniform System for the Annotation of Vertebrate microRNA Genes and the Evolution of the Human microRNAome.

Authors:  Bastian Fromm; Tyler Billipp; Liam E Peck; Morten Johansen; James E Tarver; Benjamin L King; James M Newcomb; Lorenzo F Sempere; Kjersti Flatmark; Eivind Hovig; Kevin J Peterson
Journal:  Annu Rev Genet       Date:  2015-10-14       Impact factor: 16.830

Review 2.  Multifaceted Roles of Long Non-coding RNAs in Head and Neck Cancer.

Authors:  Leslie Duncan; Chloe Shay; Yong Teng
Journal:  Adv Exp Med Biol       Date:  2021       Impact factor: 2.622

Review 3.  Role of long non-coding RNAs (LncRNAs) in multiple sclerosis: a brief review.

Authors:  Eskandar Taghizadeh; Forough Taheri; Mohammad Mahdi Samadian; Mohammad Soudyab; Abbas Abi; Seyed Mohammad Gheibi Hayat
Journal:  Neurol Sci       Date:  2020-04-30       Impact factor: 3.307

4.  lncSLdb: a resource for long non-coding RNA subcellular localization.

Authors:  Xiao Wen; Lin Gao; Xingli Guo; Xing Li; Xiaotai Huang; Ying Wang; Haifu Xu; Ruijie He; Chenglong Jia; Feixiang Liang
Journal:  Database (Oxford)       Date:  2018-01-01       Impact factor: 3.451

Review 5.  Genetic and epigenetic regulation of human aging and longevity.

Authors:  Brian J Morris; Bradley J Willcox; Timothy A Donlon
Journal:  Biochim Biophys Acta Mol Basis Dis       Date:  2018-09-01       Impact factor: 5.187

Review 6.  Insight into lncRNA biology using hybridization capture analyses.

Authors:  Matthew D Simon
Journal:  Biochim Biophys Acta       Date:  2015-09-14

7.  Exosomal lncRNAs as new players in cell-to-cell communication.

Authors:  Mihnea Dragomir; Baoqing Chen; George A Calin
Journal:  Transl Cancer Res       Date:  2018-03       Impact factor: 1.241

8.  Discovering long noncoding RNA predictors of anticancer drug sensitivity beyond protein-coding genes.

Authors:  Aritro Nath; Eunice Y T Lau; Adam M Lee; Paul Geeleher; William C S Cho; R Stephanie Huang
Journal:  Proc Natl Acad Sci U S A       Date:  2019-09-23       Impact factor: 11.205

9.  Long noncoding RNA derived from CD244 signaling epigenetically controls CD8+ T-cell immune responses in tuberculosis infection.

Authors:  Yang Wang; Huiling Zhong; Xiaodan Xie; Crystal Y Chen; Dan Huang; Ling Shen; Hui Zhang; Zheng W Chen; Gucheng Zeng
Journal:  Proc Natl Acad Sci U S A       Date:  2015-07-06       Impact factor: 11.205

10.  Identification of novel survival-related lncRNA-miRNA-mRNA competing endogenous RNA network associated with immune infiltration in colorectal cancer.

Authors:  Jianxin Li; Ting Han; Xin Wang; Yinchun Wang; Qingqiang Yang
Journal:  Am J Transl Res       Date:  2021-06-15       Impact factor: 4.060
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