Literature DB >> 29795125

Towards a complete map of the human long non-coding RNA transcriptome.

Barbara Uszczynska-Ratajczak1, Julien Lagarde2,3, Adam Frankish4, Roderic Guigó2,3, Rory Johnson5,6.   

Abstract

Gene maps, or annotations, enable us to navigate the functional landscape of our genome. They are a resource upon which virtually all studies depend, from single-gene to genome-wide scales and from basic molecular biology to medical genetics. Yet present-day annotations suffer from trade-offs between quality and size, with serious but often unappreciated consequences for downstream studies. This is particularly true for long non-coding RNAs (lncRNAs), which are poorly characterized compared to protein-coding genes. Long-read sequencing technologies promise to improve current annotations, paving the way towards a complete annotation of lncRNAs expressed throughout a human lifetime.

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Year:  2018        PMID: 29795125      PMCID: PMC6451964          DOI: 10.1038/s41576-018-0017-y

Source DB:  PubMed          Journal:  Nat Rev Genet        ISSN: 1471-0056            Impact factor:   53.242


  151 in total

1.  Estimation of alternative splicing variability in human populations.

Authors:  Mar Gonzàlez-Porta; Miquel Calvo; Michael Sammeth; Roderic Guigó
Journal:  Genome Res       Date:  2011-11-23       Impact factor: 9.043

2.  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

3.  A novel RNA motif mediates the strict nuclear localization of a long noncoding RNA.

Authors:  Bing Zhang; Lalith Gunawardane; Farshad Niazi; Fereshteh Jahanbani; Xin Chen; Saba Valadkhan
Journal:  Mol Cell Biol       Date:  2014-04-14       Impact factor: 4.272

4.  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

5.  Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression.

Authors:  Ahmad M Khalil; Mitchell Guttman; Maite Huarte; Manuel Garber; Arjun Raj; Dianali Rivea Morales; Kelly Thomas; Aviva Presser; Bradley E Bernstein; Alexander van Oudenaarden; Aviv Regev; Eric S Lander; John L Rinn
Journal:  Proc Natl Acad Sci U S A       Date:  2009-07-01       Impact factor: 11.205

6.  A G-Rich Motif in the lncRNA Braveheart Interacts with a Zinc-Finger Transcription Factor to Specify the Cardiovascular Lineage.

Authors:  Zhihong Xue; Scott Hennelly; Boryana Doyle; Arune A Gulati; Irina V Novikova; Karissa Y Sanbonmatsu; Laurie A Boyer
Journal:  Mol Cell       Date:  2016-09-08       Impact factor: 17.970

7.  A Peptide Encoded by a Putative lncRNA HOXB-AS3 Suppresses Colon Cancer Growth.

Authors:  Jin-Zhou Huang; Min Chen; Xing-Cheng Gao; Song Zhu; Hongyang Huang; Min Hu; Huifang Zhu; Guang-Rong Yan
Journal:  Mol Cell       Date:  2017-10-05       Impact factor: 17.970

8.  BLUEPRINT to decode the epigenetic signature written in blood.

Authors:  David Adams; Lucia Altucci; Stylianos E Antonarakis; Juan Ballesteros; Stephan Beck; Adrian Bird; Christoph Bock; Bernhard Boehm; Elias Campo; Andrea Caricasole; Fredrik Dahl; Emmanouil T Dermitzakis; Tariq Enver; Manel Esteller; Xavier Estivill; Anne Ferguson-Smith; Jude Fitzgibbon; Paul Flicek; Claudia Giehl; Thomas Graf; Frank Grosveld; Roderic Guigo; Ivo Gut; Kristian Helin; Jonas Jarvius; Ralf Küppers; Hans Lehrach; Thomas Lengauer; Åke Lernmark; David Leslie; Markus Loeffler; Elizabeth Macintyre; Antonello Mai; Joost H A Martens; Saverio Minucci; Willem H Ouwehand; Pier Giuseppe Pelicci; Hèléne Pendeville; Bo Porse; Vardhman Rakyan; Wolf Reik; Martin Schrappe; Dirk Schübeler; Martin Seifert; Reiner Siebert; David Simmons; Nicole Soranzo; Salvatore Spicuglia; Michael Stratton; Hendrik G Stunnenberg; Amos Tanay; David Torrents; Alfonso Valencia; Edo Vellenga; Martin Vingron; Jörn Walter; Spike Willcocks
Journal:  Nat Biotechnol       Date:  2012-03-07       Impact factor: 54.908

9.  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

10.  Transposable elements are major contributors to the origin, diversification, and regulation of vertebrate long noncoding RNAs.

Authors:  Aurélie Kapusta; Zev Kronenberg; Vincent J Lynch; Xiaoyu Zhuo; LeeAnn Ramsay; Guillaume Bourque; Mark Yandell; Cédric Feschotte
Journal:  PLoS Genet       Date:  2013-04-25       Impact factor: 5.917

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  174 in total

Review 1.  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

2.  Full-length annotation with multistrategy RNA-seq uncovers transcriptional regulation of lncRNAs in cotton.

Authors:  Xiaomin Zheng; Yanjun Chen; Yifan Zhou; Keke Shi; Xiao Hu; Danyang Li; Hanzhe Ye; Yu Zhou; Kun Wang
Journal:  Plant Physiol       Date:  2021-02-25       Impact factor: 8.340

3.  Annotation of Full-Length Long Noncoding RNAs with Capture Long-Read Sequencing (CLS).

Authors:  Sílvia Carbonell Sala; Barbara Uszczyńska-Ratajczak; Julien Lagarde; Rory Johnson; Roderic Guigó
Journal:  Methods Mol Biol       Date:  2021

Review 4.  Challenges in uncovering non-invasive biomarkers of endometriosis.

Authors:  Quanah J Hudson; Alexandra Perricos; Rene Wenzl; Iveta Yotova
Journal:  Exp Biol Med (Maywood)       Date:  2020-02-04

5.  In Vitro Silencing of lncRNA Expression Using siRNAs.

Authors:  Meike S Thijssen; Jennifer Bintz; Luis Arnes
Journal:  Methods Mol Biol       Date:  2021

6.  Bioinformatics Pipeline to Analyze lncRNA Arrays.

Authors:  Katia Todoerti; Domenica Ronchetti; Martina Manzoni; Elisa Taiana; Antonino Neri; Luca Agnelli
Journal:  Methods Mol Biol       Date:  2021

7.  An integrative proteogenomics approach reveals peptides encoded by annotated lincRNA in the mouse kidney inner medulla.

Authors:  Cameron T Flower; Lihe Chen; Hyun Jun Jung; Viswanathan Raghuram; Mark A Knepper; Chin-Rang Yang
Journal:  Physiol Genomics       Date:  2020-08-31       Impact factor: 3.107

8.  LINC01420 RNA structure and influence on cell physiology.

Authors:  Daria O Konina; Alexandra Yu Filatova; Mikhail Yu Skoblov
Journal:  BMC Genomics       Date:  2019-05-08       Impact factor: 3.969

9.  An expanded landscape of human long noncoding RNA.

Authors:  Shuai Jiang; Si-Jin Cheng; Li-Chen Ren; Qian Wang; Yu-Jian Kang; Yang Ding; Mei Hou; Xiao-Xu Yang; Yuan Lin; Nan Liang; Ge Gao
Journal:  Nucleic Acids Res       Date:  2019-09-05       Impact factor: 16.971

10.  Identification of human long noncoding RNAs associated with nonalcoholic fatty liver disease and metabolic homeostasis.

Authors:  Xiangbo Ruan; Ping Li; Yonghe Ma; Cheng-Fei Jiang; Yi Chen; Yu Shi; Nikhil Gupta; Fayaz Seifuddin; Mehdi Pirooznia; Yasuyuki Ohnishi; Nao Yoneda; Megumi Nishiwaki; Gabrijela Dumbovic; John L Rinn; Yuichiro Higuchi; Kenji Kawai; Hiroshi Suemizu; Haiming Cao
Journal:  J Clin Invest       Date:  2021-01-04       Impact factor: 14.808

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