Literature DB >> 22327834

Combined RNAi and localization for functionally dissecting long noncoding RNAs.

Debojyoti Chakraborty1, Dennis Kappei, Mirko Theis, Anja Nitzsche, Li Ding, Maciej Paszkowski-Rogacz, Vineeth Surendranath, Nicolas Berger, Herbert Schulz, Kathrin Saar, Norbert Hubner, Frank Buchholz.   

Abstract

Whereas methods to comprehensively study cellular roles of protein-coding genes are available, techniques to systematically investigate long noncoding RNAs (lncRNAs), which have been implicated in diverse biological pathways, are limited. Here we report combined knockdown and localization analysis of noncoding RNAs (c-KLAN) that merges functional characterization and localization approaches to study lncRNAs. Using this technique we identified transcripts that regulate mouse embryonic stem cell identity.

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Year:  2012        PMID： 22327834     DOI： 10.1038/nmeth.1894

Source DB:  PubMed          Journal:  Nat Methods        ISSN： 1548-7091            Impact factor:   28.547


  23 in total

1.  DEQOR: a web-based tool for the design and quality control of siRNAs.

Authors:  Andreas Henschel; Frank Buchholz; Bianca Habermann
Journal:  Nucleic Acids Res       Date:  2004-07-01       Impact factor: 16.971

2.  Production of endoribonuclease-prepared short interfering RNAs for gene silencing in mammalian cells.

Authors:  Ralf Kittler; Anne-Kristin Heninger; Kristin Franke; Bianca Habermann; Frank Buchholz
Journal:  Nat Methods       Date:  2005-10       Impact factor: 28.547

3.  A genome-scale RNAi screen for Oct4 modulators defines a role of the Paf1 complex for embryonic stem cell identity.

Authors:  Li Ding; Maciej Paszkowski-Rogacz; Anja Nitzsche; Mikolaj Michal Slabicki; Anne-Kristin Heninger; Ingrid de Vries; Ralf Kittler; Magno Junqueira; Andrej Shevchenko; Herbert Schulz; Norbert Hubner; Michael Xavier Doss; Agapios Sachinidis; Juergen Hescheler; Roberto Iacone; Konstantinos Anastassiadis; A Francis Stewart; M Teresa Pisabarro; Antonio Caldarelli; Ina Poser; Mirko Theis; Frank Buchholz
Journal:  Cell Stem Cell       Date:  2009-04-02       Impact factor: 24.633

Review 4.  Molecular mechanisms of long noncoding RNAs.

Authors:  Kevin C Wang; Howard Y Chang
Journal:  Mol Cell       Date:  2011-09-16       Impact factor: 17.970

Review 5.  Validating transcripts with probes and imaging technology.

Authors:  Shalev Itzkovitz; Alexander van Oudenaarden
Journal:  Nat Methods       Date:  2011-03-30       Impact factor: 28.547

6.  A genome-wide RNAi screen reveals determinants of human embryonic stem cell identity.

Authors:  Na-Yu Chia; Yun-Shen Chan; Bo Feng; Xinyi Lu; Yuriy L Orlov; Dimitri Moreau; Pankaj Kumar; Lin Yang; Jianming Jiang; Mei-Sheng Lau; Mikael Huss; Boon-Seng Soh; Petra Kraus; Pin Li; Thomas Lufkin; Bing Lim; Neil D Clarke; Frederic Bard; Huck-Hui Ng
Journal:  Nature       Date:  2010-10-17       Impact factor: 49.962

7.  A genome-scale DNA repair RNAi screen identifies SPG48 as a novel gene associated with hereditary spastic paraplegia.

Authors:  Mikołaj Słabicki; Mirko Theis; Dragomir B Krastev; Sergey Samsonov; Emeline Mundwiller; Magno Junqueira; Maciej Paszkowski-Rogacz; Joan Teyra; Anne-Kristin Heninger; Ina Poser; Fabienne Prieur; Jérémy Truchetto; Christian Confavreux; Cécilia Marelli; Alexandra Durr; Jean Philippe Camdessanche; Alexis Brice; Andrej Shevchenko; M Teresa Pisabarro; Giovanni Stevanin; Frank Buchholz
Journal:  PLoS Biol       Date:  2010-06-29       Impact factor: 8.029

8.  GeneCodis: interpreting gene lists through enrichment analysis and integration of diverse biological information.

Authors:  Ruben Nogales-Cadenas; Pedro Carmona-Saez; Miguel Vazquez; Cesar Vicente; Xiaoyuan Yang; Francisco Tirado; Jose María Carazo; Alberto Pascual-Montano
Journal:  Nucleic Acids Res       Date:  2009-05-22       Impact factor: 16.971

9.  Minimizing off-target effects by using diced siRNAs for RNA interference.

Authors:  Jason W Myers; Jen-Tsan Chi; Delquin Gong; Marci E Schaner; Patrick O Brown; James E Ferrell
Journal:  J RNAi Gene Silencing       Date:  2006-07-17

10.  Comparative profiling identifies C13orf3 as a component of the Ska complex required for mammalian cell division.

Authors:  Mirko Theis; Mikolaj Slabicki; Magno Junqueira; Maciej Paszkowski-Rogacz; Jana Sontheimer; Ralf Kittler; Anne-Kristine Heninger; Timo Glatter; Kristi Kruusmaa; Ina Poser; Anthony A Hyman; M Teresa Pisabarro; Matthias Gstaiger; Rudolf Aebersold; Andrej Shevchenko; Frank Buchholz
Journal:  EMBO J       Date:  2009-04-23       Impact factor: 11.598
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  27 in total

Review 1.  Long non-coding RNAs in corticogenesis: deciphering the non-coding code of the brain.

Authors:  Julieta Aprea; Federico Calegari
Journal:  EMBO J       Date:  2015-10-29       Impact factor: 11.598

Review 2.  Regulation of mammalian cell differentiation by long non-coding RNAs.

Authors:  Wenqian Hu; Juan R Alvarez-Dominguez; Harvey F Lodish
Journal:  EMBO Rep       Date:  2012-10-16       Impact factor: 8.807

Review 3.  Long noncoding RNAs: new players in the molecular mechanism for maintenance and differentiation of pluripotent stem cells.

Authors:  Suman Ghosal; Shaoli Das; Jayprokas Chakrabarti
Journal:  Stem Cells Dev       Date:  2013-05-14       Impact factor: 3.272

Review 4.  Common stemness regulators of embryonic and cancer stem cells.

Authors:  Christiana Hadjimichael; Konstantina Chanoumidou; Natalia Papadopoulou; Panagiota Arampatzi; Joseph Papamatheakis; Androniki Kretsovali
Journal:  World J Stem Cells       Date:  2015-10-26       Impact factor: 5.326

Review 5.  lncRedibly versatile: biochemical and biological functions of long noncoding RNAs.

Authors:  Emily J Shields; Ana F Petracovici; Roberto Bonasio
Journal:  Biochem J       Date:  2019-04-10       Impact factor: 3.857

Review 6.  Long noncoding RNAs during normal and malignant hematopoiesis.

Authors:  Juan R Alvarez-Dominguez; Wenqian Hu; Austin A Gromatzky; Harvey F Lodish
Journal:  Int J Hematol       Date:  2014-03-09       Impact factor: 2.490

Review 7.  Noncoding RNAs in the Regulation of Pluripotency and Reprogramming.

Authors:  Vladimir V Sherstyuk; Sergey P Medvedev; Suren M Zakian
Journal:  Stem Cell Rev Rep       Date:  2018-02       Impact factor: 5.739

8.  Evolutionarily conserved long intergenic non-coding RNAs in the eye.

Authors:  Debarshi Mustafi; Brian M Kevany; Xiaodong Bai; Tadao Maeda; Jonathan E Sears; Ahmad M Khalil; Krzysztof Palczewski
Journal:  Hum Mol Genet       Date:  2013-04-04       Impact factor: 6.150

Review 9.  Getting to the heart of the matter: long non-coding RNAs in cardiac development and disease.

Authors:  Johanna C Scheuermann; Laurie A Boyer
Journal:  EMBO J       Date:  2013-06-11       Impact factor: 11.598

Review 10.  Decoding LncRNAs.

Authors:  Lidia Borkiewicz; Joanna Kalafut; Karolina Dudziak; Alicja Przybyszewska-Podstawka; Ilona Telejko
Journal:  Cancers (Basel)       Date:  2021-05-27       Impact factor: 6.639
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