Literature DB >> 20019688

RNA processing and its regulation: global insights into biological networks.

Donny D Licatalosi1, Robert B Darnell.   

Abstract

In recent years views of eukaryotic gene expression have been transformed by the finding that enormous diversity can be generated at the RNA level. Advances in technologies for characterizing RNA populations are revealing increasingly complete descriptions of RNA regulation and complexity; for example, through alternative splicing, alternative polyadenylation and RNA editing. New biochemical strategies to map protein-RNA interactions in vivo are yielding transcriptome-wide insights into mechanisms of RNA processing. These advances, combined with bioinformatics and genetic validation, are leading to the generation of functional RNA maps that reveal the rules underlying RNA regulation and networks of biologically coherent transcripts. Together these are providing new insights into molecular cell biology and disease.

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Year:  2010        PMID: 20019688      PMCID: PMC3229837          DOI: 10.1038/nrg2673

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


  162 in total

1.  Large-scale transcriptional activity in chromosomes 21 and 22.

Authors:  Philipp Kapranov; Simon E Cawley; Jorg Drenkow; Stefan Bekiranov; Robert L Strausberg; Stephen P A Fodor; Thomas R Gingeras
Journal:  Science       Date:  2002-05-03       Impact factor: 47.728

Review 2.  An extensive network of coupling among gene expression machines.

Authors:  Tom Maniatis; Robin Reed
Journal:  Nature       Date:  2002-04-04       Impact factor: 49.962

Review 3.  RNA editing by adenosine deaminases that act on RNA.

Authors:  Brenda L Bass
Journal:  Annu Rev Biochem       Date:  2001-11-09       Impact factor: 23.643

Review 4.  Alternative pre-mRNA splicing and proteome expansion in metazoans.

Authors:  Tom Maniatis; Bosiljka Tasic
Journal:  Nature       Date:  2002-07-11       Impact factor: 49.962

5.  Intronic sequences flanking alternatively spliced exons are conserved between human and mouse.

Authors:  Rotem Sorek; Gil Ast
Journal:  Genome Res       Date:  2003-07       Impact factor: 9.043

6.  Genome-wide detection of tissue-specific alternative splicing in the human transcriptome.

Authors:  Qiang Xu; Barmak Modrek; Christopher Lee
Journal:  Nucleic Acids Res       Date:  2002-09-01       Impact factor: 16.971

7.  Mutations in the gene encoding immunoglobulin mu-binding protein 2 cause spinal muscular atrophy with respiratory distress type 1.

Authors:  K Grohmann; M Schuelke; A Diers; K Hoffmann; B Lucke; C Adams; E Bertini; H Leonhardt-Horti; F Muntoni; R Ouvrier; A Pfeufer; R Rossi; L Van Maldergem; J M Wilmshurst; T F Wienker; M Sendtner; S Rudnik-Schöneborn; K Zerres; C Hübner
Journal:  Nat Genet       Date:  2001-09       Impact factor: 38.330

8.  Glycyl tRNA synthetase mutations in Charcot-Marie-Tooth disease type 2D and distal spinal muscular atrophy type V.

Authors:  Anthony Antonellis; Rachel E Ellsworth; Nyamkhishig Sambuughin; Imke Puls; Annette Abel; Shih-Queen Lee-Lin; Albena Jordanova; Ivo Kremensky; Kyproula Christodoulou; Lefkos T Middleton; Kumaraswamy Sivakumar; Victor Ionasescu; Benoit Funalot; Jeffery M Vance; Lev G Goldfarb; Kenneth H Fischbeck; Eric D Green
Journal:  Am J Hum Genet       Date:  2003-04-10       Impact factor: 11.025

9.  Evidence for the widespread coupling of alternative splicing and nonsense-mediated mRNA decay in humans.

Authors:  Benjamin P Lewis; Richard E Green; Steven E Brenner
Journal:  Proc Natl Acad Sci U S A       Date:  2002-12-26       Impact factor: 11.205

10.  Nova regulates GABA(A) receptor gamma2 alternative splicing via a distal downstream UCAU-rich intronic splicing enhancer.

Authors:  B Kate Dredge; Robert B Darnell
Journal:  Mol Cell Biol       Date:  2003-07       Impact factor: 4.272

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  341 in total

1.  Dis3- and exosome subunit-responsive 3' mRNA instability elements.

Authors:  Daniel L Kiss; Dezhi Hou; Robert H Gross; Erik D Andrulis
Journal:  Biochem Biophys Res Commun       Date:  2012-06-02       Impact factor: 3.575

2.  Calcium-mediated histone modifications regulate alternative splicing in cardiomyocytes.

Authors:  Alok Sharma; Hieu Nguyen; Cuiyu Geng; Melissa N Hinman; Guangbin Luo; Hua Lou
Journal:  Proc Natl Acad Sci U S A       Date:  2014-11-03       Impact factor: 11.205

Review 3.  Next-generation genomics: an integrative approach.

Authors:  R David Hawkins; Gary C Hon; Bing Ren
Journal:  Nat Rev Genet       Date:  2010-07       Impact factor: 53.242

Review 4.  Alternative mRNA polyadenylation in eukaryotes: an effective regulator of gene expression.

Authors:  Carol S Lutz; Alexandra Moreira
Journal:  Wiley Interdiscip Rev RNA       Date:  2011 Jan-Feb       Impact factor: 9.957

Review 5.  Cell-context dependent TCF/LEF expression and function: alternative tales of repression, de-repression and activation potentials.

Authors:  Catherine D Mao; Stephen W Byers
Journal:  Crit Rev Eukaryot Gene Expr       Date:  2011       Impact factor: 1.807

Review 6.  Localization and dynamics of nuclear speckles in plants.

Authors:  Anireddy S N Reddy; Irene S Day; Janett Göhring; Andrea Barta
Journal:  Plant Physiol       Date:  2011-11-01       Impact factor: 8.340

Review 7.  More than Just a Phase: Prions at the Crossroads of Epigenetic Inheritance and Evolutionary Change.

Authors:  Anupam K Chakravarty; Daniel F Jarosz
Journal:  J Mol Biol       Date:  2018-07-19       Impact factor: 5.469

8.  In-cell RNA structure probing with SHAPE-MaP.

Authors:  Matthew J Smola; Kevin M Weeks
Journal:  Nat Protoc       Date:  2018-05-03       Impact factor: 13.491

9.  Mtr4-like protein coordinates nuclear RNA processing for heterochromatin assembly and for telomere maintenance.

Authors:  Nathan N Lee; Venkata R Chalamcharla; Francisca Reyes-Turcu; Sameet Mehta; Martin Zofall; Vanivilasini Balachandran; Jothy Dhakshnamoorthy; Nitika Taneja; Soichiro Yamanaka; Ming Zhou; Shiv I S Grewal
Journal:  Cell       Date:  2013-11-07       Impact factor: 41.582

10.  Allogeneic T cell responses are regulated by a specific miRNA-mRNA network.

Authors:  Yaping Sun; Isao Tawara; Meng Zhao; Zhaohui S Qin; Tomomi Toubai; Nathan Mathewson; Hiroya Tamaki; Evelyn Nieves; Arul M Chinnaiyan; Pavan Reddy
Journal:  J Clin Invest       Date:  2013-11       Impact factor: 14.808

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