Pre-mRNA Splicing: Awash in a Sea of Proteins
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TLDR
The number of new proteins emerging with no prior connection to splicing was surprising and it would be premature to label these proteins as bona fide splicing factors, yet many were identified multiple times in complexes purified under diverse conditions or from different organisms.About:
This article is published in Molecular Cell.The article was published on 2003-07-01 and is currently open access. It has received 1020 citations till now. The article focuses on the topics: Spliceosomal complex & Spliceosome.read more
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Journal ArticleDOI
The Spliceosome: Design Principles of a Dynamic RNP Machine
TL;DR: The spliceosome exhibits exceptional compositional and structural dynamics that are exploited during substrate-dependent complex assembly, catalytic activation, and active site remodeling in the pre-mRNAs.
Journal ArticleDOI
The nuclear-retained noncoding RNA MALAT1 regulates alternative splicing by modulating SR splicing factor phosphorylation.
Vidisha Tripathi,Jonathan D. Ellis,Zhen Shen,David Y. Song,Qun Pan,Andrew T. Watt,Susan M. Freier,C. Frank Bennett,Alok Sharma,Paula A. Bubulya,Benjamin J. Blencowe,Supriya G. Prasanth,Kannanganattu V. Prasanth +12 more
TL;DR: Evidence is provided for a role for the long nuclear-retained regulatory RNA, MALAT1 in AS regulation and for the role for an nrRNA in the regulation of gene expression, which suggests that MALat1 regulates AS by modulating the levels of active SR proteins.
Journal ArticleDOI
Spliceosome structure and function.
Cindy L. Will,Reinhard Lührmann +1 more
TL;DR: The extensive interplay of RNA and proteins in aligning the pre-mRNA's reactive groups, and the presence of both RNA and protein at the core of the splicing machinery, suggest that the spliceosome is an RNP enzyme, but elucidation of the precise nature of its active site awaits the generation of a high-resolution structure of its RNP core.
Journal ArticleDOI
Function of alternative splicing.
Stefan Stamm,Shani Ben-Ari,Ilona Rafalska,Yesheng Tang,Zhaiyi Zhang,Debra Toiber,Thangavel Alphonse Thanaraj,Hermona Soreq +7 more
TL;DR: Evidence is now accumulating that alternative splicing coordinates physiologically meaningful changes in protein isoform expression and is a key mechanism to generate the complex proteome of multicellular organisms.
Journal ArticleDOI
Understanding alternative splicing: towards a cellular code.
TL;DR: Traditional gene-by-gene investigations of alternative splicing mechanisms are now being complemented by global approaches that promise to reveal details of the nature and operation of cellular codes that are constituted by combinations of regulatory elements in pre-mRNA substrates and by cellular complements of splicing regulators, which together determine regulated splicing pathways.
References
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Journal ArticleDOI
Functional organization of the yeast proteome by systematic analysis of protein complexes
Anne-Claude Gavin,Markus Bösche,Roland Krause,Paola Grandi,Martina Marzioch,Andreas Bauer,Jörg Schultz,Jens Rick,Anne-Marie Michon,Cristina-Maria Cruciat,Marita Remor,Christian Höfert,Malgorzata Schelder,Miro Brajenovic,Heinz Ruffner,Alejandro Merino,Karin Klein,Manuela Hudak,David Dickson,Tatjana Rudi,Volker Gnau,Angela Bauch,Sonja Bastuck,Bettina Huhse,Christina Leutwein,Marie-Anne Heurtier,Richard R. Copley,Angela Edelmann,Erich Querfurth,Vladimir Rybin,Gerard Drewes,Manfred Raida,Tewis Bouwmeester,Peer Bork,Bertrand Séraphin,Bernhard Kuster,Gitte Neubauer,Giulio Superti-Furga +37 more
TL;DR: The analysis provides an outline of the eukaryotic proteome as a network of protein complexes at a level of organization beyond binary interactions, which contains fundamental biological information and offers the context for a more reasoned and informed approach to drug discovery.
Journal ArticleDOI
Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry
Yuen Ho,Albrecht Gruhler,Adrian Heilbut,Gary D. Bader,Gary D. Bader,Lynda Moore,Sally-Lin Adams,Anna Millar,Paul J. Taylor,Keiryn L. Bennett,Kelly Boutilier,Lingyun Yang,Cheryl Wolting,Ian Donaldson,Søren Schandorff,Juanita Shewnarane,Mai Vo,Joanne Taggart,Marilyn Goudreault,Brenda Muskat,Cris Alfarano,Danielle Dewar,Zhen Lin,Katerina Michalickova,Katerina Michalickova,Andrew Willems,Andrew Willems,Holly Sassi,Peter A Nielsen,Karina Juhl Rasmussen,Jens R. Andersen,Lene E. Johansen,Lykke Haastrup Hansen,Hans Jespersen,Alexandre V. Podtelejnikov,Eva Nielsen,Janne S. Crawford,Vibeke Poulsen,Birgitte D Sørensen,Jesper Matthiesen,Ronald C. Hendrickson,Frank Gleeson,Tony Pawson,Tony Pawson,Michael Moran,Daniel Durocher,Daniel Durocher,Matthias Mann,Christopher W. V. Hogue,Christopher W. V. Hogue,Daniel Figeys,Mike Tyers,Mike Tyers +52 more
TL;DR: Comparison of the HMS-PCI data set with interactions reported in the literature revealed an average threefold higher success rate in detection of known complexes compared with large-scale two-hybrid studies.
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The tandem affinity purification (TAP) method: a general procedure of protein complex purification.
Oscar Puig,Friederike Caspary,Guillaume Rigaut,Berthold Rutz,Emmanuelle Bouveret,Elisabeth Bragado-Nilsson,Matthias Wilm,Bertrand Séraphin +7 more
TL;DR: The TAP method is developed as a tool that allows rapid purification under native conditions of complexes, even when expressed at their natural level, and is a very useful procedure for protein purification and proteome exploration.
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Absolute quantification of proteins and phosphoproteins from cell lysates by tandem MS
TL;DR: The AQUA strategy was used to quantify low abundance yeast proteins involved in gene silencing, quantitatively determine the cell cycle-dependent phosphorylation of Ser-1126 of human separase protein, and identify kinases capable of phosphorylating Ser-1501 of separase in an in vitro kinase assay.