Insights into the regulation of protein abundance from proteomic and transcriptomic analyses
TLDR
Current understanding of the major factors regulating protein expression is summarized to demonstrate a substantial role for regulatory processes occurring after mRNA is made in controlling steady-state protein abundances.Abstract:
Recent advances in next-generation DNA sequencing and proteomics provide an unprecedented ability to survey mRNA and protein abundances. Such proteome-wide surveys are illuminating the extent to which different aspects of gene expression help to regulate cellular protein abundances. Current data demonstrate a substantial role for regulatory processes occurring after mRNA is made - that is, post-transcriptional, translational and protein degradation regulation - in controlling steady-state protein abundances. Intriguing observations are also emerging in relation to cells following perturbation, single-cell studies and the apparent evolutionary conservation of protein and mRNA abundances. Here, we summarize current understanding of the major factors regulating protein expression.read more
Citations
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Journal ArticleDOI
On the Dependency of Cellular Protein Levels on mRNA Abundance.
TL;DR: It is concluded that transcript levels by themselves are not sufficient to predict protein levels in many scenarios and to thus explain genotype-phenotype relationships and that high-quality data quantifying different levels of gene expression are indispensable for the complete understanding of biological processes.
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Ana Conesa,Pedro Madrigal,Pedro Madrigal,Sonia Tarazona,David Gomez-Cabrero,Alejandra Cervera,Andrew McPherson,Michał Wojciech Szcześniak,Daniel J. Gaffney,Laura L. Elo,Xuegong Zhang,Ali Mortazavi +11 more
TL;DR: All of the major steps in RNA-seq data analysis are reviewed, including experimental design, quality control, read alignment, quantification of gene and transcript levels, visualization, differential gene expression, alternative splicing, functional analysis, gene fusion detection and eQTL mapping.
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Genome-wide association study identifies 74 loci associated with educational attainment
Aysu Okbay,Jonathan P. Beauchamp,Mark Alan Fontana,James J. Lee,Tune H. Pers,Cornelius A. Rietveld,Patrick Turley,Guo-Bo Chen,Valur Emilsson,S. Fleur W. Meddens,Sven Oskarsson,Joseph K. Pickrell,Kevin Thom,Pascal Timshel,Ronald de Vlaming,Abdel Abdellaoui,Tarunveer S. Ahluwalia,Jonas Bacelis,Clemens Baumbach,Gyda Bjornsdottir,Johannes H. Brandsma,Maria Pina Concas,Jaime Derringer,Nicholas A. Furlotte,Tessel E. Galesloot,Giorgia Girotto,Richa Gupta,Leanne M. Hall,Sarah E. Harris,Edith Hofer,Momoko Horikoshi,Jennifer E. Huffman,Kadri Kaasik,Ioanna P. Kalafati,Robert Karlsson,Augustine Kong,Jari Lahti,Sven J. van der Lee,Christiaan de Leeuw,Penelope A. Lind,Karl-Oskar Lindgren,Tian Liu,Massimo Mangino,Jonathan Marten,Evelin Mihailov,Michael B. Miller,Peter J. van der Most,Christopher Oldmeadow,Antony Payton,Natalia Pervjakova,Wouter J. Peyrot,Yong Qian,Olli T. Raitakari,Rico Rueedi,Erika Salvi,Brge Schmidt,Katharina E. Schraut,Jianxin Shi,Albert V. Smith,Raymond A. Poot,Beate St Pourcain,Alexander Teumer,Gudmar Thorleifsson,Niek Verweij,Dragana Vuckovic,Juergen Wellmann,Harm-Jan Westra,Jingyun Yang,Wei Zhao,Zhihong Zhu,Behrooz Z. Alizadeh,Najaf Amin,Andrew Bakshi,Sebastian E. Baumeister,Ginevra Biino,Klaus Bønnelykke,Patricia A. Boyle,Harry Campbell,Francesco P. Cappuccio,Gail Davies,Jan-Emmanuel De Neve,Panos Deloukas,Ilja Demuth,Jun Ding,Peter Eibich,Lewin Eisele,Niina Eklund,David M. Evans,Jessica D. Faul,Mary F. Feitosa,Andreas J. Forstner,Ilaria Gandin,Bjarni Gunnarsson,Bjarni V. Halldorsson,Tamara B. Harris,Andrew C. Heath,Lynne J. Hocking,Elizabeth G. Holliday,Georg Homuth,Michael A. Horan,Jouke-Jan Hottenga,Philip L. De Jager,Peter K. Joshi,Astanand Jugessur,Marika Kaakinen,Mika Kähönen,Stavroula Kanoni,Liisa Keltigangas-Jarvinen,Lambertus A. Kiemeney,Ivana Kolcic,Seppo Koskinen,Aldi T. Kraja,Martin Kroh,Zoltán Kutalik,Antti Latvala,Lenore J. Launer,Maël Lebreton,Douglas F. Levinson,Paul Lichtenstein,Peter Lichtner,David C. Liewald,Anu Loukola,Pamela A. F. Madden,Reedik Mägi,Tomi Mäki-Opas,Riccardo E. Marioni,Pedro Marques-Vidal,Gerardus A. Meddens,George McMahon,Christa Meisinger,Thomas Meitinger,Y. Milaneschi,Lili Milani,Grant W. Montgomery,Ronny Myhre,Christopher P. Nelson,Dale R. Nyholt,William E R Ollier,Aarno Palotie,Lavinia Paternoster,Nancy L. Pedersen,K. Petrovic,David J. Porteous,Katri Räikkönen,Susan M. Ring,Antonietta Robino,Olga Rostapshova,Igor Rudan,Aldo Rustichini,Veikko Salomaa,Alan R. Sanders,Antti-Pekka Sarin,Helena Schmidt,Rodney J. Scott,Blair H. Smith,Jennifer A. Smith,Jan A. Staessen,Elisabeth Steinhagen-Thiessen,Konstantin Strauch,Antonio Terracciano,Martin D. Tobin,Sheila Ulivi,Simona Vaccargiu,Lydia Quaye,Frank J. A. van Rooij,Cristina Venturini,Anna A. E. Vinkhuyzen,Uwe Völker,Henry Völzke,Judith M. Vonk,Diego Vozzi,Johannes Waage,Erin B. Ware,Gonneke Willemsen,John Attia,David A. Bennett,Klaus Berger,Lars Bertram,Hans Bisgaard,Dorret I. Boomsma,Ingrid B. Borecki,Ute Bültmann,Christopher F. Chabris,Francesco Cucca,Daniele Cusi,Ian J. Deary,George Dedoussis,Cornelia M. van Duijn,Johan G. Eriksson,Barbara Franke,Lude Franke,Paolo Gasparini,Pablo V. Gejman,Christian Gieger,Hans-Jörgen Grabe,Jacob Gratten,Patrick J. F. Groenen,Vilmundur Gudnason,Pim van der Harst,Caroline Hayward,David A. Hinds,Wolfgang Hoffmann,Elina Hyppnen,William G. Iacono,Bo Jacobsson,Marjo-Riitta Järvelin,Karl-Heinz Jöckel,Jaakko Kaprio,Sharon L.R. Kardia,Terho Lehtimäki,Steven F. Lehrer,Patrik K. E. Magnusson,Nicholas G. Martin,Matt McGue,Andres Metspalu,Neil Pendleton,Brenda W.J.H. Penninx,Markus Perola,Nicola Pirastu,Mario Pirastu,Ozren Polasek,Danielle Posthuma,Christine Power,Michael A. Province,Nilesh J. Samani,David Schlessinger,Reinhold Schmidt,Thorkild I. A. Sørensen,Tim D. Spector,Kari Stefansson,Unnur Thorsteinsdottir,Roy Thurik,Nicholas J. Timpson,Henning Tiemeier,Joyce Y. Tung,André G. Uitterlinden,Veronique Vitart,Peter Vollenweider,David R. Weir,James F. Wilson,Alan F. Wright,Dalton Conley,Robert F. Krueger,George Davey Smith,Albert Hofman,David Laibson,Sarah E. Medland,Michelle N. Meyer,Jian Yang,Magnus Johannesson,Peter M. Visscher,Tõnu Esko,Philipp Koellinger,David Cesarini,Daniel J. Benjamin +254 more
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