A global view of genomic information--moving beyond the gene and the master regulator

Trends in Genetics : TIG
John S MattickG Faulkner

Abstract

The current view of gene regulation in complex organisms holds that gene expression is largely controlled by the combinatoric actions of transcription factors and other regulatory proteins, some of which powerfully influence cell type. Recent large-scale studies have confirmed that cellular differentiation involves many different regulatory factors. However, other studies indicate that the genome is pervasively transcribed to produce a variety of short and long non-protein-coding RNAs, including those derived from retrotransposed sequences, which also play important roles in the epigenetic regulation of gene expression. The evidence suggests that ontogenesis requires interplay between state-specific regulatory proteins, multitasked effector complexes and target-specific RNAs that recruit these complexes to their sites of action. Moreover, the semi-continuous nature of the transcriptome prompts the reassessment of 'genes' as discrete entities and indicates that the mammalian genome might be more accurately viewed as islands of protein-coding information in a sea of cis- and trans-acting regulatory sequences.

References

Jun 1, 1971·The Quarterly Review of Biology·R J Britten, E H Davidson
Mar 10, 2001·Genes & Development·F GiudicelliP Gilardi-Hebenstreit
May 4, 2002·Science·Philipp KapranovThomas R Gingeras
May 15, 2002·Evolution & Development·Matthew W Hahn, Gregory A Wray
Nov 26, 2002·The Journal of Biological Chemistry·Stefan MaasKazuko Nishikura
Dec 6, 2002·Nature·Y OkazakiUNKNOWN RIKEN Genome Exploration Research Group Phase I & II Team
Jul 11, 2003·Nature·Michael Levine, Robert Tjian
Jan 1, 1956·Cold Spring Harbor Symposia on Quantitative Biology·B MCCLINTOCK
Sep 25, 2003·BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology·John S Mattick
Nov 19, 2004·American Journal of Human Genetics·Dirk A Kleinjan, Veronica van Heyningen
Mar 26, 2005·Science·Jill ChengThomas R Gingeras
Sep 1, 2005·Annals of Anatomy = Anatomischer Anzeiger : Official Organ of the Anatomische Gesellschaft·Beate Brand-Saberi
Sep 6, 2005·Science·P CarninciUNKNOWN RIKEN Genome Exploration Research Group and Genome Science Group (Genome Network Project Core Group)
Sep 6, 2005·Science·S KatayamaUNKNOWN FANTOM Consortium
Jan 31, 2006·Proceedings of the National Academy of Sciences of the United States of America·Roy Britten
Apr 29, 2006·Nature Genetics·Piero CarninciYoshihide Hayashizaki
May 3, 2006·Human Molecular Genetics·John S Mattick, Igor V Makunin
May 9, 2006·PLoS Computational Biology·Orjan SvenssonJens Lagergren
May 10, 2006·PLoS Genetics·Martin C FrithLukasz Huminiecki
May 25, 2006·International Journal of Hematology·Naveenan Navaratnam, Rizwan Sarwar
Jan 11, 2007·Genes & Development·Kannanganattu V Prasanth, David L Spector
Feb 14, 2007·BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology·Ryan J TaftJohn S Mattick
Feb 24, 2007·Nature Reviews. Molecular Cell Biology·A Gregory MateraMichael P Terns
Feb 27, 2007·Cell·Vicki L Chandler
Feb 27, 2007·Cell·Bradley E BernsteinEric S Lander
Feb 27, 2007·Cell·Tony Kouzarides
Mar 27, 2007·Trends in Genetics : TIG·Deyou Zheng, Mark B Gerstein
Apr 24, 2007·The Journal of Experimental Biology·John S Mattick
Apr 28, 2007·Proceedings of the National Academy of Sciences of the United States of America·Craig B LoweDavid Haussler
May 9, 2007·Nature Reviews. Genetics·Philipp KapranovThomas R Gingeras
May 19, 2007·Science·Philipp KapranovThomas R Gingeras
Jun 15, 2007·Molecular Cell·Lasse Peters, Gunter Meister
Jun 15, 2007·Trends in Genetics : TIG·Chang Seob Kwon, Doris Wagner
Jun 15, 2007·Genome Research·Mark B GersteinMichael Snyder
Jul 3, 2007·Cell·Brendan D Manning, Lewis C Cantley
Jul 12, 2007·Journal of Cell Science·Masamitsu SoneShinichi Nakagawa
Aug 11, 2007·Genome Research·Michael Pheasant, John S Mattick
Nov 6, 2007·Trends in Genetics : TIG·Giorgio DieciAldo Pagano
Nov 13, 2007·Trends in Neurosciences·Georges St Laurent, Claes Wahlestedt

❮ Previous
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Citations

Apr 30, 2014·Nature Reviews. Genetics·Kevin V Morris, John S Mattick
Jul 13, 2013·Nucleic Acids Research·Martin A SmithJohn S Mattick
Dec 18, 2013·Journal of Bone and Mineral Metabolism·Layla PanachMiguel Ángel García-Pérez
May 4, 2010·Neurogenetics·Guido J BreedveldVincenzo Bonifati
Aug 19, 2010·Nucleic Acids Research·Nayef Jarrous, Venkat Gopalan
Sep 3, 2010·Pharmacogenetics and Genomics·Vadim YuferovMary Jeanne Kreek
Sep 14, 2010·American Journal of Physiology. Heart and Circulatory Physiology·F HaddadK M Baldwin
Oct 5, 2010·The Journal of Physical Chemistry. B·Zhen XiaPengyu Ren
May 31, 2011·BMC Bioinformatics·Fernando MeyerMichael Beckstette
Aug 11, 2011·Genetics·Kenneth M Weiss, Anne V Buchanan
Aug 11, 2011·PLoS Computational Biology·Jan Gorodkin, Ivo L Hofacker
Nov 22, 2011·Clinical Chemistry·Renate B SchnabelEmelia J Benjamin
Feb 9, 2012·International Journal of Molecular Sciences·Nicola A Maiorano, Robert Hindges
Sep 29, 2012·Science·Sue Mei Tan-WongNick J Proudfoot
May 30, 2013·PLoS Genetics·Jafar KianiMinoo Rassoulzadegan
Jun 1, 2013·BMC Biology·Aleksandra E KornienkoFlorian M Pauler
Jun 15, 2011·Current Neurology and Neuroscience Reports·Irfan A Qureshi, Mark F Mehler
Nov 15, 2011·Mammalian Genome : Official Journal of the International Mammalian Genome Society·Thomas DerrienChristophe Hitte
Apr 27, 2010·Pharmacogenomics·Magnus Ingelman-Sundberg, Alvin Gomez
Mar 8, 2012·Molekuliarnaia biologiia·V V Grechko
Jan 29, 2016·APMIS : Acta Pathologica, Microbiologica, Et Immunologica Scandinavica·Luis P Villarreal
Jan 30, 2016·Nucleic Acids Research·Elisa N SalasIstvan Ladunga
Aug 13, 2011·Trends in Genetics : TIG·Ulf Andersson Orom, Ramin Shiekhattar
Jul 16, 2011·Trends in Biotechnology·Paul M LizardiNarendra Wajapeyee
May 31, 2011·Seminars in Cell & Developmental Biology·John S Mattick
Aug 25, 2015·Biochimica Et Biophysica Acta·Brian S Gloss, Marcel E Dinger
Jan 25, 2011·Seminars in Cell & Developmental Biology·Michael B Clark, John S Mattick
Aug 7, 2010·Biochemical Pharmacology·Katarzyna Szarc vel SzicWim Vanden Berghe
Mar 3, 2010·New Biotechnology·Ebbe Sloth Andersen
Jan 1, 2015·BMC Bioinformatics·Christina OttoSebastian Will
May 12, 2011·FEBS Letters·John S Mattick
Dec 17, 2015·Nature Reviews. Genetics·Jeffrey J Quinn, Howard Y Chang
Sep 4, 2015·Seminars in Cell & Developmental Biology·Minoo Rassoulzadegan, François Cuzin
Oct 5, 2014·Journal of Molecular Evolution·Folkert K de Boer, Paulien Hogeweg
Oct 26, 2013·Scientific Reports·James A BoothJessica M Lindvall
Jan 22, 2011·Annals of the New York Academy of Sciences·Moncef Zouali
Jun 24, 2011·IUBMB Life·Julius LukešMichael W Gray
Dec 2, 2011·Wiley Interdisciplinary Reviews. Nanomedicine and Nanobiotechnology·Nicole MichelottiNils G Walter
Dec 24, 2010·Journal of Neurochemistry·Greg T SutherlandJillian J Kril
Sep 17, 2013·Alcoholism, Clinical and Experimental Research·Greg T SutherlandJillian J Kril

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