Genome-wide analysis of mammalian promoter architecture and evolution.

Nature Genetics
Piero CarninciYoshihide Hayashizaki

Abstract

Mammalian promoters can be separated into two classes, conserved TATA box-enriched promoters, which initiate at a well-defined site, and more plastic, broad and evolvable CpG-rich promoters. We have sequenced tags corresponding to several hundred thousand transcription start sites (TSSs) in the mouse and human genomes, allowing precise analysis of the sequence architecture and evolution of distinct promoter classes. Different tissues and families of genes differentially use distinct types of promoters. Our tagging methods allow quantitative analysis of promoter usage in different tissues and show that differentially regulated alternative TSSs are a common feature in protein-coding genes and commonly generate alternative N termini. Among the TSSs, we identified new start sites associated with the majority of exons and with 3' UTRs. These data permit genome-scale identification of tissue-specific promoters and analysis of the cis-acting elements associated with them.

References

Oct 25, 1990·Nucleic Acids Research·T D Schneider, R M Stephens
Dec 9, 1998·Proceedings of the National Academy of Sciences of the United States of America·M B EisenD Botstein
Jun 22, 2002·Proceedings of the National Academy of Sciences of the United States of America·Elizabeth M Prescott, Nick J Proudfoot
Oct 17, 2002·Genes & Development·Jennifer E F Butler, James T Kadonaga
Dec 6, 2002·Nature·Y OkazakiUNKNOWN RIKEN Genome Exploration Research Group Phase I & II Team
Jan 8, 2003·Experimental & Molecular Medicine·James T Kadonaga
Jan 10, 2003·Nucleic Acids Research·D KarolchikUNKNOWN University of California Santa Cruz
Mar 26, 2003·Annual Review of Biochemistry·Stephen T Smale, James T Kadonaga
May 23, 2003·Journal of Biology·Boris LenhardWyeth W Wasserman
Jun 24, 2003·Genome Research·Piero CarninciYoshihide Hayashizaki
Oct 31, 2003·Trends in Genetics : TIG·Josette-Renée LandryBrian T Wilhelm
Nov 5, 2003·Proceedings of the National Academy of Sciences of the United States of America·Peter D Keightley, Daniel J Gaffney
Dec 10, 2003·Proceedings of the National Academy of Sciences of the United States of America·Toshiyuki ShirakiYoshihide Hayashizaki
Jan 7, 2004·Genome Research·Nathan D TrinkleinRichard M Myers
May 18, 2004·Trends in Immunology·Giuseppina Bonizzi, Michael Karin
Aug 3, 2004·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Adam Siepel, David Haussler
Aug 25, 2004·Biochemical and Biophysical Research Communications·Takuya ImamuraKunio Shiota
Oct 23, 2004·Science·UNKNOWN ENCODE Project Consortium
Nov 6, 2004·Nature Biotechnology·Vladimir B BajicSumio Sugano
Jan 14, 2005·Nucleic Acids Research·Nils BlüthgenHanspeter Herzel
Mar 26, 2005·Science·Jill ChengThomas R Gingeras
Apr 19, 2005·Genome Biology·Jonathan SchugChristian J Stoeckert
May 20, 2005·Current Opinion in Cell Biology·David L Bentley
Jul 12, 2005·Genomics·Yongchun WuJiong Zhang
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
Feb 21, 2006·Nature Methods·Rimantas KodziusPiero Carninci

❮ Previous
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Citations

Apr 28, 2012·Cellular and Molecular Life Sciences : CMLS·Lucy W BarrettSteve D Wilton
Oct 8, 2008·Mammalian Genome : Official Journal of the International Mammalian Genome Society·Paulo P Amaral, John S Mattick
Sep 23, 2008·Mammalian Genome : Official Journal of the International Mammalian Genome Society·David A Hume
May 16, 2009·Mammalian Genome : Official Journal of the International Mammalian Genome Society·Yu-Lan S LoChristine A Wells
Jul 1, 2011·Mammalian Genome : Official Journal of the International Mammalian Genome Society·Hong-Seok HaHeui-Soo Kim
Sep 25, 2009·Molecular and Cellular Biochemistry·Anastasiia AleksandrovaJoseph D Fontes
Dec 20, 2011·Virus Genes·Zhiqiang BaiShou-Jiang Gao
Aug 4, 2010·Cell Research·Susan C WuYi Zhang
Aug 20, 2009·Molecular Therapy : the Journal of the American Society of Gene Therapy·Jeroen GeurtsFons A J van de Loo
Jan 27, 2009·Nature·UNKNOWN Affymetrix ENCODE Transcriptome Project, UNKNOWN Cold Spring Harbor Laboratory ENCODE Transcriptome Project
Apr 26, 2013·Nature·Vicent PelechanoLars M Steinmetz
Nov 17, 2009·Nature Biotechnology·Rupali P PatwardhanJay Shendure
Jan 23, 2009·Nature Cell Biology·Miki EbisuyaEisuke Nishida
Apr 21, 2009·Nature Genetics·Ryan J TaftJohn S Mattick
Apr 21, 2009·Nature Genetics·Geoffrey J FaulknerPiero Carninci
Apr 21, 2009·Nature Genetics·UNKNOWN FANTOM ConsortiumYoshihide Hayashizaki
Jul 1, 2010·Nature Methods·John A Stamatoyannopoulos
Jul 12, 2012·Neuropsychopharmacology : Official Publication of the American College of Neuropsychopharmacology·Lisa D MooreGuoping Fan
Dec 31, 2010·Nature Reviews. Genetics·Fatih Ozsolak, Patrice M Milos
Jun 19, 2012·Nature Reviews. Genetics·Ross C Hardison, James Taylor
Jul 19, 2011·Nature Structural & Molecular Biology·Frederic KochJean-Christophe Andrau
Aug 9, 2011·Nature Structural & Molecular Biology·Eivind ValenTorben Heick Jensen
Jan 16, 2008·Proceedings of the National Academy of Sciences of the United States of America·Tomohito YagiAlbert C Shaw
Sep 26, 2008·Proceedings of the National Academy of Sciences of the United States of America·Yuichi KumakiHiroki R Ueda
Dec 29, 2011·Proceedings of the National Academy of Sciences of the United States of America·Matthieu GiraudChristophe Benoist
Jul 28, 2009·The Journal of Biological Chemistry·Pierre TissièresJérôme Pugin
Oct 20, 2011·The Journal of Biological Chemistry·Thomas K FelderWolfgang Patsch
Jan 21, 2010·Journal of Biomolecular Structure & Dynamics·Padmavathi Putta, Chanchal K Mitra
Sep 9, 2011·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Emmanuel MonginMathieu Blanchette
Mar 28, 2009·Briefings in Functional Genomics & Proteomics·Bart Deplancke
Jun 6, 2009·Briefings in Functional Genomics & Proteomics·Leelavati Narlikar, Ivan Ovcharenko
Jul 17, 2009·Briefings in Functional Genomics & Proteomics·David FredmanBoris Lenhard
Oct 17, 2009·Briefings in Functional Genomics & Proteomics·Harm van Bakel, Timothy R Hughes
Sep 23, 2009·Briefings in Functional Genomics & Proteomics·Marcel E DingerJohn S Mattick

❮ Previous
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