title: Human Lineage-Specific Transcriptional Regulation through GA-Binding Protein Transcription Factor Alpha (GABPa).
abstract: A substantial fraction of phenotypic differences between closely related species are likely caused by differences in gene regulation. While this has already been postulated over 30 years ago, only few examples of evolutionary changes in gene regulation have been verified. Here, we identified and investigated binding sites of the transcription factor GA-binding protein alpha (GABPa) aiming to discover cis-regulatory adaptations on the human lineage. By performing chromatin immunoprecipitation-sequencing experiments in a human cell line, we found 11,619 putative GABPa binding sites. Through sequence comparisons of the human GABPa binding regions with orthologous sequences from 34 mammals, we identified substitutions that have resulted in 224 putative human-specific GABPa binding sites. To experimentally assess the transcriptional impact of those substitutions, we selected four promoters for promoter-reporter gene assays using human and African green monkey cells. We compared the activities of wild-type promoters to mutated forms, where we have introduced one or more substitutions to mimic the ancestral state devoid of the GABPa consensus binding sequence. Similarly, we introduced the human-specific substitutions into chimpanzee and macaque promoter backgrounds. Our results demonstrate that the identified substitutions are functional, both in human and nonhuman promoters. In addition, we performed GABPa knock-down experiments and found 1,215 genes as strong candidates for primary targets. Further analyses of our data sets link GABPa to cognitive disorders, diabetes, KRAB zinc finger (KRAB-ZNF), and human-specific genes. Thus, we propose that differences in GABPa binding sites played important roles in the evolution of human-specific phenotypes.
authors.affiliation: Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University Leipzig, Leipzig, Germany Paul-Flechsig Institute for Brain Research, University of Leipzig, Leipzig, Germany.
authors.forename: Alvaro
authors.initials: A
authors.lastname: Perdomo-Sabogal
authors.affiliation: Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University Leipzig, Leipzig, Germany Paul-Flechsig Institute for Brain Research, University of Leipzig, Leipzig, Germany nowick@bioinf.uni-leipzig.de Robert.Querfurth@gmx.de.
authors.forename: Katja
authors.initials: K
authors.lastname: Nowick
authors.affiliation: Institute of Genetics of Heart Diseases (IfGH), Department of Cardiovascular Medicine, University Hospital Münster, 48149 Münster, Germany Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Berlin, Germany.
authors.forename: Ilaria
authors.initials: I
authors.lastname: Piccini
authors.affiliation: European Centre for Public Heath Genomics, UNU-MERIT, Unsiversity Maastricht,PO Box 616, 6200 MD Maastricht, The Netherlands Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Berlin, Germany.
authors.forename: Ralf
authors.initials: R
authors.lastname: Sudbrak
authors.affiliation: Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Berlin, Germany.
authors.forename: Hans
authors.initials: H
authors.lastname: Lehrach
authors.affiliation: Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Berlin, Germany.
authors.forename: Marie-Laure
authors.initials: ML
authors.lastname: Yaspo
authors.affiliation: Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Berlin, Germany.
authors.forename: Hans-Jörg
authors.initials: HJ
authors.lastname: Warnatz
authors.affiliation: Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Berlin, Germany nowick@bioinf.uni-leipzig.de Robert.Querfurth@gmx.de.
authors.forename: Robert
authors.initials: R
authors.lastname: Querfurth
mesh_terms: D000818:Animals; D001665:Binding Sites; D005075:Biological Evolution; D019556:COS Cells; D002522:Chlorocebus aethiops; D047369:Chromatin Immunoprecipitation; D002874:Chromosome Mapping; D019143:Evolution, Molecular; D051268:GA-Binding Protein Transcription Factor / Q000235:genetics* / Q000378:metabolism*; D005786:Gene Expression Regulation; D049810:Genetic Speciation; D057809:HEK293 Cells; D006801:Humans; D011401:Promoter Regions, Genetic; D011485:Protein Binding; D016415:Sequence Alignment; D016335:Zinc Fingers / Q000235:genetics
chemical_list: D051268:GA-Binding Protein Transcription Factor; C495661:GABPA protein, human
keywords: ChIP-Seq; GABP; KRAB zinc finger genes; comparative genomics.; human molecular evolution; human-specific binding sites; promoter assay
references.citation: Nature. 2004 Mar 25;428(6981):415-8
references.pmid: 15042088
references.citation: Science. 2008 Aug 15;321(5891):956-60
references.pmid: 18599741
references.citation: Ageing Res Rev. 2009 Jul;8(3):150-9
references.pmid: 19491040
references.citation: Diabetologia. 2007 Mar;50(3):676-81
references.pmid: 17216280
references.citation: Diabetologia. 2007 Dec;50(12):2486-94
references.pmid: 17906960
references.citation: Genome Res. 2007 Jun;17(6):818-27
references.pmid: 17568000
references.citation: Am J Hum Genet. 2013 May 2;92(5):774-80
references.pmid: 23643384
references.citation: Nat Rev Genet. 2007 Mar;8(3):206-16
references.pmid: 17304246
references.citation: Nat Genet. 2008 Nov;40(11):1262-3; author reply 1263-4
references.pmid: 18957975
references.citation: Glycobiology. 2007 Sep;17(9):922-31
references.pmid: 17580316
references.citation: Bioinformatics. 2010 Nov 15;26(22):2924-6
references.pmid: 20861032
references.citation: BMC Bioinformatics. 2007;8:41
references.pmid: 17284313
references.citation: Biochem Biophys Res Commun. 2006 Sep 1;347(3):747-51
references.pmid: 16842759
references.citation: Nature. 2011 Oct 6;478(7367):57-63
references.pmid: 21937992
references.citation: Prog Neuropsychopharmacol Biol Psychiatry. 2013 Jan 10;40:236-9
references.pmid: 23046827
references.citation: J Biol Chem. 2011 Jul 1;286(26):23521-32
references.pmid: 21555518
references.citation: Genomics. 2009 Mar;93(3):227-34
references.pmid: 19056481
references.citation: Genetics. 2007 Aug;176(4):2069-76
references.pmid: 17565944
references.citation: Science. 1975 Apr 11;188(4184):107-16
references.pmid: 1090005
references.citation: Bioinformatics. 2003 Jan 22;19(2):185-93
references.pmid: 12538238
references.citation: Mol Biol Evol. 2007 Aug;24(8):1586-91
references.pmid: 17483113
references.citation: Genome Res. 2006 May;16(5):584-94
references.pmid: 16606703
references.citation: Mol Cell Biol. 2007 Jul;27(13):5040-6
references.pmid: 17485447
references.citation: Genome Res. 2012 Sep;22(9):1813-31
references.pmid: 22955991
references.citation: Bioinformatics. 2004 Feb 12;20(3):307-15
references.pmid: 14960456
references.citation: Nat Genet. 2007 Apr;39(4):534-9
references.pmid: 17384640
references.citation: Genome Biol. 2007;8(6):R124
references.pmid: 17594489
references.citation: J Biol Chem. 2001 Jun 22;276(25):22209-14
references.pmid: 11301336
references.citation: Rev Diabet Stud. 2008 Winter;5(4):225-31
references.pmid: 19290383
references.citation: Nucleic Acids Res. 2009 Jul;37(Web Server issue):W202-8
references.pmid: 19458158
references.citation: Mol Biol Evol. 2010 Nov;27(11):2606-17
references.pmid: 20573777
references.citation: Genome Res. 2004 Dec;14(12):2412-23
references.pmid: 15574820
references.citation: Mol Genet Genomic Med. 2015 Jan;3(1):59-68
references.pmid: 25629079
references.citation: J Comput Biol. 2007 May;14(4):446-61
references.pmid: 17572023
references.citation: Mol Cell Biol. 2004 Jul;24(13):5844-9
references.pmid: 15199140
references.citation: Proc Natl Acad Sci U S A. 2009 Dec 29;106(52):22358-63
references.pmid: 20007773
references.citation: Bioinformatics. 2006 May 1;22(9):1036-46
references.pmid: 16500937
references.citation: Nucleic Acids Res. 2004 Jan 1;32(Database issue):D493-6
references.pmid: 14681465
references.citation: Nature. 2000 Mar 2;404(6773):99-103
references.pmid: 10716451
references.citation: Nat Methods. 2008 Sep;5(9):829-34
references.pmid: 19160518
references.citation: J Neurosci. 2002 Nov 15;22(22):9800-9
references.pmid: 12427836
references.citation: PLoS Biol. 2010;8(10). pii: e1000494. doi: 10.1371/journal.pbio.1000494
references.pmid: 20957185
references.citation: Nat Genet. 2007 Sep;39(9):1140-4
references.pmid: 17694055
references.citation: BMC Genet. 2007;8:43
references.pmid: 17601350
references.citation: PLoS Biol. 2011 Oct;9(10):e1001179
references.pmid: 22028629
references.citation: Mol Biol Evol. 2011 Aug;28(8):2173-83
references.pmid: 21335606
references.citation: Genome Res. 2006 May;16(5):669-77
references.pmid: 16606702
references.citation: PLoS Biol. 2005 Dec;3(12):e387
references.pmid: 16274263
references.citation: Proc Natl Acad Sci U S A. 2008 Aug 12;105(32):11043-9
references.pmid: 18682559
references.citation: J Biol Chem. 1997 Nov 14;272(46):29060-7
references.pmid: 9360980
references.citation: PLoS One. 2012;7(12):e49892
references.pmid: 23284628
references.citation: Q Rev Biol. 1971 Jun;46(2):111-38
references.pmid: 5160087
references.citation: J Neurosci. 2004 Nov 3;24(44):9878-87
references.pmid: 15525772
references.citation: PLoS Genet. 2007 Nov;3(11):e208
references.pmid: 18020712
references.citation: Science. 1998 Feb 13;279(5353):1037-41
references.pmid: 9461436
references.citation: J Neurochem. 2012 Feb;120(3):419-29
references.pmid: 22077634
references.citation: Proc Natl Acad Sci U S A. 2006 Nov 7;103(45):16716-21
references.pmid: 17065319
references.citation: Blood Cells Mol Dis. 2004 Jan-Feb;32(1):143-54
references.pmid: 14757430
references.citation: Blood. 2011 Aug 25;118(8):2243-53
references.pmid: 21705494
references.citation: PLoS One. 2009;4(2):e4582
references.pmid: 19242545
references.citation: Philos Trans R Soc Lond B Biol Sci. 2013 Dec 19;368(1632):20130025
references.pmid: 24218637
references.citation: Trends Genet. 2013 Mar;29(3):130-9
references.pmid: 23253430
references.citation: Science. 2008 Sep 5;321(5894):1346-50
references.pmid: 18772437
references.citation: Genome Biol. 2007;8(5):R84
references.pmid: 17506886
references.citation: PLoS One. 2011;6(6):e20284
references.pmid: 21695124