Highly conserved upstream sequences for transcription factor genes and implications for the regulatory network.
Identifying evolutionarily conserved blocks in orthologous genomic sequences is an effective way to detect regulatory elements. In this study, with the aim of elucidating the architecture of the regulatory network, we systematically estimated the degree of conservation of the upstream sequences of 3,750 human-mouse orthologue pairs along 8-kb stretches. We found that the genes with high upstream conservation are predominantly transcription factor (TF) genes. In particular, developmental process-related TF genes showed significantly higher conservation of the upstream sequences than other TF genes. Such extreme upstream conservation of the developmental process-related TF genes suggests that the regulatory networks involved with developmental processes have been evolutionarily well conserved in both human and mouse lineages.
19 references, click to expand
-
Gene ontology: tool for the unification of biology. The Gene Ontology Consortium.Nat Genet. 2000 May;25(1):25-9 PMID: 10802651
-
dbSNP-database for single nucleotide polymorphisms and other classes of minor genetic variation.Genome Res. 1999 Aug;9(8):677-9 PMID: 10447503
-
RefSeq and LocusLink: NCBI gene-centered resources.Nucleic Acids Res. 2001 Jan 1;29(1):137-40 PMID: 11125071
-
Initial sequencing and analysis of the human genome.Nature. 2001 Feb 15;409(6822):860-921 PMID: 11237011
-
Genomic strategies to identify mammalian regulatory sequences.Nat Rev Genet. 2001 Feb;2(2):100-9 PMID: 11253049
-
Mutations in SIP1, encoding Smad interacting protein-1, cause a form of Hirschsprung disease.Nat Genet. 2001 Apr;27(4):369-70 PMID: 11279515
-
Nonsense and frameshift mutations in ZFHX1B, encoding Smad-interacting protein 1, cause a complex developmental disorder with a great variety of clinical features.Am J Hum Genet. 2001 Dec;69(6):1178-85 PMID: 11592033
-
Discovery of regulatory elements by a computational method for phylogenetic footprinting.Genome Res. 2002 May;12(5):739-48 PMID: 11997340
-
Transcriptional regulatory networks in Saccharomyces cerevisiae.Science. 2002 Oct 25;298(5594):799-804 PMID: 12399584
-
Initial sequencing and comparative analysis of the mouse genome.Nature. 2002 Dec 5;420(6915):520-62 PMID: 12466850
-
Mowat-Wilson syndrome.J Med Genet. 2003 May;40(5):305-10 PMID: 12746390
-
Sequencing and comparison of yeast species to identify genes and regulatory elements.Nature. 2003 May 15;423(6937):241-54 PMID: 12748633
-
Finding functional features in Saccharomyces genomes by phylogenetic footprinting.Science. 2003 Jul 4;301(5629):71-6 PMID: 12775844
-
Evolutionary conservation of motif constituents in the yeast protein interaction network.Nat Genet. 2003 Oct;35(2):176-9 PMID: 12973352
-
The Eukaryotic Promoter Database EPD: the impact of in silico primer extension.Nucleic Acids Res. 2004 Jan 1;32(Database issue):D82-5 PMID: 14681364
-
The spandrels of San Marco and the Panglossian paradigm: a critique of the adaptationist programme.Proc R Soc Lond B Biol Sci. 1979 Sep 21;205(1161):581-98 PMID: 42062
-
BLAST 2 Sequences, a new tool for comparing protein and nucleotide sequences.FEMS Microbiol Lett. 1999 May 15;174(2):247-50 PMID: 10339815
-
SIP1, a novel zinc finger/homeodomain repressor, interacts with Smad proteins and binds to 5'-CACCT sequences in candidate target genes.J Biol Chem. 1999 Jul 16;274(29):20489-98 PMID: 10400677
-
Human-mouse genome comparisons to locate regulatory sites.Nat Genet. 2000 Oct;26(2):225-8 PMID: 11017083
Contact
No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong
Qilu Normal University · Genelibs Bioinformatics Lab
750 Shunhua Rd, Jinan
2F, Bldg F, University Science Park
Tel: 0531-88819269
WeChat Official Account
Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.
Business Email
E-mail: [email protected]
Copyright © 2026.Genelibs Jinan Honghui Biotechnology Co., Ltd. 鲁ICP备20007159号-2
