Evolution of transcription factor binding sites in mammalian gene regulatory regions: Conservation and turnover

Molecular Biology and Evolution

Volumn 19, Issue 7, 2002, Pages 1114-1121

  Dermitzakis, Emmanouil T ^a,b   Clark, Andrew G ^a  

^a PENNSYLVANIA STATE UNIVERSITY   (United States)

^b UNIVERSITY OF GENEVA   (Switzerland)

Author keywords

Binding site turnover; Mammals; Regulatory evolution

Indexed keywords

ADENOSINE DEAMINASE; APOLIPOPROTEIN A1; APOLIPOPROTEIN A2; APOLIPOPROTEIN C3; APOLIPOPROTEIN E; ATRIAL NATRIURETIC FACTOR; BLOOD CLOTTING FACTOR 9; C REACTIVE PROTEIN; CD68 ANTIGEN; CHEMOKINE RECEPTOR CCR5; ERYTHROPOIETIN; FRUCTOSE BISPHOSPHATE ALDOLASE; GLYCOPROTEIN IB; GONADORELIN; GROWTH HORMONE; HUNTINGTIN; INTERLEUKIN 3; INTERLEUKIN 5; MUCIN 1; MYOGLOBIN; NEUROFILAMENT PROTEIN; OXYTOCIN; PADGEM PROTEIN; PREPROINSULIN; PROTEIN C MYB; THYROGLOBULIN; TRANSCRIPTION FACTOR; TRANSMEMBRANE CONDUCTANCE REGULATOR; TROPONIN C; TUMOR NECROSIS FACTOR ALPHA;

ARTICLE; BINDING SITE; DNA FOOTPRINTING; EVOLUTION; GENETIC CONSERVATION; GENETIC VARIABILITY; HUMAN; MAMMALIAN GENETICS; NONHUMAN; PHYLOGENY; PRIMATE; PROMOTER REGION; RODENT; SEQUENCE HOMOLOGY; SPECIES DIFFERENCE; ANIMAL; BIOLOGICAL MODEL; COMPARATIVE STUDY; GENE EXPRESSION REGULATION; GENETIC TRANSCRIPTION; GENETICS; METABOLISM; MOLECULAR EVOLUTION; NUCLEOTIDE SEQUENCE; REGULATORY SEQUENCE;

MAMMALIA; PRIMATES; RODENTIA;

ANIMALS; BINDING SITES; CONSERVED SEQUENCE; DNA FOOTPRINTING; EVOLUTION, MOLECULAR; GENE EXPRESSION REGULATION; HUMANS; MODELS, GENETIC; PROMOTER REGIONS (GENETICS); REGULATORY SEQUENCES, NUCLEIC ACID; RODENTIA; TRANSCRIPTION FACTORS; TRANSCRIPTION, GENETIC;

EID: 0035986888     PISSN: 07374038     EISSN: None     Source Type: Journal    
DOI: 10.1093/oxfordjournals.molbev.a004169     Document Type: Article

References (26)

1. Selection of DNA binding sites by regulatory proteins. Statistical-mechanical theory and application to operators and promoters
2. Regulatory element detection using correlation with expression
3. Variations on a theme: Cataloging human DNA sequence variation
4. Active conservation of noncoding sequences revealed by three-way species comparisons
5. Profile hidden markov models
6. Validating computer programs for functional genomics in gene regulatory regions
7. Long human-mouse sequence alignments reveal novel regulatory elements: A reason to sequence the mouse genome
8. Comparative analysis of noncoding regions of 77 orthologous mouse and human gene pairs
9. Identification of phylogenetic footprints in primate tumor necrosis factor-alpha promoters
10. Evidence for stabilizing selection in a eukaryotic enhancer element
11. Evolutionary parameters of the transcribed mammalian genome: An analysis of 2,820 orthologous rodent and human sequences
12. Mutually compensatory mutations during evolution of the tetramerization domain of tumor suppressor p53 lead to impaired hetero-oligomerization
13. CCR5 promoter polymorphism and HIV-1 disease progression. Multicenter AIDS Cohort Study (MACS)
14. Transcriptional control of the factor IX gene: Analysis of five cis-acting elements and the deleterious effects of naturally occurring hemophilia B Leyden mutations
15. Genome-wide location and function of DNA binding proteins
16. The future of genetic studies of complex human diseases
17. PipMaker - A web server for aligning two genomic DNA sequences
18. Comparative studies on mammalian Hoxc8 early enhancer sequence reveal a baleen whale-specific deletion of a cis-acting element
19. An efficient cis-element discovery method using multiple sequence comparisons based on evolutionary relationships
20. Human-mouse genome comparisons to locate regulatory sites
21. The NOTCH4 locus is associated with susceptibility to schizophrenia
22. Association of a promoter polymorphism of tumor necrosis factor-alpha with subacute cutaneous lupus erythematosus and distinct photoregulation of transcription
23. TRANSFAC: An integrated system for gene expression regulation
24. Bayesian adaptive alignment and inference