Exceptional expansion and conservation of a CT-repeat complex in the core promoter of PAXBP1 in primates

American Journal of Primatology

Volumn 76, Issue 8, 2014, Pages 747-756

  Mohammadparast, Saeid ^a   Bayat, Hadi ^a   Biglarian, Akbar ^a   Ohadi, Mina ^a  

^a UNIVERSITY OF SOCIAL WELFARE AND REHABILITATION SCIENCES   (Iran)

Author keywords

Core promoter; CT repeat; Evolution; Homo sapiens; PAXBP1; Primate

Indexed keywords

AMPHIBIA; AVES; CALLITHRIX; CALLITHRIX JACCHUS; GALAGONIDAE; HAPLORHINI; HOMO SAPIENS; LEMUR; MACACA MULATTA; MAMMALIA; MICROCEBUS MURINUS; OTOLEMUR GARNETTII; PRIMATES; REPTILIA; STREPSIRHINI; VERTEBRATA;

MICROSATELLITE DNA;

ANIMAL; EVOLUTION; GENETIC DATABASE; GENETIC VARIABILITY; GENETICS; HEK293 CELL LINE; HUMAN; PRIMATE; PROMOTER REGION;

ANIMALS; BIOLOGICAL EVOLUTION; DATABASES, GENETIC; GENETIC VARIATION; HEK293 CELLS; HUMANS; MICROSATELLITE REPEATS; PRIMATES; PROMOTER REGIONS, GENETIC;

EID: 84904566470     PISSN: 02752565     EISSN: 10982345     Source Type: Journal    
DOI: 10.1002/ajp.22266     Document Type: Article

References (46)

1. Bajard L, Relaix F, Lagha M, et al. 2006. A novel genetic hierarchy functions during hypaxial myogenesis: Pax3 directly activates Myf5 in muscle progenitor cells in the limb. Genes & Development 20:2450-2464.
2. Bastir M, Rosas A, Stringer C, et al. 2010. Effects of brain and facial size on basicranial form in human and primate evolution. Journal of Human Evolution 58:424-431.
3. Bayés A, Collins MO, Croning MD, et al. 2012. Comparative study of human and mouse postsynaptic proteomes finds high compositional conservation and abundance differences for key synaptic proteins. PLoS ONE 7:e46683.
4. Borel C, Migliavacca E, Letourneau A, et al. 2012. Tandem repeat sequence variation as causative cis-eQTLs for protein-coding gene expression variation: the case of CSTB. Human Mutation 33:1302-1309.
5. Brawand D, Soumillon M, Necsulea A, et al. 2011. The evolution of gene expression levels in mammalian organs. Nature 478:343-348.
6. Bolton KA, Ross JP, Grice DM, et al. 2013. STaRRRT: a table of short tandem repeats in regulatory regions of the human genome. BMC Genomics 14:795.
7. Buchberger A, Freitag D, Arnold HH. 2007. A homeo-paired domain-binding motif di-rects Myf5 expression in progenitor cells of limb muscle. Development 134:1171-1180.
8. Buckingham M, Relaix F. 2007. The role of Pax genes in the development of tissues and organs: Pax3 and Pax7 regulate muscle progenitor cell functions. Annual Review of Cell and Developmental Biology 23:645-673.
9. Crockford SJ. 2003. Thyroid rhythm phenotypes and hominid evolution: a new paradigm implicates pulsatile hormone secretion in speciation and adaptation changes. Comparative Biochemistry and Physiology. Part A, Molecular & Integrative Physiology 135:105-129.
10. Darvish H, Oladnabi O, Ghasemi Firouzabadi S, et al. 2011. Exceptional human core promoter nucleotide compositions. Gene 475:79-86.
11. Darvish H, Heidari A, Hosseinkhani S, et al. 2013. Biased homozygous haplotypes across the human caveolin 1 upstream purine complex in Parkinson's disease. Journal of Molecular Neuroscience 51:389-393.
12. Dereeper A, Guignon V, Blanc G, et al. 2008. Phylogeny.fr: robust phylogenetic analysis for the non-specialist. Nucleic Acids Research 36 (Web Server issue): W465-W469.
13. Diao Y, Guo X, Li Y, et al. 2012. Pax3/7BP is a Pax7- and Pax3-binding protein that regulates the proliferation of muscle precursor cells by an epigenetic mechanism. Cell Stem Cell 11:231-241.
14. Donaldson ZR, Bai Y, Kondrashov FA, et al. 2008. Evolution of a behavior-linked microsatellite-containing element of the 5' flanking region of the primate AVPR1A gene. BMC Evolutionary Biology 8:180-188.
15. Edgar RC. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research 32(5):1792-1797.
16. Esmaeilzadeh-Gharehdaghi E, et al. 2011. Support for down-tuning of the calreticulin gene in the process of human evolution. Prog Neuropsychopharmacol Biol Psychiatry 35(7):1770-1773.
17. Estruch SB, Buzón V, Carbó LR, et al. 2012. The oncoprotein BCL11A binds to orphan nuclear receptor TLX and potentiates its transrepressive function. PLoS ONE 7(6):e37963.
18. Giordani J, Bajard L, Demignon J, et al. 2007. Six proteins regulate the activation of Myf5 expression in embryonic mouse limbs. Proceedings of the National Academy of Sciences of the United States of America 104:11310-11315.
19. Guerreiro I, Nunes A, Woltering JM, et al. 2013. Role of a polymorphism in a Hox/Pax-responsive enhancer in the evolution of the vertebrate spine. Proceedings of the National Academy of Sciences of the United States of America 110:10682-10686.
20. Hammock EA, Young LJ. 2005. Microsatellite instability generates diversity in brain and sociobehavioral traits. Science 728:1630-1634.
21. Han YJ, de Lanerolle P. 2008. Naturally extended CT. AG repeats increase H-DNA structures and promoter activity in the smooth muscle myosin light chain kinase gene. Molecular and Cellular Biology 28:863-872.
22. Heidari A, Nariman Saleh Fam Z, Esmaeilzadeh-Gharedaghi E, et al. 2012. Core promoter STRs: novel mechanism for inter-individual variation in gene expression in humans. Gene 492:195-198.
23. Hopkins WD, Donaldson ZR, Young LJ. 2012. A polymorphic indel containing the RS3 microsatellite in the 5' flanking region of the vasopressin V1a receptor gene is associated with chimpanzee (Pan troglodytes) personality. Genes, Brain, and Behaviour 11:552-558.
24. Kashi Y, King DG. 2006. Simple sequence repeats as advantageous mutators in evolution. Trends in Genetics 22:253-259.
25. King DG. 2012. Evolution of simple sequence repeats as mutable sites. Advances in Experimental Medicine and Biology 769:10-25.
26. Li Y, Seidel K, Marschall P. 2012. A polymorphic microsatellite repeat within the ECE-1c promoter is involved in transcriptional start site determination, human evolution, and Alzheimer's disease. Journal of Neuroscience 32:16807-16820.
27. Lieberman DE, Ross CF, Ravosa MJ. 2000. The primate cranial base: ontogeny, function, and integration. American Journal of Physical Anthropology Suppl 31:117-169.
28. Liu F, van der Lijn F, Schurmann C, Zhu G, Mallar Chakravarty M. 2012. A genome-wide association study identifies five loci influencing facial morphology in Europeans. PLoS ONE 8(9):e1002932.
29. Maczkowiak F, Matéos S, Wang E, et al. 2010. The Pax3 and Pax7 paralogs cooperate in neural and neural crest patterning using distinct molecular mechanisms, in Xenopus laevis embryos. Developmental Biology 340:381-396.
30. Magli A, Schnettler E, Rinaldi F, Bremer P, Perlingeiro RC. 2013. Functional dissection of Pax3 in paraxial mesoderm development and myogenesis. Stem Cells 31:59-70.
31. Marie B, Pym E, Bergquist S, Davis GW. 2010. Synaptic homeostasis is consolidated by the cell fate gene gooseberry, a Drosophila pax3/7 homolog. Journal of Neuroscience 30:8071-8082.
32. Murdoch M, DelConte C, Garci{dotless}'a-Castro MI. 2012. Pax7 lineage contributions to the mammalian neural crest. PLoS ONE 7:e41089.
33. Ohadi M, Mohammadparast S, Darvish H. 2012. Evolutionary trend of exceptionally long human core promoter STRs. Gene 501:61-67.
34. Paternoster L, Zhurov AI, Toma AM, Kemp JP, Pourcain BS. 2012. Genome-wide association study of three-dimensional facial morphology identifies a variant in Pax3 associated with nasion position. American Journal of Human Genetics 90:478-485.
35. Relaix F, Rocancourt D, Mansouri A, Buckingham M. 2005. A Pax3/Pax7-dependent population of skeletal muscle progenitor cells. Nature 435:948-953.
36. Relaix F, Montarras D, Zaffran S, et al. 2006. Pax3 and Pax7 have distinct and overlapping functions in adult muscle progenitor cells. Journal of Cell Biology 172:91-102.
37. Rockman MV, Wray GA. 2002. Abundant raw material for cis-regulatory evolution in humans. Molecular Biology and Evolution 19:1991-2004.
38. Sankaran VG, Xu J, Ragoczy T, et al. 2009. Developmental and species-divergent globin switching are driven by BCL11A. Nature 460:1093-1097.
39. Sawaya SM, Lennon D, Buschiazzo E, Gemmell N, Minin VN. 2012. Measuring microsatellite conservation in mammalian evolution with a phylogenetic birth-death model. Genome Biology and Evolution 4:636-647.
40. Seyfarth J, Garred P, Madsen HO. 2005. The 'involution' of mannose-binding lectin. Human Molecular Genetics 14:2859-2869.
41. Smale ST, Kadonaga JT. 2003. The RNA polymerase II core promoter. Annual Review of Biochemistry 72:449-479.
42. Valipour E, Kowsari A, Bayat H, et al. 2013. Polymorphic core promoter GA-repeats alter gene expression of the early embryonic development genes. Gene 531:175-179.
43. Vinces MD, Legendre M, Caldara M, Hagihara M, Verstrepen KJ. 2009. Unstable tandem repeats in promoters confer transcriptional evolvability. Science 324:1213-1216.
44. Webster MT, Smith NG, Ellegren H. 2002. Microsatellite evolution inferred from human-Pan troglodytes genomic sequence alignments. Proceedings of the National Academy of Sciences of the United States of America 99:8748-8753.
45. Williams SA, Ostrofsky KR, Frater N, et al. 2013. The vertebral column of Australopithecus sediba. Science 340:1232996.
46. Yang C, Bolotin E, Jiang T, Sladek FM, Martinez E. 2007. Prevalence of the initiator over the TATA box in human and yeast genes and identification of DNA motifs enriched in human TATA-less core promoters. Gene 389:52-65.