Core promoter short tandem repeats as evolutionary switch codes for primate speciation

American Journal of Primatology

Volumn 77, Issue 1, 2015, Pages 34-43

  Ohadi, Mina ^a   Valipour, Elaheh ^a   Ghadimi Haddadan, Saeed ^a   Namdar Aligoodarzi, Pegah ^a   Bagheri, Abouzar ^a   Kowsari, Ali ^b   Rezazadeh, Maryam ^a   Darvish, Hossein ^c   Kazeminasab, Somayeh ^a  

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

^b GOLESTAN UNIVERSITY OF MEDICAL SCIENCES   (Iran)

^c SHAHID BEHESHTI UNIVERSITY OF MEDICAL SCIENCES   (Iran)

Author keywords

Core promoter; Evolution; Non primate; Primate; Short tandem repeat

Indexed keywords

AFROTHERIA; GORILLA GORILLA GORILLA; HOMO SAPIENS; LAURASIATHERIA; MAMMALIA; PAN TROGLODYTES; PRIMATES; SCANDENTIA; XENARTHRA;

MICROSATELLITE DNA;

ANIMAL; DOG; EVOLUTION; GENETIC DATABASE; GENETICS; GENOME; GORILLA; HUMAN; MAMMAL; MOUSE; PAN TROGLODYTES; PRIMATE; PROMOTER REGION; SPECIES DIFFERENTIATION;

ANIMALS; BIOLOGICAL EVOLUTION; DATABASES, GENETIC; DOGS; GENETIC SPECIATION; GENOME; GORILLA GORILLA; HUMANS; MAMMALS; MICE; MICROSATELLITE REPEATS; PAN TROGLODYTES; PRIMATES; PROMOTER REGIONS, GENETIC;

EID: 84919876762     PISSN: 02752565     EISSN: 10982345     Source Type: Journal    
DOI: 10.1002/ajp.22308     Document Type: Article

References (41)

1. 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.
2. 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.
3. Brawand D, Soumillon M, Necsulea A., et al. 2011. The evolution of gene expression levels in mammalian organs. Nature 478:343-348.
4. Buschiazzo E, Gemmel NJ. 2006. The rise, fall and renaissance of microsatellites in eukaryotic genomes. BioEssays 28:1040-1050.
5. 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.
6. Darvish H, Nabi MO, Firouzabadi SG, et al. 2011. Exceptional human core promoter nucleotide compositions. Gene 475:79-86.
7. 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.
8. Donaldson ZR, Kondrashov FA, Putnam A, et al. 2008. Evolution of a behavior-linked microsatellite-containing element in the 5' flanking region of the primate AVPR1A gene. BMC Evolutionary Biology 8:180.
9. Esmaeilzadeh-Gharehdaghi E, Banan M, Farashi S, et al. 2011. Support for down-tuning of the calreticulin gene in the process of human evolution. Progress in Neuropsychopharmacology and Biological Psychiatry 35:1770-1773.
10. Fondon JW III, Garner HR. 2004. Molecular origins of rapid and continuous morphological evolution. Proceedings of the National Academy of Science United States of America 101:18058.
11. Gemayel R, Vinces MD, Legendre M, Verstrepen KJ. 2010. Variable tandem repeats accelerate evolution of coding and regulatory sequences. Annual Review of Genetics 44:445-477. Review.
12. 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 Science United States of America 110:10682-10686.
13. Hammock EAD, Young LJ. 2005. Microsatellite instability generates diversity in brain and sociobehavioral traits. Science 308:1630-1634.
14. Heidari A, Nariman Saleh Fam Z, Esmaeilzadeh-Gharehdaghi E, et al. 2012. Core promoter STRs: novel mechanism for inter-individual variation in gene expression in humans. Gene 492:195-198.
15. Iglesias AR, Kindlund E, Tammi M, Wadelius C. 2004. Some microsatellites may act as novel polymorphic cis-regulatory elements through transcription factor binding. Gene 341:149-165.
16. Jansen A, Gemayel R, Verstrepen KJ. 2012. Unstable microsatellite repeats facilitate rapid evolution of coding and regulatory sequences. Genome Dynamics 7:108-125. Review.
17. Kashi Y, King DG. 2006. Simple sequence repeats as advantageous mutators in evolution. Trends in Genetics 22:253-259.
18. King DG. 2012. Evolution of simple sequence repeats as mutable sites. Advances in Experimental Medical Biology 769:10-25.
19. King DG, Trifonov EN, Kashi Y. 2006. Chapter 4. Tuning knobs in the genome: evolution of simple sequence repeats by indirect selection In: Caporale LH, editor. The implicit genome. UK: Oxford Press.
20. Li Y, Seidel K, Marschall P, et al. 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.
21. 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:e1002932.
22. Milunsky JM, Maher TA, Zhao G, et al. 2008. TFAP2A mutations result in branchio-oculo-facial syndrome. American Journal of Human Genetics 82:1171-1177.
23. Mohammadparast S, Bayat H, Biglarian A, Ohadi M. 2014. Exceptional expansion and conservation of the CT-STR complex in the core promoter of PAXBP1 in primates. American Journal of Primatology doi: 10.1002/ajp.22266.
24. Moshonov S, Elfakess R, Golan-Mashiach M, Sinvani H, Dikstein R. 2008. Links between core promoter and basic gene features influence gene expression. BMC Genomics 9:92.
25. Mouse Genome Sequencing Consortium. 2002. Initial sequencing and comparative analysis of the mouse genome. Nature 420:520-562.
26. Murdoch M, DelConte C, García-Castro MI. 2012. Pax7 lineage contributions to the mammalian neural crest. PLoS ONE 7:e41089.
27. Ohadi M, Mohammadparast S, Darvish H. 2012. Evolutionary trend of exceptionally long human core promoter short tandem repeats. Gene 507:61-67.
28. 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.
29. Rockman MV, Wray GA. 2002. Abundant raw material for cis-regulatory evolution in humans. Molecular Biology and Evolution 19:1991-2004.
30. Sandelin A, Carninci P, Lenhard B, et al. 2007. Mammalian RNA polymerase II core promoters: insights from genome-wide studies Nature Reviews Genetics 8:424-436.
31. 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.
32. Singh DP, Bhargavan B, Chhunchha B, et al. 2012. Transcriptional protein Sp1 regulates LEDGF transcription by directly interacting with its cis-elements in GC-rich region of TATA-less gene promoter. PLoS ONE 7:e37012.
33. Trivedi S, Hancock JM. 2012. Low microsatellite frequencies in neuron and brain expressed microRNAs. Gene 508:73-77.
34. Valipour E, Kowsari A, Bayat H, et al. 2013. Polymorphic core promoter GA-repeats alter gene expression of the early embryonic developmental genes. Gene 531:175-179.
35. Verstrepen KJ, Jansen A, Lewitter F, Fink GR. 2005. Intragenic tandem repeats generate functional variability. Nature Genetics 37:986.
36. Vinces MD, Legendre M, Caldara M, Hagihara M, Verstrepen KJ. 2009. Unstable tandem repeats in promoters confer transcriptional evolvability. Science 324:1213-1216.
37. Vowles EJ, Amos W. 2006. Quantifying ascertainment bias and species-specific length differences in human and chimpanzee microsatellites using genome sequences. Molecular Biology Evolution 23:598-607.
38. Wang Y, Rekaya R. 2009. A comprehensive analysis of gene expression evolution between humans and mice. Evolutionary Bioinformatics Online 5:81-90.
39. 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.
40. Zarif Yeganeh M, Ghaffarpour M, Farhud DD, et al. 2009. Skew in the human caveolin 1 gene upstream purine complex homozygote haplotype compartment in multiple sclerosis. Journal of Neuroimmunology 216:103-107.
41. Zarif Yeganeh M, Mirabzadeh A, Khorram Khorshid HR, et al. 2010. Novel extreme homozygote haplotypes at the human caveolin 1 gene upstream purine complex in sporadic Alzheimer's disease. American Journal of Medical Genetics B Neuropsychiatric Genetics 153B:347-349.