Epigenetic variability across human populations: A Focus on DNA Methylation Profiles of the KRTCAP3, MAD1L1 and BRSK2 Genes

Genome Biology and Evolution

Volumn 8, Issue 9, 2016, Pages 2760-2773

  Giuliani, Cristina ^a   Sazzini, Marco ^a   Bacalini, Maria Giulia ^a   Pirazzini, Chiara ^a   Marasco, Elena ^a   Fontanesi, Elisa ^a   Franceschi, Claudio ^a,b   Luiselli, Donata ^a   Garagnani, Paolo ^a,c  

^a UNIVERSITY OF BOLOGNA   (Italy)

^b IRCCS ISTITUTO DELLE SCIENZE NEUROLOGICHE DI BOLOGNA   (Italy)

^c UNIVERSITY OF BOLOGNA   (Italy)

Author keywords

DNA methylation variability; environmental interaction; human adaptation; population epigenetics

Indexed keywords

BRSK2 PROTEIN, HUMAN; CELL CYCLE PROTEIN; KERATIN; MAD1L1 PROTEIN, HUMAN; NUCLEAR PROTEIN; PROTEIN SERINE THREONINE KINASE;

ADAPTATION; ANCESTRY GROUP; CPG ISLAND; DNA METHYLATION; GENETIC EPIGENESIS; GENETIC VARIATION; GENETICS; HUMAN;

ADAPTATION, PHYSIOLOGICAL; CELL CYCLE PROTEINS; CONTINENTAL POPULATION GROUPS; CPG ISLANDS; DNA METHYLATION; EPIGENESIS, GENETIC; GENETIC VARIATION; HUMANS; KERATINS; NUCLEAR PROTEINS; PROTEIN-SERINE-THREONINE KINASES;

EID: 84995478823     PISSN: None     EISSN: 17596653     Source Type: Journal    
DOI: 10.1093/gbe/evw186     Document Type: Article

References (54)

1. Ai S, Shen L, Guo J, Feng X, Tang B. 2012. DNA methylation as a biomarker for neuropsychiatric diseases. Int J Neurosci. 122:165-176. doi: 10.3109/00207454.2011.637654.
2. Alisch RS, et al. 2012. Age-Associated DNA methylation in pediatric populations. Genome Res. 22:623-632. doi: 10.1101/gr.125187.111.
3. Andres AM, et al. 2009. Targets of Balancing Selection in the Human. Genome. Mol Biol Evol. 26:2755-2764. doi: 10.1093/molbev/msp190.
4. Arciero E, et al. 2015. Genes regulated by Vitamin D in bone cells are positively selected in East Asians. Plos One 10(12):e0146072. doi: 10.1371/journal.pone.0146072.
5. Auton A, et al. 2015. A global reference for human genetic variation. Nature 526:68-74. doi: 10.1038/nature15393.
6. Bacalini MG, et al. 2015. A meta-Analysis on age-Associated change in blood DNA methylation: results from an original analysis pipeline for Infinium 450k data. Aging 7(2):97-109.
7. Bierne H, Hamon M, Cossart P. 2012. Epigenetics and bacterial infections. Cold Spring Harb Perspect Med. 2:a010272. doi: 10.1101/cshperspect.a010272.
8. Botigué LR, et al. 2013. Gene flow from North Africa contributes to differential human genetic diversity in southern Europe. Proc Natl Acad Sci U S A. 110:11791-11796. doi: 10.1073/pnas.1306223110.
9. Calvano SE, et al. 2005. A network-based analysis of systemic inflammation in humans. Nature 437:1032-1037. doi: 10.1038/nature03985.
10. Chen X-Y, et al. 2012. Brain-selective kinase 2 (BRSK2) phosphorylation on PCTAIRE1 negatively regulates glucose-stimulated insulin secretion in pancreatic b-cells. J Biol Chem. 287:30368-30375. doi: 10.1074/jbc.M112.375618.
11. Consortium T, 1000 GP. 2010. A map of human genome variation from population-scale sequencing. Nature 467:1061-1073. doi: 10.1038/nature09534.
12. Du P, Kibbe WA, Lin SM. 2008. lumi: A pipeline for processing Illumina microarray. Bioinforma Oxf Engl. 24:1547-1548. doi: 10.1093/bioinformatics/btn224.
13. Fagny M, et al. 2015. The epigenomic landscape of African rainforest hunter-gatherers and farmers. Nat Commun. 6:10047. doi: 10.1038/ncomms10047.
14. Feinberg AP, Irizarry RA. 2009. Stochastic epigenetic variation as a driving force of development, evolutionary adaptation, and disease. Proc Natl Acad Sci U S A. 200906183. 107 Suppl 1:1757-1764. doi: 10.1073/pnas.0906183107.
15. Fraser HB, Lam LL, Neumann SM, Kobor MS. 2012. Population-specificity of human DNA methylation. Genome Biol. 13(2):R8.
16. Friemel C, et al. 2014. Array-based DNA methylation profiling in male infertility reveals allele-specific DNA methylation in PIWIL1 and PIWIL2. Fertil Steril. 101:1097-1103.e1. doi: 10.1016/j.fertnstert.2013.12.054.
17. Fumagalli M, et al. 2011. Signatures of environmental genetic adaptation pinpoint pathogens as the main selective pressure through human evolution. PLoS Genet. 7:e1002355. doi: 10.1371/journal.pgen.1002355.
18. George RD, et al. 2011. Trans genomic capture and sequencing of primate exomes reveals new targets of positive selection. Genome Res. 21:1686-1694. doi: 10.1101/gr.121327.111.
19. Giuliani C, et al. 2015. The epigenetic side of human adaptation: hypotheses, evidences and theories. Ann Hum Biol. 42:1-9. doi: 10.3109/03014460.2014.961960.
20. Gluckman PD, Hanson MA, Spencer HG. 2005. Predictive adaptive responses and human evolution. Trends Ecol Evol. 20:527-533. doi: 10.1016/j.tree.2005.08.001.
21. Han M, Fan L, Qin Z, Lavingia B, Stastny P. 2013. Alleles of keratin 1 in families and populations. Hum Immunol. 74:1453-1458. doi: 10.1016/j.humimm.2013.05.003.
22. Henn BM, et al. 2012. Genomic ancestry of North Africans Supports Backto-AfricaMigrations Schierup. PLoS Genet. 8:e1002397. doi: 10.1371/journal.pgen.1002397.
23. Heyn H, et al. 2013. DNA methylation contributes to natural human variation. Genome Res. 23:1363-1372. doi: 10.1101/gr.154187.112.
24. Hubisz MJ, Pollard KS. 2014. Exploring the genesis and functions of Human Accelerated Regions sheds light on their role in human evolution. Curr Opin Genet Dev. 29:15-21. doi: 10.1016/j.gde.2014.07.005.
25. Jablonka E, Lamb MJ. 2005. Evolution in Four Dimensions: Genetic, Epigenetic, Behavioral, and Symbolic Variation in the History of Life. Cambridge, MA: MIT Press.
26. Jablonski NG, Chaplin G. 2010. Human skin pigmentation as an adaptation to UV radiation. Proc Natl Acad Sci U S A. 107:8962-8968. doi: 10.1073/pnas.0914628107.
27. Karsli-Ceppioglu S, et al. 2015. Genome-wide DNA methylation modified by soy phytoestrogens: role for epigenetic therapeutics in prostate cancer? OMICS J Integr Biol. 19:209-219. doi: 10.1089/omi.2014.0142.
28. Khan I, et al. 2014. Mammalian keratin associated proteins (KRTAPs) subgenomes: disentangling hair diversity and adaptation to terrestrial and aquatic environments. BMC Genomics 15:779. doi: 10.1186/1471-2164-15-779.
29. Klironomos FD, Berg J, Collins S. 2013. How epigenetic mutations can affect genetic evolution: model and mechanism. BioEssays News Rev Mol Cell Dev Biol. 35:571-578. doi: 10.1002/bies.201200169.
30. Lane N, et al. 2003. Resistance of IAPs to methylation reprogramming may provide a mechanism for epigenetic inheritance in the mouse. Genesis 35:88-93. doi: 10.1002/gene.10168.
31. Lemire M, et al. 2015. Long-range epigenetic regulation is conferred by genetic variation located at thousands of independent loci. Nat Commun. 6:6326. doi: 10.1038/ncomms7326.
32. Li L, et al. 2012. DNA methylation in peripheral blood: A potential biomarker for cancer molecular epidemiology. J Epidemiol Jpn Epidemiol Assoc. 22:384-394.
33. Marr AK, et al. 2014. Leishmania donovani infection causes distinct epigenetic DNA methylation changes in hostmacrophages. PLoS Pathog. 10:e1004419. doi: 10.1371/journal.ppat.1004419.
34. Marsit C, Christensen B. 2013. Blood-derived DNA methylationmarkers of cancer risk. Adv Exp Med Biol. 754:233-252. doi: 10.1007/978-1-4419-9967-2-12.
35. Menozzi FD, et al. 2002. Enhanced bacterial virulence through exploitation of host glycosaminoglycans. Mol Microbiol. 43:1379-1386.
36. Pollard KS, et al. 2006. Forces Shaping the Fastest Evolving Regions in the Human Genome. PLoS Genet. 2:e168. doi: 10.1371/journal.pgen.0020168.
37. Richards EJ., 2008 Population epigenetics. Curr Opin Genet Dev. 18:221-226. doi: 10.1016/j.gde.2008.01.014.
38. Robins AH. 2009. The evolution of light skin color: role of vitamin D disputed. Am J Phys Anthropol. 139:447-450. doi: 10.1002/ajpa.21077.
39. Santoro MG. 2003. NEW EMBOMEMBERS REVIEW: NF-kappaB and virus infection: who controls whom. Embo J. 22:2552-2560. doi: 10.1093/emboj/cdg267.
40. Schmitz RJ, et al. 2011. Transgenerational epigenetic instability is a source of novel methylation variants. Science 334:369-373. doi: 10.1126/science.1212959.
41. Schroder K, Hertzog PJ, Ravasi T, Hume DA. 2004. Interferon-g: An overview of signals, mechanisms and functions. J Leukoc Biol. 75:163-189. doi: 10.1189/jlb.0603252.
42. Seisenberger S, et al. 2012. The dynamics of genome-wide DNA methylation reprogramming in mouse primordial germ cells. Mol Cell. 48:849-862. doi: 10.1016/j.molcel.2012.11.001.
43. Shea N, Pen I, Uller T. 2011 Three epigenetic information channels and their different roles in evolution. J Evol Biol. 24:1178-1187. doi: 10.1111/j.1420-9101.2011.02235.x.
44. Sternini C, Anselmi L, Rozengurt E. 2008. Enteroendocrine cells: A site of taste in gastrointestinal chemosensing. Curr Opin Endocrinol Diabetes Obes. 15:73-78. doi: 10.1097/MED.0b013e3282f43a73.
45. Sturm RA, Duffy DL. 2012. Human pigmentation genes under environmental selection. Genome Biol. 13:248. doi: 10.1186/gb-2012-13-9-248.
46. Szyf M. 2015. Nongenetic inheritance and transgenerational epigenetics. Trends Mol Med. 21:134-144. doi: 10.1016/j.molmed.2014.12.004.
47. Tanaka T, et al. 2009. Genome-wide association study of vitamin B6, vitamin B12, Folate, and homocysteine blood concentrations. Am J Hum Genet. 84:477-482. doi: 10.1016/j.ajhg.2009.02.011.
48. Thompson RF, SuzukiM, Lau KW, Greally JM. 2009. A pipeline for the quantitative analysis of CG dinucleotide methylation using mass spectrometry. Bioinformatics 25:2164-2170. doi: 10.1093/bioinformatics/btp382.
49. Tolg C, et al. 2011. Uropathogenic E. Coli infection provokes epigenetic downregulation of CDKN2A (p16INK4A) in uroepithelial cells. Lab Investig J Tech Methods Pathol. 91:825-836. doi: 10.1038/labinvest.2010.197.
50. Trowbridge JM, Gallo RL. 2002. Dermatan sulfate: new functions from an old glycosaminoglycan. Glycobiology 12:117R-125R.
51. Tukey RH, Strassburg CP. 2000. Human UDP-glucuronosyltransferases: metabolism, expression, and disease. Annu Rev Pharmacol Toxicol. 40:581-616. doi: 10.1146/annurev.pharmtox.40.1.581.
52. Wang TJ, et al. 2010. Common genetic determinants of vitamin D insufficiency: A genome-wide association study. The Lancet 376:180-188. doi: 10.1016/S0140-6736(10)60588-0.
53. Wang Y, et al. 2012. BRSK2 is regulated by ER stress in protein level and involved in ER stress-induced apoptosis. Biochem Biophys Res Commun. 423:813-818. doi: 10.1016/j.bbrc.2012.06.046.
54. Wessely F, Emes RD. 2012. Identification of DNA methylation biomarkers from Infinium arrays. Front Genet. 3:(161)1-8.