A model for transgenerational imprinting variation in complex traits

PLoS ONE

Volumn 5, Issue 7, 2010, Pages

  Wang, Chenguang ^a   Wang, Zhong ^b   Luo, Jiangtao ^b   Li, Qin ^a   Li, Yao ^c   Ahn, Kwangmi ^b   Prows, Daniel R ^d   Wu, Rongling ^b  

^a University of Florida   (United States)

^b PENN STATE COLLEGE OF MEDICINE   (United States)

^c WEST VIRGINIA UNIVERSITY   (United States)

^d UNIVERSITY OF CINCINNATI COLLEGE OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALLELE; ANIMAL EXPERIMENT; ARTICLE; CHROMOSOME 1; CHROMOSOME 15; CHROMOSOME 4; CHROMOSOME 9; CONTROLLED STUDY; FEMALE; GENE SEGREGATION; GENETIC ALGORITHM; GENOME IMPRINTING; GENOTYPE; HERITABILITY; INBRED STRAIN; MALE; MATING; MODEL; MOUSE STRAIN; NONHUMAN; PEDIGREE; QUANTITATIVE TRAIT LOCUS; QUANTITATIVE TRAIT LOCUS MAPPING; SURVIVAL TIME; ALGORITHM; COMPUTER SIMULATION; GENETICS; STATISTICAL MODEL;

ALGORITHMS; COMPUTER SIMULATION; GENOMIC IMPRINTING; GENOTYPE; LIKELIHOOD FUNCTIONS; QUANTITATIVE TRAIT LOCI;

EID: 77955398983     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0011396     Document Type: Article

References (51)

1. Lander E, Botstein D (1989) Mapping Mendelian factors underlying quantitative traits using RFLP linkage maps. Genetics 121: 185-199.
2. Zeng Z (1994) Precision mapping of quantitative trait loci. Genetics 136: 1457-1468.
3. Ma C, Casella G, Wu R (2002) Functional mapping of quantitative trait loci underlying the character process: a theoretical framework. Genetics 161: 1751-1762.
4. Xu S (2003) Estimating polygenic effects using markers of the entire genome. Genetics 163: 789-801.
5. Li C, Zhou A, Sang T (2006) Rice domestication by reducing shattering. Science 311: 1936-1939.
6. Anholt R, Mackay T (2004) Genetic analysis of complex behaviors in Drosophila. Nat Rev Genet 5: 838-849.
7. Paterson A (2006) Leafing through the genomes of our major crop plants: strategies for capturing unique information. Nature Reviews Genetics 7: 174-184.
8. Veyrieras J, Kudaravalli S, Kim S, Dermitzakis E, Gilad Y, et al. (2008) Highresolution mapping of expression-QTLs yields insight into human gene regulation. PLoS genetics 4: e1000214. doi:10.1371/journal.pgen.1000214.
9. Martienssen R, Colot V (2001) DNA methylation and epigenetic inheritance in plants and filamentous fungi. Science 293: 1070-1074.
10. Richards E (2006) Inherited epigenetic variation-revisiting soft inheritance. Nature Reviews Genetics 7: 395-401.
11. Richards E (2008) Population epigenetics. Current Opinion in Genetics & Development 18: 221-226.
12. Johannes F, Porcher E, Teixeira F, Saliba-Colombani V, Simon M, et al. (2009) Assessing the impact of transgenerational epigenetic variation on complex traits. PLoS Genetics 5: e1000530. doi:10.1371/journal.pgen.1000530.
13. Manning K, Tor M, Poole M, Hong Y, Thompson A, et al. (2006) A naturally occurring epigenetic mutation in a gene encoding an SBP-box transcription factor inhibits tomato fruit ripening. Nature genetics 38: 948-952.
14. Rakyan V, Chong S, Champ M, Cuthbert P, Morgan H, et al. (2003) Transgenerational inheritance of epigenetic states at the murine AxinFu allele occurs after maternal and paternal transmission. Proceedings of the National Academy of Sciences 100: 2538-2543.
15. Kahn A, Fraga M (2009) Epigenetics and aging: status, challenges, and needs for the future. The Journals of Gerontology: Series A 64: 195-198.
16. Kakutani T (2002) Epi-alleles in plants: inheritance of epigenetic information over generations. Plant and cell physiology 43: 1106-1111.
17. Kalisz S, Purugganan M (2004) Epialleles via DNA methylation: consequences for plant evolution. Trends in Ecology & Evolution 19: 309-314.
18. Reik W, Walter J (2001) Genomic imprinting: parental influence on the genome. Nature Reviews Genetics 2: 21-32.
19. Sasaki H, Matsui Y (2008) Epigenetic events in mammalian germ-cell development: reprogramming and beyond. Nature Reviews Genetics 9:129-140.
20. Sha K (2008) A mechanistic view of genomic imprinting. Annu Res Genomics Hum Genet 9: 197-216.
21. Itier J, Tremp G, Léonard J, Multon M, Ret G, et al. (1998) Imprinted gene in postnatal growth role. Nature 393: 125-126.
22. Li L, Keverne E, Aparicio S, Ishino F, Barton S, et al. (1999) Regulation of maternal behavior and offspring growth by paternally expressed Peg3. Science 284: 330-333.
23. Isles A, Wilkinson L (2000) Imprinted genes, cognition and behaviour. Trends in Cognitive Sciences 4: 309-318.
24. Constância M, Kelsey G, Reik W (2004) Resourceful imprinting. Nature 432:53-57.
25. Wilkinson L, Davies W, Isles A (2007) Genomic imprinting effects on brain development and function. Nature Reviews Neuroscience 8: 832-843.
26. Cheverud J, Hager R, Roseman C, Fawcett G, Wang B, et al. (2008) Genomic imprinting effects on adult body composition in mice. Proceedings of the National Academy of Sciences 105: 4253-4258.
27. Wolf J, Cheverud J, Roseman C, Hager R (2008) Genome-wide analysis reveals a complex pattern of genomic imprinting in mice. PLoS Genetics 4: e1000091.
28. Li Y, Coelho C, Liu T, Wu S, Wu J, et al. (2008) A statistical model for estimating maternal-zygotic interactions and parent-of-origin effects of QTLs for seed development. PLoS One 3: e3131.
29. Liu T, Todhunter R, Wu S, Hou W, Mateescu R, et al. (2007) A random model for mapping imprinted quantitative trait loci in a structured pedigree: An implication for mapping canine hip dysplasia. Genomics 90: 276-284.
30. Morgan H, Santos F, Green K, Dean W, Reik W (2005) Epigenetic reprogramming in mammals. Human molecular genetics 14: R47-R58.
31. Li E (2002) Chromatin modification and epigenetic reprogramming in mammalian development. Nature Reviews Genetics 3: 662-673.
32. Surani M, Barton S, Norris M (1984) Development of reconstituted mouse eggs suggests imprinting of the genome during gametogenesis. Nature 308: 548-550.
33. McGrath J, Solter D (1984) Inability of mouse blastomere nuclei transferred to enucleated zygotes to support development in vitro. Science 226: 1317-1319.
34. Morgan H, Sutherland H, Martin D, Whitelaw E (1999) Epigenetic inheritance at the agouti locus in the mouse. Nature Genetics 23: 314-318.
35. Cropley J, Suter C, Beckman K, Martin D (2006) Germ-line epigenetic modification of the murine Avy allele by nutritional supplementation. Proceedings of the National Academy of Sciences 103: 17308-17312.
36. Dolinoy D, Weidman J, Waterland R, Jirtle R (2006) Maternal genistein alters coat color and protects Avy mouse offspring from obesity by modifying the fetal epigenome. Environmental health perspectives 114: 567-572.
37. Skinner M (2008) What is an epigenetic transgenerational phenotype?:: F3 or F2. Reproductive toxicology 25: 2-6.
38. Youngson N, Whitelaw E (2008) Transgenerational epigenetic effects. Annu Rev Genomics Hum Genet 9: 233-257.
39. Whitelaw N, Whitelaw E (2008) Transgenerational epigenetic inheritance in health and disease. Current opinion in genetics & development 18: 273-279.
40. Pembrey M, Bygren L, Kaati G, Edvinsson S, Northstone K, et al. (2005) Sexspecific, male-line transgenerational responses in humans. European Journal of Human Genetics 14: 159-166.
41. Wu R, Ma C, Casella G (2007) Statistical genetics of quantitative traits: linkage, maps, and QTL Springer Verlag.
42. Churchill G, Doerge R (1994) Empirical threshold values for quantitative trait mapping. Genetics 138: 963-971.
43. Prows D, Hafertepen A, Winterberg A, Gibbons Jr W, Liu C, et al. (2007) Genetic analysis of hyperoxic acute lung injury survival in reciprocal intercross mice. Physiological genomics 30: 271-281.
44. Wilkins J, Haig D (2003) What good is genomic imprinting: the function of parent-specific gene expression. Nature Reviews Genetics 4: 359-368.
45. Cui Y (2007) A statistical framework for genome-wide scanning and testing of imprinted quantitative trait loci. Journal of theoretical biology 244: 115-126.
46. Yang R, Wang X, Wu Z, Prows D, Lin M (2010) Bayesian model selection for characterizing genomic imprinting effects and patterns. Bioinformatics 26:235-241.
47. Jirtle R, Skinner M (2007) Environmental epigenomics and disease susceptibility. Nature Reviews Genetics 8: 253-262.
48. Kaati G, Bygren L, Pembrey M, Sjostrom M (2007) Transgenerational response to nutrition, early life circumstances and longevity. European Journal of Human Genetics 15: 784-790.
49. Cheng Y, Berg A, Wu S, Li Y, Wu R (2009) Computing genetic imprinting expressed by haplotypes. Methods in molecular biology (Clifton, NJ) 573:189-212.
50. Wen S, Wang C, Berg A, Li Y, Chang M, et al. (2009) Modeling genetic imprinting effects of DNA sequences with multilocus polymorphism data. Algorithms for Molecular Biology 4: 11.
51. Schalkwyk L, Meaburn E, Smith R, Dempster E, Jeffries A, et al. (2010) Allelic Skewing of DNA Methylation Is Widespread across the Genome. The American Journal of Human Genetics 86: 196-212.