Analysis of a four generation family reveals the widespread sequence-dependent maintenance of allelic DNA methylation in somatic and germ cells

Scientific Reports

Volumn 6, Issue , 2016, Pages

  Tang, Aifa ^a,b   Huang, Yi ^a,c   Li, Zesong ^a,b   Wan, Shengqing ^d   Mou, Lisha ^a,b   Yin, Guangliang ^e   Li, Ning ^e   Xie, Jun ^b   Xia, Yudong ^e   Li, Xianxin ^b   Luo, Liya ^a   Zhang, Junwen ^b   Chen, Shen ^b   Wu, Song ^a,c,d   Sun, Jihua ^e   Sun, Xiaojuan ^a   Jiang, Zhimao ^b   Chen, Jing ^b   Li, Yingrui ^e   Wang, Jian ^e   Wang, Jun ^e   Cai, Zhiming ^a   Gui, Yaoting ^b   more..

^a THE FIRST AFFILIATED HOSPITAL OF SHENZHEN UNIVERSITY   (China)

^b PEKING UNIVERSITY SHENZHEN HOSPITAL   (China)

^c WASHINGTON UNIVERSITY   (United States)

^d Department of Respiratory Diseases   (China)

^e BGI SHENZHEN   (China)

Author keywords

[No Author keywords available]

Indexed keywords

DNA METHYLATION; EPIGENETICS; FAMILY; FAMILY STUDY; GENETIC VARIABILITY; GERM CELL; HUMAN; SPERMATOGENESIS; ALLELE; BIOLOGY; CLUSTER ANALYSIS; GENE LOCUS; GENETIC EPIGENESIS; GENETICS; GENOTYPE; HIGH THROUGHPUT SEQUENCING; MALE; METABOLISM; MOLECULAR GENETICS; PEDIGREE; PROCEDURES; REPRODUCIBILITY; SINGLE NUCLEOTIDE POLYMORPHISM; SPERMATOZOON; X CHROMOSOME INACTIVATION;

ALLELES; CLUSTER ANALYSIS; COMPUTATIONAL BIOLOGY; DNA METHYLATION; EPIGENESIS, GENETIC; FAMILY; GENETIC LOCI; GENOTYPE; GERM CELLS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; MALE; MOLECULAR SEQUENCE ANNOTATION; PEDIGREE; POLYMORPHISM, SINGLE NUCLEOTIDE; REPRODUCIBILITY OF RESULTS; SPERMATOZOA; X CHROMOSOME INACTIVATION;

EID: 84954503464     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep19260     Document Type: Article

References (23)

1. Robertson, K. D. DNA methylation and human disease. Nat Rev Genet 6, 597-610 (2005).
2. Kelsey, G. DNA methylation: a new twist in the tail. Cell Res 21, 1155-6 (2011).
3. Smith, Z. D. and Meissner, A. DNA methylation: roles in mammalian development. Nat Rev Genet 14, 204-20 (2013).
4. Kerkel, K. et al. Genomic surveys by methylation-sensitive SNP analysis identify sequence-dependent allele-specific DNA methylation. Nat Genet 40, 904-8 (2008).
5. Schalkwyk, L. C. et al. Allelic skewing of DNA methylation is widespread across the genome. Am J Hum Genet 86, 196-212 (2010).
6. Choufani, S. et al. A novel approach identifies new differentially methylated regions (DMRs) associated with imprinted genes. Genome Res 21, 465-76 (2011).
7. Li, H., Ruan, J. and Durbin, R. Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res 18, 1851-8 (2008).
8. Bock, C. et al. Quantitative comparison of genome-wide DNA methylation mapping technologies. Nat Biotechnol 28, 1106-14 (2010).
9. Weber, M. et al. Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome. Nat Genet 39, 457-66 (2007).
10. Tycko, B. Allele-specific DNA methylation: beyond imprinting. Hum Mol Genet 19, R210-20 (2010).
11. Schilling, E., El Chartouni, C. and Rehli, M. Allele-specific DNA methylation in mouse strains is mainly determined by cis-acting sequences. Genome Res 19, 2028-35 (2009).
12. Gibbs, J. R. et al. Abundant quantitative trait loci exist for DNA methylation and gene expression in human brain. PLoS Genet 6, e1000952 (2010).
13. Gertz, J. et al. Analysis of DNA methylation in a three-generation family reveals widespread genetic influence on epigenetic regulation. PLoS Genet 7, e1002228 (2011).
14. Shoemaker, R., Deng, J., Wang, W. and Zhang, K. Allele-specific methylation is prevalent and is contributed by CpG-SNPs in the human genome. Genome Res 20, 883-9 (2010).
15. Bartolomei, M. S. Genomic imprinting: employing and avoiding epigenetic processes. Genes Dev 23, 2124-33 (2009).
16. Feng, S., Jacobsen, S. E. and Reik, W. Epigenetic reprogramming in plant and animal development. Science 330, 622-7 (2010).
17. Yang, Y. et al. The epigenetically-regulated miR-663 targets H-ras in K-562 cells. FEBS J 280, 5109-17 (2013).
18. Yan-Fang, T. et al. The promoter of miR-663 is hypermethylated in Chinese pediatric acute myeloid leukemia (AML). BMC Med Genet 14, 74 (2013).
19. Liu, Z. Y., Zhang, G. L., Wang, M. M., Xiong, Y. N. and Cui, H. Q. MicroRNA-663 targets TGFB1 and regulates lung cancer proliferation. Asian Pac J Cancer Prev 12, 2819-23 (2011).
20. Li, Y. et al. The DNA methylome of human peripheral blood mononuclear cells. PLoS Biol 8, e1000533 (2010).
21. Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078-9 (2009).
22. Li, L. C. and Dahiya, R. MethPrimer: designing primers for methylation PCRs. Bioinformatics 18, 1427-31 (2002).
23. Rohde, C., Zhang, Y., Reinhardt, R. and Jeltsch, A. BISMA-fast and accurate bisulfite sequencing data analysis of individual clones from unique and repetitive sequences. BMC Bioinformatics 11, 230 (2010).