title: Analysis of a four generation family reveals the widespread sequence-dependent maintenance of allelic DNA methylation in somatic and germ cells.
abstract: Differential methylation of the homologous chromosomes, a well-known mechanism leading to genomic imprinting and X-chromosome inactivation, is widely reported at the non-imprinted regions on autosomes. To evaluate the transgenerational DNA methylation patterns in human, we analyzed the DNA methylomes of somatic and germ cells in a four-generation family. We found that allelic asymmetry of DNA methylation was pervasive at the non-imprinted loci and was likely regulated by cis-acting genetic variants. We also observed that the allelic methylation patterns for the vast majority of the cis-regulated loci were shared between the somatic and germ cells from the same individual. These results demonstrated the interaction between genetic and epigenetic variations and suggested the possibility of widespread sequence-dependent transmission of DNA methylation during spermatogenesis.
authors.affiliation: Shenzhen Key Laboratory of Genitourinary Tumor, National-Regional Key Engineering Technology Laboratory for Clinical Application of Cancer Genomics, Shenzhen Second People's Hospital, the First Affiliated Hospital of Shenzhen University, Shenzhen 518035, China.|Guangdong and Shenzhen Key Laboratory of Male Reproductive Medicine and Genetics, Institute of Urology, Peking University Shenzhen Hospital, Shenzhen PKU-HKUST Medical Center, Shenzhen 518036, China.
authors.forename: Aifa
authors.initials: A
authors.lastname: Tang
authors.affiliation: Shenzhen Key Laboratory of Genitourinary Tumor, National-Regional Key Engineering Technology Laboratory for Clinical Application of Cancer Genomics, Shenzhen Second People's Hospital, the First Affiliated Hospital of Shenzhen University, Shenzhen 518035, China.|The Genome Institute, Washington University in St Louis, Missouri 63108, USA.
authors.forename: Yi
authors.initials: Y
authors.lastname: Huang
authors.affiliation: Shenzhen Key Laboratory of Genitourinary Tumor, National-Regional Key Engineering Technology Laboratory for Clinical Application of Cancer Genomics, Shenzhen Second People's Hospital, the First Affiliated Hospital of Shenzhen University, Shenzhen 518035, China.|Guangdong and Shenzhen Key Laboratory of Male Reproductive Medicine and Genetics, Institute of Urology, Peking University Shenzhen Hospital, Shenzhen PKU-HKUST Medical Center, Shenzhen 518036, China.
authors.forename: Zesong
authors.initials: Z
authors.lastname: Li
authors.affiliation: Luohu People's Hospital, Shezhen 518001, China.
authors.forename: Shengqing
authors.initials: S
authors.lastname: Wan
authors.affiliation: Shenzhen Key Laboratory of Genitourinary Tumor, National-Regional Key Engineering Technology Laboratory for Clinical Application of Cancer Genomics, Shenzhen Second People's Hospital, the First Affiliated Hospital of Shenzhen University, Shenzhen 518035, China.|Guangdong and Shenzhen Key Laboratory of Male Reproductive Medicine and Genetics, Institute of Urology, Peking University Shenzhen Hospital, Shenzhen PKU-HKUST Medical Center, Shenzhen 518036, China.
authors.forename: Lisha
authors.initials: L
authors.lastname: Mou
authors.affiliation: BGI-Shenzhen, Shenzhen 518083, China.
authors.forename: Guangliang
authors.initials: G
authors.lastname: Yin
authors.affiliation: BGI-Shenzhen, Shenzhen 518083, China.
authors.forename: Ning
authors.initials: N
authors.lastname: Li
authors.affiliation: Guangdong and Shenzhen Key Laboratory of Male Reproductive Medicine and Genetics, Institute of Urology, Peking University Shenzhen Hospital, Shenzhen PKU-HKUST Medical Center, Shenzhen 518036, China.
authors.forename: Jun
authors.initials: J
authors.lastname: Xie
authors.affiliation: BGI-Shenzhen, Shenzhen 518083, China.
authors.forename: Yudong
authors.initials: Y
authors.lastname: Xia
authors.affiliation: Guangdong and Shenzhen Key Laboratory of Male Reproductive Medicine and Genetics, Institute of Urology, Peking University Shenzhen Hospital, Shenzhen PKU-HKUST Medical Center, Shenzhen 518036, China.
authors.forename: Xianxin
authors.initials: X
authors.lastname: Li
authors.affiliation: Shenzhen Key Laboratory of Genitourinary Tumor, National-Regional Key Engineering Technology Laboratory for Clinical Application of Cancer Genomics, Shenzhen Second People's Hospital, the First Affiliated Hospital of Shenzhen University, Shenzhen 518035, China.
authors.forename: Liya
authors.initials: L
authors.lastname: Luo
authors.affiliation: Guangdong and Shenzhen Key Laboratory of Male Reproductive Medicine and Genetics, Institute of Urology, Peking University Shenzhen Hospital, Shenzhen PKU-HKUST Medical Center, Shenzhen 518036, China.
authors.forename: Junwen
authors.initials: J
authors.lastname: Zhang
authors.affiliation: Guangdong and Shenzhen Key Laboratory of Male Reproductive Medicine and Genetics, Institute of Urology, Peking University Shenzhen Hospital, Shenzhen PKU-HKUST Medical Center, Shenzhen 518036, China.
authors.forename: Shen
authors.initials: S
authors.lastname: Chen
authors.affiliation: Shenzhen Key Laboratory of Genitourinary Tumor, National-Regional Key Engineering Technology Laboratory for Clinical Application of Cancer Genomics, Shenzhen Second People's Hospital, the First Affiliated Hospital of Shenzhen University, Shenzhen 518035, China.|The Genome Institute, Washington University in St Louis, Missouri 63108, USA.|Luohu People's Hospital, Shezhen 518001, China.
authors.forename: Song
authors.initials: S
authors.lastname: Wu
authors.affiliation: BGI-Shenzhen, Shenzhen 518083, China.
authors.forename: Jihua
authors.initials: J
authors.lastname: Sun
authors.affiliation: Shenzhen Key Laboratory of Genitourinary Tumor, National-Regional Key Engineering Technology Laboratory for Clinical Application of Cancer Genomics, Shenzhen Second People's Hospital, the First Affiliated Hospital of Shenzhen University, Shenzhen 518035, China.
authors.forename: Xiaojuan
authors.initials: X
authors.lastname: Sun
authors.affiliation: Guangdong and Shenzhen Key Laboratory of Male Reproductive Medicine and Genetics, Institute of Urology, Peking University Shenzhen Hospital, Shenzhen PKU-HKUST Medical Center, Shenzhen 518036, China.
authors.forename: Zhimao
authors.initials: Z
authors.lastname: Jiang
authors.affiliation: Guangdong and Shenzhen Key Laboratory of Male Reproductive Medicine and Genetics, Institute of Urology, Peking University Shenzhen Hospital, Shenzhen PKU-HKUST Medical Center, Shenzhen 518036, China.
authors.forename: Jing
authors.initials: J
authors.lastname: Chen
authors.affiliation: BGI-Shenzhen, Shenzhen 518083, China.
authors.forename: Yingrui
authors.initials: Y
authors.lastname: Li
authors.affiliation: BGI-Shenzhen, Shenzhen 518083, China.
authors.forename: Jian
authors.initials: J
authors.lastname: Wang
authors.affiliation: BGI-Shenzhen, Shenzhen 518083, China.
authors.forename: Jun
authors.initials: J
authors.lastname: Wang
authors.affiliation: Shenzhen Key Laboratory of Genitourinary Tumor, National-Regional Key Engineering Technology Laboratory for Clinical Application of Cancer Genomics, Shenzhen Second People's Hospital, the First Affiliated Hospital of Shenzhen University, Shenzhen 518035, China.
authors.forename: Zhiming
authors.initials: Z
authors.lastname: Cai
authors.affiliation: Guangdong and Shenzhen Key Laboratory of Male Reproductive Medicine and Genetics, Institute of Urology, Peking University Shenzhen Hospital, Shenzhen PKU-HKUST Medical Center, Shenzhen 518036, China.
authors.forename: Yaoting
authors.initials: Y
authors.lastname: Gui
mesh_terms: D000483:Alleles; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods; D019175:DNA Methylation; D044127:Epigenesis, Genetic; D005190:Family; D056426:Genetic Loci; D005838:Genotype; D005854:Germ Cells / Q000378:metabolism*; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D008297:Male; D058977:Molecular Sequence Annotation; D010375:Pedigree; D020641:Polymorphism, Single Nucleotide; D015203:Reproducibility of Results; D013094:Spermatozoa / Q000378:metabolism; D049951:X Chromosome Inactivation / Q000235:genetics