287
Views
0
CrossRef citations to date
0
Altmetric
Research Article

Development of a Method for Identifying and Functionally Analyzing Allele-Specific DNA Methylation Based on BS-Seq Data

, , , , , , , & show all
Pages 1679-1692 | Received 22 Jan 2019, Accepted 10 Oct 2019, Published online: 08 Nov 2019

References

  • Luedi PP , DietrichFS , WeidmanJR , BoskoJM , JirtleRL , HarteminkAJ. Computational and experimental identification of novel human imprinted genes. Genome Res.17(12), 1723–1730 (2007).
  • Lim DH , MaherER. Genomic imprinting syndromes and cancer. Adv. Genet.70, 145–175 (2010).
  • Fang F , HodgesE , MolaroA , DeanM , HannonGJ , SmithAD. Genomic landscape of human allele-specific DNA methylation. Proc. Natl Acad. Sci. USA109(19), 7332–7337 (2012).
  • Bartolomei MS , WebberAL , BrunkowME , TilghmanSM. Epigenetic mechanisms underlying the imprinting of the mouse H19 gene. Genes Dev.7(9), 1663–1673 (1993).
  • Ferguson-Smith AC , SasakiH , CattanachBM , SuraniMA. Parental-origin-specific epigenetic modification of the mouse H19 gene. Nature362(6422), 751–755 (1993).
  • Hu B , JiY , XuY , TingAH. Screening for SNPs with allele-specific methylation based on next-generation sequencing data. Stat. Biosci.5(1), 179–197 (2013).
  • Prendergast JG , TongP , HayDC , FarringtonSM , SempleCA. A genome-wide screen in human embryonic stem cells reveals novel sites of allele-specific histone modification associated with known disease loci. Epigenet. Chromatin5(1), 6 (2012).
  • Stelzer Y , RonenD , BockC , BoyleP , MeissnerA , BenvenistyN. Identification of novel imprinted differentially methylated regions by global analysis of human-parthenogenetic-induced pluripotent stem cells. Stem Cell Rep.1(1), 79–89 (2013).
  • Peng Q , EckerJR. Detection of allele-specific methylation through a generalized heterogeneous epigenome model. Bioinformatics28(12), i163–171 (2012).
  • Shoemaker R , DengJ , WangW , ZhangK. Allele-specific methylation is prevalent and is contributed by CpG-SNPs in the human genome. Genome Res.20(7), 883–889 (2010).
  • Liu Y , SiegmundKD , LairdPW , BermanBP. Bis-SNP: combined DNA methylation and SNP calling for Bisulfite-seq data. Genome Biol.13(7), R61 (2012).
  • Li R , LiY , FangXet al. SNP detection for massively parallel whole-genome resequencing. Genome Res.19(6), 1124–1132 (2009).
  • Li H , HandsakerB , WysokerAet al. The sequence alignment/map format and SAMtools. Bioinformatics25(16), 2078–2079 (2009).
  • Depristo MA , BanksE , PoplinRet al. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat. Genet.43(5), 491–498 (2011).
  • Zhao Z , BoerwinkleE. Neighboring-nucleotide effects on single nucleotide polymorphisms: a study of 2.6 million polymorphisms across the human genome. Genome Res.12(11), 1679–1686 (2002).
  • Cancer Genome Atlas Research N , WeinsteinJN , CollissonEAet al.The Cancer Genome Atlas Pan-Cancer analysis project. Nat. Genet.45(10), 1113–1120 (2013).
  • Krueger F , AndrewsSR. Bismark: a flexible aligner and methylation caller for bisulfite-Seq applications. Bioinformatics27(11), 1571–1572 (2011).
  • Li H , DurbinR. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics25(14), 1754–1760 (2009).
  • Li D , ZhangB , XingX , WangT. Combining MeDIP-seq and MRE-seq to investigate genome-wide CpG methylation. Methods72, 29–40 (2015).
  • Elliott G , HongC , XingXet al. Intermediate DNA methylation is a conserved signature of genome regulation. Nat. Commun.6, 6363 (2015).
  • Huang Da W , ShermanBT , LempickiRA. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat. Protoc.4(1), 44–57 (2009).
  • Lister R , PelizzolaM , DowenRHet al. Human DNA methylomes at base resolution show widespread epigenomic differences. Nature462(7271), 315–322 (2009).
  • Thorvaldsdottir H , RobinsonJT , MesirovJP. Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Brief Bioinform.14(2), 178–192 (2013).
  • Wei Y , SuJ , LiuHet al. MetaImprint: an information repository of mammalian imprinted genes. Development141(12), 2516–2523 (2014).
  • Gibbs JR , VanDer Brug MP , HernandezDGet al. Abundant quantitative trait loci exist for DNA methylation and gene expression in human brain. PLoS Genet.6(5), e1000952 (2010).
  • Schilling E , ElChartouni C , RehliM. Allele-specific DNA methylation in mouse strains is mainly determined by cis-acting sequences. Genome Res.19(11), 2028–2035 (2009).
  • Zhang D , ChengL , BadnerJAet al. Genetic control of individual differences in gene-specific methylation in human brain. Am. J. Hum. Genet.86(3), 411–419 (2010).
  • Kerkel K , SpadolaA , YuanEet al. Genomic surveys by methylation-sensitive SNP analysis identify sequence-dependent allele-specific DNA methylation. Nat. Genet.40(7), 904–908 (2008).
  • Zhang Y , RohdeC , ReinhardtR , Voelcker-RehageC , JeltschA. Non-imprinted allele-specific DNA methylation on human autosomes. Genome Biol.10(12), R138 (2009).
  • Xie W , BarrCL , KimAet al. Base-resolution analyses of sequence and parent-of-origin dependent DNA methylation in the mouse genome. Cell148(4), 816–831 (2012).
  • Gertz J , VarleyKE , ReddyTEet al. Analysis of DNA methylation in a three-generation family reveals widespread genetic influence on epigenetic regulation. PLoS Genet.7(8), e1002228 (2011).

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.