Abstract
Epigenetics is an upcoming field that studies the gene regulation of mitotically heritable genes which change the physiology of cells without altering the DNA sequence. Various epigenetic elements such as modification of histone proteins, methylation of DNA, chromatin modeling, and RNA-mediating silencing influence the regulation of genes at many levels, which leads to diseases such as cancer. All of these factors modulate gene expression in a tissue-specific manner. Bioinformatics is a successful approach in the field of molecular biology for studying epigenomics data. To generate these epigenomic data which can be analyzed using various bioinformatics tools and software, a variety of technologies are being used by researchers. Many biological databases which store a huge amount of information related to the modifications due to epigenetics are available online. With the help of these data, we can identify key target genes that can be manipulated to achieve some resistance against diseases caused by epigenetic factors.
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References
Arand J et al (2012) In vivo control of CpG and non-CpG DNA methylation by DNA methyltransferases. PLoS Genet 8:e1002750
Bannister AJ, Kouzarides T (2011) Regulation of chromatin by histone modifications. Cell Res 21:381–395
Berger SL (2002) Histone modifications in transcriptional regulation. Curr Opin Genet Dev 12:142–148
Bird A (2002) DNA methylation patterns and epigenetic memory. Genes Dev 16:6–21
Bowman GD, Poirier MG (2014) Post-translational modifications of histones that influence nucleosome dynamics. Chem Rev 115:2274–2295
Brunet AS, Berger L (2014) Epigenetics of aging and aging-related disease. J Gerontol A Biol Sci Med Sci 69:S17–S20
Calvanese V et al (2009) The role of epigenetics in aging and age-related diseases. Ageing Res Rev 8:268–276
Carey MF et al (2009) Chromatin immunoprecipitation (ChIP). Cold Spring Harb Protoc,pdb prot5279
Deaton AM, Bird A (2011) CpG islands and the regulation of transcription. Genes Dev 25:1010–1022
Dupont C et al (2009) Epigenetics: definition, mechanisms and clinical perspective. Semin Reprod Med 27:351–357
Eberharter A, Becker PB (2002) Histone acetylation: a switch between repressive and permissive chromatin. EMBO Rep 3:224–229
Egger G et al (2004) Epigenetics in human disease and prospects for epigenetic therapy. Nature 429:457–463
Ehrich M et al (2007) A new method for accurate assessment of DNA quality after bisulfite treatment. Nucleic Acids Res 35:e29
Furey TS (2012) ChIP-seq and beyond: new and improved methodologies to detect and characterize protein-DNA interactions. Nat Rev Genet 13:840–852
Gangaraju VK, Bartholomew B (2007) Mechanisms of ATP dependent chromatin remodeling. Mutat Res/Fundam Mol Mech Mutagen 618:3–17
Hackett JA, Surani MA (2013) DNA methylation dynamics during the mammalian life cycle. Philos Trans R Soc Lond Ser B Biol Sci 368:20110328
Hirst M, Marra MA (2010) Next generation sequencing based approaches to epigenomics. Brief Funct Genomics 9:455–465
Holoch D, Moazed D (2015) RNA-mediated epigenetic regulation of gene expression. Nat Rev Genet 16:71–84
Jaenisch R, Bird A (2003) Epigenetic regulation of gene expression: how the genome integrates intrinsic and environmental signals. Nat Genet 33:245–254
Jiang YH et al (2004) Epigenetics and human disease. Annu Rev Genomics Hum Genet 5:479–510
Jones PA (2012) Functions of DNA methylation: islands, start sites, gene bodies and beyond. Nat Rev Genet 13:484–492
Jothi R et al (2008) Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data. Nucleic Acids Res 36:5221–5231
Kadonaga JT (2004) Regulation of RNA polymerase II transcription by sequence-specific DNA binding factors. Cell 116:247–257
Lee TI et al (2006) Chromatin immunoprecipitation and microarray-based analysis of protein location. Nat Protoc 1:729–748
Lim SJ et al (2010) Computational epigenetics: the new scientific paradigm. Bioinformation 4:331–337
Patterson K et al (2011) DNA methylation: bisulphite modification and analysis. J Vis Exp 56:3170
Villeneuve LM, Natarajan R (2010) The role of epigenetics in the pathology of diabetic complications. Am J Physiol Renal Physiol 299:F14–F25
Visel A et al (2009) ChIP-seq accurately predicts tissue-specific activity of enhancers. Nature 457:854–858
Wilkinson KA, Henley JM (2010) Mechanisms, regulation and consequences of protein SUMOylation. Biochem J 428:133–145
Wolffe AP (1998) Packaging principle: how DNA methylation and histone acetylation control the transcriptional activity of chromatin. J Exp Zool 282:239–244
Wolffe AP, Matzke MA (1999) Epigenetics: regulation through repression. Science 286:481–486
Yang HH, Lee MP (2004) Application of bioinformatics in cancer epigenetics. Ann N Y Acad Sci 1020:67–76
Yang Z, Wu J (2007) MicroRNAs and regenerative medicine. DNA Cell Biol 26:257–264
Zou C, Mallampalli RK (2014) Regulation of histone modifying enzymes by the ubiquitin-proteasome system. Biochim Biophys Acta 1843:694–702
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The authors are grateful to the Sam Higginbottom University of Agriculture, Technology & Sciences, Allahabad, India, for providing the facilities and support to complete the present research work.
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Gautam, B., Goswami, K., Mishra, N.S., Wadhwa, G., Singh, S. (2018). The Role of Bioinformatics in Epigenetics. In: Wadhwa, G., Shanmughavel, P., Singh, A., Bellare, J. (eds) Current trends in Bioinformatics: An Insight. Springer, Singapore. https://doi.org/10.1007/978-981-10-7483-7_3
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DOI: https://doi.org/10.1007/978-981-10-7483-7_3
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