Multi-omics integration strategies for animal epigenetic studies — A review
2
조회
0
다운로드
1
인용
0
참고문헌
키워드
초록
Genome-wide studies provide considerable insights into the genetic background of animals; however, the inheritance of several heritable factors cannot be elucidated. Epigenetics explains these heritabilities, including those of genes influenced by environmental factors. Knowledge of the mechanisms underlying epigenetics enables understanding the processes of gene regulation through interactions with the environment. Recently developed next-generation sequencing (NGS) technologies help understand the interactional changes in epigenetic mechanisms. There are large sets of NGS data available; however, the integrative data analysis approaches still have limitations with regard to reliably interpreting the epigenetic changes. This review focuses on the epigenetic mechanisms and profiling methods and multi-omics integration methods that can provide comprehensive biological insights in animal genetic studies.
Abstract
Genome-wide studies provide considerable insights into the genetic background of animals; however, the inheritance of several heritable factors cannot be elucidated. Epigenetics explains these heritabilities, including those of genes influenced by environmental factors. Knowledge of the mechanisms underlying epigenetics enables understanding the processes of gene regulation through interactions with the environment. Recently developed next-generation sequencing (NGS) technologies help understand the interactional changes in epigenetic mechanisms. There are large sets of NGS data available; however, the integrative data analysis approaches still have limitations with regard to reliably interpreting the epigenetic changes. This review focuses on the epigenetic mechanisms and profiling methods and multi-omics integration methods that can provide comprehensive biological insights in animal genetic studies.
참고문헌 (104)
- Eichler EE, "Missing heritability and strategies for finding the underlying causes of complex disease", Nat Rev Genet, 11, pp.446~450 (2010)[DOI]
- Egger G, "Epigenetics in human disease and prospects for epigenetic therapy", Nature, 429, pp.457~463 (2004)[DOI]
- Bonasio R, "Molecular signals of epigenetic states", Science, 330, pp.612~616 (2010)[DOI]
- Luger K, "Crystal structure of the nucleosome core particle at 2. 8Å resolution", Nature, 389, pp.251~260 (1997)[DOI]
- Kouzarides T, "Chromatin modifications and their function", Cell, 128, pp.693~705 (2007)[DOI]
- Bannister AJ, "Regulation of chromatin by histone modifications", Cell Res, 21, pp.381~395 (2011)[DOI]
- Sterner DE, "Acetylation of histones and transcription-related factors", Microbiol Mol Biol R, 64, pp.435~459 (2000)[DOI]
- Davie JR, "Control of histone modifications", J Cell Biochem, 75, pp.141~148 (1999)[DOI]
- Roth SY, "Histone acetyltransferases", Annu Rev Biochem, 70, pp.81~120 (2001)[DOI]
- Kundu TK, "Activator-dependent transcription from chromatin in vitro involving targeted histone acetylation by p300", Mol Cell, 6, pp.551~561 (2000)[DOI]
- An W, "Chromatin and disease", pp.351~369 (2007), SpringerVerlag
- Strahl BD, "The language of covalent histone modifications", Nature, 403, pp.41~45 (2000)[DOI]
- Turner BM, "Histone acetylation and an epigenetic code", Bioessays, 22, pp.836~845 (2000)[DOI]
- Jenuwein T, "Translating the histone code", Science, 293, pp.1074~1080 (2001)[DOI]
- Ng SS, "Dynamic protein methylation in chromatin biology", Cell Mol Life Sci, 66, pp.407~ (2009)[DOI]
- Bedford MT, "Protein arginine methylation in mammals : who, what, and why", Mol Cell, 33, pp.1~13 (2009)[DOI]
- Lan F, "Epigenetic regulation : methylation of histone and non-histone proteins", Sci China Ser C Life Sci, 52, pp.311~322 (2009)[DOI]
- Neidhart M, "DNA methylation and complex human disease", pp.2016, Elsevier
- Chen SY, "Histone deacetylase inhibitors : the epigenetic therapeutics that repress hypoxia-inducible factors", J Biomed Biotechnol, 2011 (2011)[DOI]
- Crea F, "Histone modifications, stem cells and prostate cancer", Curr Pharm Design, 20, pp.1687~1697 (2014)[DOI]
- Santos-Rosa H, "Active genes are tri-methylated at K4 of histone H3", Nature, 419, pp.407~411 (2002)[DOI]
- Vermeulen M, "Grasping trimethylation of histone H3 at lysine 4", Epigenomics-Uk, 2, pp.395~406 (2010)[DOI]
- Noma K, "Transitions in distinct histone H3 methylation patterns at the heterochromatin domain boundaries", Science, 293, pp.1150~1155 (2001)[DOI]
- Pinskaya M, "Histone H3 lysine 4 di-methylation A novel mark for transcriptional fidelity", Epigenetics-Us, 4, pp.302~306 (2009)[DOI]
- Hassan MQ, "Non-coding RNAs : Epigenetic regulators of bone development and homeostasis", Bone, 81, pp.746~756 (2015)[DOI]
- Wang KC, "Molecular mechanisms of long noncoding RNAs", Mol Cell, 43, pp.904~914 (2011)[DOI]
- Ghildiyal M, "Small silencing RNAs : an expanding universe", Nat Rev Genet, 10, pp.94~108 (2009)[DOI]
- Costa FF, "Non-coding RNAs, epigenetics and complexity", Gene, 410, pp.9~17 (2008)[DOI]
- Peschansky VJ, "Non-coding RNAs as direct and indirect modulators of epigenetic regulation", EpigeneticsUs, 9, pp.3~12 (2014)[DOI]
- Tang X, "Transcriptomic analysis of mRNAlncRNA-miRNA interactions in hepatocellular carcinoma", Sci Rep, 9, pp.16096~ (2019)[DOI]
- Zhang W, "LncRNA-miRNA interaction prediction through sequence-derived linear neighborhood propagation method with information combination", BMC Genomics, 20, pp.946~ (2019)[DOI]
- Ruvkun G, "Molecular biology. Glimpses of a tiny RNA world", Science, 294, pp.797~799 (2001)[DOI]
- Krol J, "The widespread regulation of microRNA biogenesis, function and decay", Nat Rev Genet, 11, pp.597~610 (2010)[DOI]
- Lewis BP, "Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets", Cell, 120, pp.15~20 (2005)[DOI]
- Bartel DP, "MicroRNAs : target recognition and regulatory functions", Cell, 136, pp.215~233 (2009)[DOI]
- Nikolaus Rajewsky, "microRNA target predictions in animals", Nature Genetics, 38(S6), pp.S8~S13 (2006), Springer Science and Business Media LLC[DOI]
- Lee Y, "The nuclear RNase III Drosha initiates microRNA processing", Nature, 425, pp.415~419 (2003)[DOI]
- Hutvagner G, "A microRNA in a multiple-turnover RNAi enzyme complex", Science, 297, pp.2056~2060 (2002)[DOI]
- Mourelatos Z, "miRNPs : a novel class of ribonucleoproteins containing numerous microRNAs", Genes Dev, 16, pp.720~728 (2002)[DOI]
- Wightman B, "Posttranscriptional regulation of the heterochronic gene lin-14 by lin-4 mediates temporal pattern formation in C. elegans", Cell, 75, pp.855~862 (1993)[DOI]
- Ponting CP, "Evolution and functions of long noncoding RNAs", Cell, 136, pp.629~641 (2009)[DOI]
- Cao X, "Noncoding RNAs in the mammalian central nervous system", Annu Rev Neurosci, 29, pp.77~103 (2006)[DOI]
- Wilusz JE, "Long noncoding RNAs : functional surprises from the RNA world", Genes Dev, 23, pp.1494~1504 (2009)[DOI]
- Jin B, "DNA methylation : superior or subordinate in the epigenetic hierarchy", Genes Cancer, 2, pp.607~617 (2011)[DOI]
- Newell-Price J, "DNA methylation and silencing of gene expression", Trends Endocrinol Metab, 11, pp.142~148 (2000)[DOI]
- Lister R, "Human DNA methylomes at base resolution show widespread epigenomic differences", Nature, 462, pp.315~322 (2009)[DOI]
- Lee J, "Presence of 5-methylcytosine in CpNpG trinucleotides in the human genome", Genomics, 96, pp.67~72 (2010)[DOI]
- Kim KD, "Accessing epigenetic variation in the plant methylome", Brief Funct Genomics, 13, pp.318~327 (2014)[DOI]
- Saxonov S, "A genome-wide analysis of CpG dinucleotides in the human genome distinguishes two distinct classes of promoters", Proc Natl Acad Sci USA, 103, pp.1412~1417 (2006)[DOI]
- Jones PA, "Functions of DNA methylation : islands, start sites, gene bodies and beyond", Nat Rev Genet, 13, pp.484~492 (2012)[DOI]
- Li E, "Chromatin modification and epigenetic reprogramming in mammalian development", Nat Rev Genet, 3, pp.662~673 (2002)[DOI]
- Sadakierska-Chudy A, "A comprehensive view of the epigenetic landscape part I : DNA methylation, passive and active DNA demethylation pathways and histone variants", Neurotox Res, 27, pp.84~97 (2015)[DOI]
- Jin SG, "Genomic mapping of 5-hydroxymethylcytosine in the human brain", Nucleic Acids Res, 39, pp.5015~5024 (2011)[DOI]
- Nestor CE, "Tissue type is a major modifier of the 5-hydroxymethylcytosine content of human genes", Genome Res, 22, pp.467~477 (2012)[DOI]
- Li X, "RNA Sequencing in Schizophrenia", Bioinform Biol Insights, 9, pp.53~60 (2015)[DOI]
- Wang Z, "RNA-Seq : a revolutionary tool for transcriptomics", Nat Rev Genet, 10, pp.57~63 (2009)[DOI]
- Miller MB, "Basic concepts of microarrays and potential applications in clinical microbiology", Clin Microbiol Rev, 22, pp.611~633 (2009)[DOI]
- Russo G, "Advantages and limitations of microarray technology in human cancer", Oncogene, 22, pp.6497~6507 (2003)[DOI]
- Marioni JC, "RNA-seq : an assessment of technical reproducibility and comparison with gene expression arrays", Genome Res, 18, pp.1509~1517 (2008)[DOI]
- Morrissy AS, "Next-generation tag sequencing for cancer gene expression profiling", Genome Res, 19, pp.1825~1835 (2009)[DOI]
- Levin JZ, "Targeted next-generation sequencing of a cancer transcriptome enhances detection of sequence variants and novel fusion transcripts", Genome Biol, 10, pp.R115~ (2009)[DOI]
- Shapiro E, "Single-cell sequencingbased technologies will revolutionize whole-organism science", Nat Rev Genet, 14, pp.618~630 (2013)[DOI]
- Hafner M, "Identification of microRNAs and other small regulatory RNAs using cDNA library sequencing", Methods, 44, pp.3~12 (2008)[DOI]
- Kriukiene E, "DNA unmethylome profiling by covalent capture of CpG sites", Nat Commun, 4, pp.2190~ (2013)[DOI]
- Maunakea AK, "Conserved role of intragenic DNA methylation in regulating alternative promoters", Nature, 466, pp.253~257 (2010)[DOI]
- Cokus SJ, "Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning", Nature, 452, pp.215~219 (2008)[DOI]
- Meissner A, "Reduced representation bisulfite sequencing for comparative high-resolution DNA methylation analysis", Nucleic Acids Res, 33, pp.5868~5877 (2005)[DOI]
- Laurent L, "Dynamic changes in the human methylome during differentiation", Genome Res, 20, pp.320~331 (2010)[DOI]
- Weber M, "Chromosome-wide and promoter-specific analyses identify sites of differential DNA methylation in normal and transformed human cells", Nat Genet, 37, pp.853~862 (2005)[DOI]
- Serre D, "MBD-isolated Genome Sequencing provides a high-throughput and comprehensive survey of DNA methylation in the human genome", Nucleic Acids Res, 38, pp.391~399 (2010)[DOI]
- Yong WS, "Profiling genome-wide DNA methylation", Epigenetics Chromatin, 9, pp.26~ (2016)[DOI]
- Nair SS, "Comparison of methylDNA immunoprecipitation(MeDIP)and methyl-CpG binding domain(MBD)protein capture for genome-wide DNA methylation analysis reveal CpG sequence coverage bias", Epigenetics-Us, 6, pp.34~44 (2011)[DOI]
- Harris RA, "Comparison of sequencingbased methods to profile DNA methylation and identification of monoallelic epigenetic modifications", Nat Biotechnol, 28, pp.1097~1105 (2010)[DOI]
- Bock C, "Quantitative comparison of genome-wide DNA methylation mapping technologies", Nat Biotechnol, 28, pp.1106~1114 (2010)[DOI]
- Greally JM, "DNA methylation protocols", pp.191~207 (2018), Humana Press
- Khulan B, "Comparative isoschizomer profiling of cytosine methylation : The HELP assay", Genome Res, 16, pp.1046~1055 (2006)[DOI]
- Suzuki M, "DNA methylation profiling using HpaII tiny fragment enrichment by ligation-mediated PCR(HELP)", Methods, 52, pp.218~222 (2010)[DOI]
- Suzuki M, "Optimized design and data analysis of tag-based cytosine methylation assays", Genome Biol, 11, pp.R36~ (2010)[DOI]
- Gu H, "Preparation of reduced representation bisulfite sequencing libraries for genome-scale DNA methylation profiling", Nat Protoc, 6, pp.468~481 (2011)[DOI]
- Rakyan VK, "Epigenomewide association studies for common human diseases", Nat Rev Genet, 12, pp.529~541 (2011)[DOI]
- Mohn F, "DNA methylation", pp.55~64 (2009), Humana Press
- Hu Q, "Genome-wide DNA methylation and RNA analysis reveal potential mechanism of resistance to Streptococcus agalactiae in GIFT strain of nile tilapia(Oreochromis niloticus)", J Immunol, 204, pp.3182~3190 (2020)[DOI]
- Guo K, "Genome-wide profiling of DNA methylation and gene expression identifies candidate genes for human diabetic neuropathy", Clin Epigenetics, 12, pp.123~ (2020)[DOI]
- Zhang M, "Genome-wide DNA methylation profiles reveal novel candidate genes associated with meat quality at different age stages in hens", Sci Rep, 7, pp.45564~ (2017)[DOI]
- Kanehisa M, "KEGG : Kyoto encyclopedia of genes and genomes", Nucleic Acids Res, 28, pp.27~30 (2000)[DOI]
- Franceschini A, "STRING v9. 1:protein-protein interaction networks, with increased coverage and integration", Nucleic Acids Res, 41, pp.D808~D815 (2013)[DOI]
- Fabregat A, "Reactome pathway analysis : a high-performance in-memory approach", BMC Bioinformatics, 18, pp.142~ (2017)[DOI]
- Shen J, "Integrated analysis of the gene expression profile and DNA methylation profile of obese patients with type 2diabetes", Mol Med Rep, 17, pp.7636~7644 (2018)[DOI]
- Wilson S, "A network of epigenomic and transcriptional cooperation encompassing an epigenomic master regulator in cancer", NPJ Syst Biol Appl, 4, pp.24~ (2018)[DOI]
- Kim JM, "Integrated transcriptomes throughout swine oestrous cycle reveal dynamic changes in reproductive tissues interacting networks", Sci Rep, 8, pp.5436~ (2018)[DOI]
- Lim B, "Integrated time-serial transcriptome networks reveal common innate and tissue-specific adaptive immune responses to PRRSV infection", Vet Res, 51, pp.128~ (2020)[DOI]
- Lu Y, "Comparative transcriptomic and metabolomic analysis of fenofibrate and fish oil treatments in mice", Physiol Genomics, 43, pp.1307~1318 (2011)[DOI]
- Audrey P Gasch, "Exploring the conditional coregulation of yeast gene expression through fuzzy k-means clustering", Genome Biology, 3(11) (2002), Springer Science and Business Media LLC[DOI]
- Animesh Acharjee, "Integration of multi-omics data for prediction of phenotypic traits using random forest", BMC Bioinformatics, 17(S5), pp.180~ (2016), Springer Science and Business Media LLC[DOI]
- Meng C, "Dimension reduction techniques for the integrative analysis of multi-omics data", Brief Bioinform, 17, pp.628~641 (2016)[DOI]
- Meng C, "A multivariate approach to the integration of multi-omics datasets", BMC Bioinformatics, 15, pp.162~ (2014)[DOI]
- Dennis G Jr, "DAVID : Database for annotation, visualization, and integrated discovery", Genome Biol, 4, pp.R60~ (2003)[DOI]
- Voigt A, "Assessment of weighted topological overlap(wTO)to improve fidelity of gene co-expression networks", BMC Bioinformatics, 20, pp.58~ (2019)[DOI]
- Lipshutz RJ, "High density synthetic oligonucleotide arrays", Nat Genet, 21, pp.20~24 (1999)[DOI]
- Xu W, "Integrative analysis of DNA methylation and gene expression identified cervical cancerspecific diagnostic biomarkers", Signal Transduct Target Ther, 4, pp.55~ (2019)[DOI]
- Silverbush D, "Simultaneous integration of multi-omics data improves the identification of cancer driver modules", Cell Syst, 8, pp.456~466 (2019)[DOI]
- Moreno-Estrada A, "Reconstructing the population genetic history of the Caribbean", PLoS Genet, 9, pp.e1003925~ (2013)[DOI]
- Wang L, "Integrating multi-omics for uncovering the architecture of cross-talking pathways in breast cancer", PLoS One, 9, pp.e104282~ (2014)[DOI]
- Chella Krishnan K, "Integration of multi-omics data from mouse diversity panel highlights mitochondrial dysfunction in non-alcoholic fatty liver disease", Cell Syst, 6, pp.103~115 (2018)[DOI]
