Advances in Next Generation Sequencing Technologies and Cancer Epigenomics

Abstract

Epigenetics refers to the heritable yet reversible chemical modifications to the deoxyribonucleic acid (DNA) sequence and histone protein such as DNA methylation and histone modification resulting in modulation of gene expression without direct alteration to the DNA sequence itself. It also includes post‐transcriptional regulation of protein coding ribonucleic acids (RNAs) by microRNAs (miRNAs), which subsequently affect protein translation. Although the development of microarray technologies has transformed the interrogation of epigenetics from targeted regions to whole epigenome scale, next generation sequencing has brought another wave of technological revolution that allows a more thorough investigation of the epigenome at a single nucleotide resolution. Since the arrival of next generation sequencing technologies, several studies have applied next generation sequencing‐based methods to dissect cancer epigenome, such as whole methylome sequencing of one colon cancer and adjacent normal as well as small RNA sequencing in several cancer tissues for discovery of novel miRNAs. In addition to individual studies, next‐generation sequencing technologies have enabled international consortia such as NIH Roadmap Epigenomics Programme and the International Human Epigenome Consortium to perform in‐depth investigation of epigenetics in a wide range of tissues. These international consortia ensures the standardisation of experimental methods across different groups to generate high quality data that can be compared and integrated into larger epigenomic datasets. The completion of these projects will undoubtedly contribute to significant advances in the knowledge and understanding of the roles of epigenetics underlying human diseases.

Key Concepts:

  • Epigenetics has advanced considerably after the arrival of whole genome interrogation tools such as microarray and next generation sequencing technologies.

  • Epigenetic aberration plays an equally important role as with genetic aberration in contributing to diseases such as cancers.

  • Next generation sequencing‐based methods permit a thorough investigation of DNA methylation, histone modifications and miRNAs throughout the whole genome at a single nucleotide resolution.

  • Sequencing of the entire methylome in embryonic stem cells has unravelled non‐CG methylation patterns, which would not have been discovered using microarrays focus primarily on CpG sites.

  • Sequencing of the first cancer methylome in colon cancer has also documented substantial differences in DNA methylation patterns between cancer and normal tissue.

  • ChIP‐seq has been used to compare histone modification patterns in human breast cancer and normal mammary epithelial cell lines revealing that H3K4me3 and H3K9/14ac were both highly enriched in promoter regions, whereas H3K4me1 was more broadly distributed.

  • The production of a large number of sequence reads by NGS technologies has also allowed deep sequencing of noncoding RNAs (including miRNAs) or a more comprehensive analysis of RNA species.

  • The arrival of NGS technologies has brought a paradigm shift in the approaches used for epigenomics studies, as well as improving our understanding of biology and diseases.

  • As TGS technologies mature, the investigation of cancer epigenomics will likely be provided with a greater depth and breadth of analysis through single DNA molecule sequencing.

  • Although NGS has brought new opportunities to the study of epigenetics, challenges ranging from technical difficulties to bioinformatics analysis must be noted.

Keywords: next generation sequencing technologies; epigenetics; DNA methylation; histone modification; microRNA; cancer epigenome; whole genome bisulfite sequencing; chromatin immunoprecipitation sequencing; small RNA sequencing; microarray

Figure 1.

Epigenetics refers to the heritable and yet reversible chemical modifications to the chromatin structure (e.g. modification of histone tails that alter chromatin condensation and thus accessibility of transcription binding proteins) and deoxyribonucleic acid (DNA) sequence (e.g. addition of a methyl group to CpG sites) that result in modulation of gene expression levels without a direct alteration to the DNA sequence itself. In addition, gene expression levels can also be modulated post‐transcriptionally through microRNA (miRNA) mediated mechanisms that lead to degradation or translational repression of messenger ribonucleic acid (mRNA). These mechanisms interact with transcription factors and other DNA‐binding proteins to regulate gene‐expression patterns inherited from cell to cell. These epigenetic mechanisms play a critical role in the normal stages of cellular developmental processes, and thus epigenetic abnormalities have been linked to a wide range of diseases. Reprinted by permission from Macmillan Publishers Ltd: Moving AHEAD with an international Human epigenome project. Nature, 2008; 454 (7205): 711–715.

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Further Reading

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Ng, Hong Kiat, Ku, Chee Seng, Wu, Mengchu, Iacopetta, Barry, and Soong, Richie(Jun 2012) Advances in Next Generation Sequencing Technologies and Cancer Epigenomics. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0023507]