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Diversity of Human CpG Islands

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Handbook of Nutrition, Diet, and Epigenetics

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Abstract

CpG islands (CGIs) are the most extensively studied regulatory features in mammalian genomes. Identified first in the early 1980s using methylation-sensitive restriction enzymes, CpG islands were defined as clusters of unmethylated CpG dinucleotides. Compared to the highly methylated nature of the bulk human genome, CGIs constitute as much as 1% of the DNA of all types of tissues including embryonic, somatic, and germ lines. Earlier analyses revealed strong associations between CGIs and transcription start sites, rendering researchers to use CGIs as markers for genes. Utilizing the particular sequence-nature of CGIs, many methods to identify CGIs from genome sequences have been developed throughout the years. These methods were highly useful to guide researchers to focus on specific regions of the genome. With the recent advent of efficient experimental tools to analyze DNA methylation, CpG island research has entered a new era. Newly accumulating data on genome-wide DNA methylation allowed researchers to identify clusters of unmethylated CpGs, regardless of their sequence characteristics. Efforts on this end have produced comprehensive, experimentally verified catalogues of “epigenetic” CpG islands from the human genome. Notably, many epigenetic CpG islands that were previously not detected by sequence-based methods are now known. Epigenetically determined CpG islands reveal tremendous insights into the molecular, functional, and evolutionary diversity of these elements as well as how they affect key regulatory processes of the human genome.

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Abbreviations

CAP:

CXXC affinity purification

CGI:

CpG island

CpG O/E:

Observed/expected CpG ratio

CpG:

Cytosine-phosphate-guanine

GC:

Guanine-cytosine

MeDIP-chip:

Methylated DNA immunoprecipitation chip

MeDIP-seq:

Methylated DNA immunoprecipitation sequencing

PCR:

Polymerase chain reaction

RRBS:

Reduced representation bisulfite sequencing

SMRT:

Single-molecule real-time sequencing

TSS:

Transcription start site

UCSC:

University of California, Santa Cruz

WGBS:

Whole-genome bisulfite sequencing

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Authors and Affiliations

  1. School of Biological Sciences, Georgia Institute of Technology, 950 Atlantic Drive, Atlanta, GA, 30332, USA

    Isabel Mendizabal & Soojin V. Yi

  2. Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country UPV/EHU, 48940, Leioa, Spain

    Isabel Mendizabal

Authors
  1. Isabel Mendizabal
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  2. Soojin V. Yi
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Correspondence to Soojin V. Yi .

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Editors and Affiliations

  1. c/o Editorial Board 978-0-387-78665 , Heidelberg, Baden-Württemberg, Germany

    Vinood Patel

  2. Kings College , London, United Kingdom

    Victor Preedy

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Mendizabal, I., Yi, S. (2017). Diversity of Human CpG Islands. In: Patel, V., Preedy, V. (eds) Handbook of Nutrition, Diet, and Epigenetics. Springer, Cham. https://doi.org/10.1007/978-3-319-31143-2_67-1

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  • DOI: https://doi.org/10.1007/978-3-319-31143-2_67-1

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  • Print ISBN: 978-3-319-31143-2

  • Online ISBN: 978-3-319-31143-2

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