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Diversity of Human CpG Islands

  • Isabel Mendizabal
  • Soojin V. YiEmail author
Reference work entry

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.

Keywords

CpG island CGI CpG island identification DNA methylation Ttranscriptional regulation Sequence-based algorithm Epigenomics Unmethylated sequences Transcription initiation Active chromatin Tissue-specific regulation Differentially methylated regions Whole- genome bisulfite sequencing 

List of 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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Copyright information

© Springer Nature Switzerland AG 2019

Authors and Affiliations

  1. 1.School of Biological SciencesGeorgia Institute of TechnologyAtlantaUSA
  2. 2.Department of Genetics, Physical Anthropology and Animal PhysiologyUniversity of the Basque Country UPV/EHULeioaSpain

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