Diversity of Human CpG Islands

Handbook of Nutrition, Diet, and Epigenetics pp 265-280| Cite as

• Authors
• Authors and affiliations

• Isabel Mendizabal
• Soojin V. Yi

1. 1.
2. 2.

Reference work entry

First Online: 05 January 2019

• 32Downloads

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

This is a preview of subscription content, log in to check access.

References

1. Antequera F (2003) Structure, function and evolution of CpG island promoters. Cell Mol Life Sci 60:1647–1658CrossRefGoogle Scholar
2. Antequera F, Bird A (1993) Number of CpG islands and genes in human and mouse. Proc Natl Acad Sci USA 90:11995–11999CrossRefGoogle Scholar
3. Bajic VB, Tan SL, Suzuki Y, Sugano S (2004) Promoter prediction analysis on the whole human genome. Nat Biotechnol 22:1467–1473CrossRefGoogle Scholar
4. Bird AP (1986) CpG-rich islands and the function of DNA methylation. Nature 321:209–213CrossRefGoogle Scholar
5. Bird A, Taggart M, Frommer M, Miller OJ, Macleod D (1985) A fraction of the mouse genome that is derived from islands of nonmethylated, CpG-rich DNA. Cell 40(1):91–99Google Scholar
6. Blackledge NP, Long HK, Zhou JC, Kriaucionis S, Patient R, Klose RJ (2012) Bio-CAP: a versatile and highly sensitive technique to purify and characterise regions of non-methylated DNA. Nucleic Acids Res 40:e32CrossRefGoogle Scholar
7. Cohen NM, Kenigsberg E, Tanay A (2011) Primate CpG islands are maintained by heterogeneous evolutionary regimes involving minimal selection. Cell 145:773–786CrossRefGoogle Scholar
8. Cokus SJ, Feng S, Zhang X, Chen Z, Merriman B, Haudenschild CD et al (2008) Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature 452:215–219CrossRefGoogle Scholar
9. Cooper DN, Taggart MH, Bird AP (1983) Unmethylated domains in vertebrate DNA. Nucleic Acids Res 11:647–658CrossRefGoogle Scholar
10. Coulondre C, Miller JH, Farabaugh PJ, Gilbert W (1978) Molecular basis of base substitution hotspots in Escherichia coli. Nature 274:775–780CrossRefGoogle Scholar
11. Eckhardt F, Lewin J, Cortese R, Rakyan VK, Attwood J, Burger M et al (2006) DNA methylation profiling of human chromosomes 6, 20 and 22. Nat Genet 38:1378–1385CrossRefGoogle Scholar
12. Elango N, Yi SV (2008) DNA methylation and structural and functional bimodality of vertebrate promoters. Mol Biol Evol 25:1602–1608CrossRefGoogle Scholar
13. Feschotte C (2008) Transposable elements and the evolution of regulatory networks. Nat Rev Genet 9:397–405CrossRefGoogle Scholar
14. Frommer M, Mcdonald LE, Millar DS, Collis CM, Watt F, Grigg GW et al (1992) A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands. Proc Natl Acad Sci USA 89:1827–1831CrossRefGoogle Scholar
15. Gardiner-Garden M, Frommer M (1987) CpG islands in vertebrate genomes. J Mol Biol 196:261–282CrossRefGoogle Scholar
16. Grunau C, Clark SJ, Rosenthal A (2001) Bisulfite genomic sequencing: systematic investigation of critical experimental parameters. Nucleic Acids Res 29:e65CrossRefGoogle Scholar
17. Illingworth RS, Bird AP (2009) CpG islands–‘a rough guide’. FEBS Lett 583:1713–1720CrossRefGoogle Scholar
18. Illingworth R, Kerr A, Desousa D, Jorgensen H, Ellis P, Stalker J et al (2008) A novel CpG island set identifies tissue-specific methylation at developmental gene loci. PLoS Biol 6:e22CrossRefGoogle Scholar
19. Illingworth RS, Gruenewald-Schneider U, Webb S, Kerr AR, James KD, Turner DJ et al (2010) Orphan CpG islands identify numerous conserved promoters in the mammalian genome. PLoS Genet 6:e1001134CrossRefGoogle Scholar
20. Irizarry RA, Ladd-Acosta C, Wen B, Wu Z, Montano C, Onyango P et al (2009) The human colon cancer methylome shows similar hypo- and hypermethylation at conserved tissue-specific CpG island shores. Nat Genet 41:178–186CrossRefGoogle Scholar
21. Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, Zahler AM et al (2002) The human genome browser at UCSC. Genome Res 12:996–1006CrossRefGoogle Scholar
22. Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J et al (2001) Initial sequencing and analysis of the human genome. Nature 409:860–921CrossRefGoogle Scholar
23. Larsen F, Gundersen G, Lopez R, Prydz H (1992) CpG islands as gene markers in the human genome. Genomics 13:1095–1107CrossRefGoogle Scholar
24. Lister R, Pelizzola M, Dowen RH, Hawkins RD, Hon G, Tonti-Filippini J et al (2009) Human DNA methylomes at base resolution show widespread epigenomic differences. Nature 462:315–322CrossRefGoogle Scholar
25. Long HK, Sims D, Heger A, Blackledge NP, Kutter C, Wright ML et al (2013) Epigenetic conservation at gene regulatory elements revealed by non-methylated DNA profiling in seven vertebrates. Elife 2:e00348CrossRefGoogle Scholar
26. Meissner A, Gnirke A, Bell GW, Ramsahoye B, Lander ES, Jaenisch R (2005) Reduced representation bisulfite sequencing for comparative high-resolution DNA methylation analysis. Nucleic Acids Res 33:5868–5877CrossRefGoogle Scholar
27. Meissner A, Mikkelsen TS, Gu H, Wernig M, Hanna J, Sivachenko A, Zhang X, Bernstein BE, Nusbaum C, Jaffe DB, Gnirke A, Jaenisch R, Lander ES (2008) Genome-scale DNA methylation maps of pluripotent and differentiated cells. Nature 454:766–70Google Scholar
28. Mendizabal I, Yi SV (2016) Whole-genome bisulfite sequencing maps from multiple human tissues reveal novel CpG islands associated with tissue-specific regulation. Hum Mol Genet 25:69–82CrossRefGoogle Scholar
29. Sarda S, Zeng J, Hunt BG, Yi SV (2012) The evolution of invertebrate gene body methylation. Mol Biol Evol 29:1907–1016CrossRefGoogle Scholar
30. Saxonov S, Berg P, Brutlag DL (2006) A genome-wide analysis of CpG dinucleotides in the human genome distinguishes two distinct classes of promoters. Proc Natl Acad Sci USA 103:1412–1417CrossRefGoogle Scholar
31. Schultz MD, He Y, Whitaker JW, Hariharan M, Mukamel EA, Leung D et al (2015) Human body epigenome maps reveal noncanonical DNA methylation variation. Nature 523:212–216CrossRefGoogle Scholar
32. Shiota K (2004) DNA methylation profiles of CpG islands for cellular differentiation and development in mammals. Cytogenet Genome Res 105:325–334CrossRefGoogle Scholar
33. Singer-Sam J, Lebon JM, Tanguay RL, Riggs AD (1990) A quantitative Hpall-PCR assay to measure methylation of DNA from a small number of cells. Nucleic Acids Res 18:687–687CrossRefGoogle Scholar
34. Slotkin RK, Martienssen R (2007) Transposable elements and the epigenetic regulation of the genome. Nat Rev Genet 8:272–285CrossRefGoogle Scholar
35. Stein R, Sciaky-Gallili N, Razin A, Cedar H (1983) Pattern of methylation of two genes coding for housekeeping functions. Proc Natl Acad Sci USA 80:2422–2426CrossRefGoogle Scholar
36. Su AI, Wiltshire T, Batalov S, Lapp H, Ching KA, Block D et al (2004) A gene atlas of the mouse and human protein-encoding transcriptomes. Proc Natl Acad Sci USA 101:6062–6067CrossRefGoogle Scholar
37. Takai D, Jones PA (2002) Comprehensive analysis of CpG islands in human chromosomes 21 and 22. Proc Natl Acad Sci USA 99:3740–3745CrossRefGoogle Scholar
38. Tykocinski ML, Max EE (1984) CG dinucleotide clusters in MHC genes and in 5′ demethylated genes. Nucleic Acids Res 12:4385–4396CrossRefGoogle Scholar
39. Varley KE, Gertz J, Bowling KM, Parker SL, Reddy TE, Pauli-Behn F et al (2013) Dynamic DNA methylation across diverse human cell lines and tissues. Genome Res 23:555–567CrossRefGoogle Scholar
40. Weber M, Hellmann I, Stadler MB, Ramos L, Paabo S, Rebhan M et al (2007) Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome. Nat Genet 39:457–466CrossRefGoogle Scholar
41. Yamada Y, Toyota M, Hirokawa Y, Suzuki H, Takagi A, Matsuzaki T et al (2004a) Identification of differentially methylated CpG islands in prostate cancer. Int J Cancer 112(5):840CrossRefGoogle Scholar
42. Yamada Y, Watanabe H, Miura F, Soejima H, Uchiyama M, Iwasaka T et al (2004b) A comprehensive analysis of allelic methylation status of CpG islands on human chromosome 21q. Genome Res 14:247–266CrossRefGoogle Scholar
43. Zeng J, Nagrajan HK, Yi SV (2014) Fundamental diversity of human CpG islands at multiple biological levels. Epigenetics (9):483–91Google Scholar
44. Ziller MJ, Gu H, Muller F, Donaghey J, Tsai LT, Kohlbacher O et al (2013) Charting a dynamic DNA methylation landscape of the human genome. Nature 500:477–481CrossRefGoogle Scholar