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Cited by 550Genomics and Chromatin DynamicsEpigenetics and DNA MethylationChromosomal and Genetic Variations

Orphan CpG Islands Identify Numerous Conserved Promoters in the Mammalian Genome

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Illingworth, Robert S., Gruenewald-Schneider, Ulrike, Webb, Shaun, Kerr, Alastair R. W., James, Keith D., Turner, Daniel J., Smith, Colin, Harrison, David J. +2 more·2010·PLoS Genetics
DOI 10.1371/journal.pgen.1001134PMC PMC2944787
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Abstract

CpG islands (CGIs) are vertebrate genomic landmarks that encompass the promoters of most genes and often lack DNA methylation. Querying their apparent importance, the number of CGIs is reported to vary widely in different species and many do not co-localise with annotated promoters. We set out to quantify the number of CGIs in mouse and human genomes using CXXC Affinity Purification plus deep sequencing (CAP-seq). We also asked whether CGIs not associated with annotated transcripts share properties with those at known promoters. We found that, contrary to previous estimates, CGI abundance in humans and mice is very similar and many are at conserved locations relative to genes. In each species CpG density correlates positively with the degree of H3K4 trimethylation, supporting the hypothesis that these two properties are mechanistically interdependent. Approximately half of mammalian CGIs (>10,000) are "orphans" that are not associated with annotated promoters. Many orphan CGIs show evidence of transcriptional initiation and dynamic expression during development. Unlike CGIs at known promoters, orphan CGIs are frequently subject to DNA methylation during development, and this is accompanied by loss of their active promoter features. In colorectal tumors, however, orphan CGIs are not preferentially methylated, suggesting that cancer does not recapitulate a developmental program. Human and mouse genomes have similar numbers of CGIs, over half of which are remote from known promoters. Orphan CGIs nevertheless have the characteristics of functional promoters, though they are much more likely than promoter CGIs to become methylated during development and hence lose these properties. The data indicate that orphan CGIs correspond to previously undetected promoters whose transcriptional activity may play a functional role during development.

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  • Thousands of genes have CGIs in their gene bodies that can act as novel alternative promoters during development.

    “thousands of genes have CGIs in their gene bodies (intragenic CGIs) that can act as novel alternative promoters during development36.”

    From Alternative promoters in CpG depleted regions are prevalently associated with epigenetic misregulation of liver cancer transcriptomes (2023) · cites this paper as [36]

    The Discussion (‘CGI methylation is conserved even at sites distal to annotated gene promoters’; page unavailable) proposes that many intragenic orphan CGIs may serve as alternative promoters with spatially or temporally restricted use. The Concluding remarks describe thousands of orphan CGIs as functional promoters, but do not establish that thousands of distinct genes have intragenic CGIs acting as alternative promoters. (LLM, conf=0.86)

    Experimental — accuracy not yet measured

  • Depletion of HCC alternative promoters from intragenic CGIs is notably different than alternative promoters usage from intragenic CGIs during developmental stages or gene upstream CGIs in adult tissues.

    “Depletion of HCC alternative promoters from intragenic CGIs is notably different than alternative promoters usage from intragenic CGIs during developmental stages36 or gene upstream CGIs61 in adult tissues”

    From Alternative promoters in CpG depleted regions are prevalently associated with epigenetic misregulation of liver cancer transcriptomes (2023) · cites this paper as [36]

    The Discussion (‘CGI methylation is conserved even at sites distal to annotated gene promoters’; page not available) proposes that many intragenic orphan CGIs may be alternative promoters used in a spatially or temporally restricted fashion. It presents this as an ‘intriguing possibility,’ not established alternative-promoter usage during developmental stages. The citation attaches to the developmental comparison, not the citing authors’ finding about HCC. (LLM, conf=0.83)

    Experimental — accuracy not yet measured

  • Intragenic CGIs are less favorable to act as alternative promoters in cancer, though they can act as alternative promoters during embryonic development and cell differentiation.

    “Thus, intragenic CGIs are less favorable to act as alternative promoters in cancer, though they can act as alternative promoters during embryonic development and cell differentiation36”

    From Alternative promoters in CpG depleted regions are prevalently associated with epigenetic misregulation of liver cancer transcriptomes (2023) · cites this paper as [36]

    The Discussion (‘CGI methylation is conserved even at sites distal to annotated gene promoters’; page unavailable) proposes that many intragenic orphan CGIs may be alternative promoters used in a spatially or temporally restricted fashion. But the paper does not establish their use specifically during cell differentiation, and its colorectal-cancer analysis measures CGI methylation, not whether intragenic CGIs are less likely to act as alternative promoters in cancer. (LLM, conf=0.84)

    Experimental — accuracy not yet measured

  • Approximately half of the annotated CGI are distributed between gene bodies and intergenic regions.

    “However approximately half of the annotated CGI are distributed between gene bodies and intergenic regions [24].”

    From Comprehensive in silico CpG methylation analysis in hepatocellular carcinoma identifies tissue- and tumor-type specific marks disconnected from gene expression (2024) · cites this paper as [24]

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Authors
Illingworth, R. S., Gruenewald-Schneider, U., Webb, S., Kerr, A. R. W., James, K. D., Turner, D. J., Smith, C., Harrison, D. J., Andrews, R., & Bird, A. P.
Affiliations
  • Wellcome Centre for Cell Biology (GB)
  • Wellcome Sanger Institute (GB)
  • University of Edinburgh (GB)
  • Western General Hospital (GB)
Corresponding author
Bird, Adrian P.
ORCID
Venue
PLoS Genetics
Publisher
Public Library of Science (PLoS)
Published
2010-09-23
Volume
6
Issue
9
Pages
e1001134
ISSN
  • 1553-7390 (ISSN-L)
  • 1553-7404
DOI
10.1371/journal.pgen.1001134
PMC
PMC2944787
OpenAlex
W2122277359
Cited by
550
References
5
Citations by year
2026: 11 · 2025: 19 · 2024: 13 · 2023: 25 · 2022: 40 · 2021: 47 · 2020: 36 · 2019: 32 · 2018: 33 · 2017: 34 · 2016: 28 · 2015: 42 · 2014: 44 · 2013: 63 · 2012: 49
FWCI
18.90
Type
journal article
Language
en
Open access
Licence
Locations
  • PLoS Genetics (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
  • Figshare (submittedVersion, cc-by)
  • Edinburgh Research Explorer (University of Edinburgh) (submittedVersion, cc-by)
  • St Andrews Research Repository (St Andrews Research Repository) (submittedVersion, cc-by)
Funders
  • Wellcome Trust (077224)
  • Medical Research Council
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
  • Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
Keywords
CpG islands, DNA methylation, H3K4 trimethylation, transcription initiation, developmental gene regulation, colorectal neoplasia
MeSH terms
Adult, Animals, Base Sequence, Chromatography, Affinity, Female, Histones, Humans, Lysine, Male, Mammals, Middle Aged, Organ Specificity, Promoter Regions, Genetic, Transcription, Genetic, Colorectal Neoplasms, Genome, Conserved Sequence, Sequence Analysis, DNA, CpG Islands, DNA Methylation, Mice, Young Adult

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