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CG dinucleotide clustering is a species-specific property of the genome
Cytosines at cytosine-guanine (CG) dinucleotides are the near-exclusive target of DNA methyltransferases in mammalian genomes. Spontaneous deamination of methylcytosine to thymine makes methylated cytosines unusually susceptible to mutation and consequent depletion. The loci where CG dinucleotides r...
Autores principales: | , , , , , , , , , , , |
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Formato: | Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2007
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2175314/ https://www.ncbi.nlm.nih.gov/pubmed/17932072 http://dx.doi.org/10.1093/nar/gkm489 |
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author | Glass, Jacob L. Thompson, Reid F. Khulan, Batbayar Figueroa, Maria E. Olivier, Emmanuel N. Oakley, Erin J. Van Zant, Gary Bouhassira, Eric E. Melnick, Ari Golden, Aaron Fazzari, Melissa J. Greally, John M. |
author_facet | Glass, Jacob L. Thompson, Reid F. Khulan, Batbayar Figueroa, Maria E. Olivier, Emmanuel N. Oakley, Erin J. Van Zant, Gary Bouhassira, Eric E. Melnick, Ari Golden, Aaron Fazzari, Melissa J. Greally, John M. |
author_sort | Glass, Jacob L. |
collection | PubMed |
description | Cytosines at cytosine-guanine (CG) dinucleotides are the near-exclusive target of DNA methyltransferases in mammalian genomes. Spontaneous deamination of methylcytosine to thymine makes methylated cytosines unusually susceptible to mutation and consequent depletion. The loci where CG dinucleotides remain relatively enriched, presumably due to their unmethylated status during the germ cell cycle, have been referred to as CpG islands. Currently, CpG islands are solely defined by base compositional criteria, allowing annotation of any sequenced genome. Using a novel bioinformatic approach, we show that CG clusters can be identified as an inherent property of genomic sequence without imposing a base compositional a priori assumption. We also show that the CG clusters co-localize in the human genome with hypomethylated loci and annotated transcription start sites to a greater extent than annotations produced by prior CpG island definitions. Moreover, this new approach allows CG clusters to be identified in a species-specific manner, revealing a degree of orthologous conservation that is not revealed by current base compositional approaches. Finally, our approach is able to identify methylating genomes (such as Takifugu rubripes) that lack CG clustering entirely, in which it is inappropriate to annotate CpG islands or CG clusters. |
format | Text |
id | pubmed-2175314 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2007 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-21753142008-01-07 CG dinucleotide clustering is a species-specific property of the genome Glass, Jacob L. Thompson, Reid F. Khulan, Batbayar Figueroa, Maria E. Olivier, Emmanuel N. Oakley, Erin J. Van Zant, Gary Bouhassira, Eric E. Melnick, Ari Golden, Aaron Fazzari, Melissa J. Greally, John M. Nucleic Acids Res Genomics Cytosines at cytosine-guanine (CG) dinucleotides are the near-exclusive target of DNA methyltransferases in mammalian genomes. Spontaneous deamination of methylcytosine to thymine makes methylated cytosines unusually susceptible to mutation and consequent depletion. The loci where CG dinucleotides remain relatively enriched, presumably due to their unmethylated status during the germ cell cycle, have been referred to as CpG islands. Currently, CpG islands are solely defined by base compositional criteria, allowing annotation of any sequenced genome. Using a novel bioinformatic approach, we show that CG clusters can be identified as an inherent property of genomic sequence without imposing a base compositional a priori assumption. We also show that the CG clusters co-localize in the human genome with hypomethylated loci and annotated transcription start sites to a greater extent than annotations produced by prior CpG island definitions. Moreover, this new approach allows CG clusters to be identified in a species-specific manner, revealing a degree of orthologous conservation that is not revealed by current base compositional approaches. Finally, our approach is able to identify methylating genomes (such as Takifugu rubripes) that lack CG clustering entirely, in which it is inappropriate to annotate CpG islands or CG clusters. Oxford University Press 2007-11 2007-10-10 /pmc/articles/PMC2175314/ /pubmed/17932072 http://dx.doi.org/10.1093/nar/gkm489 Text en © 2007 The Author(s) http://creativecommons.org/licenses/by-nc/2.0/uk/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Genomics Glass, Jacob L. Thompson, Reid F. Khulan, Batbayar Figueroa, Maria E. Olivier, Emmanuel N. Oakley, Erin J. Van Zant, Gary Bouhassira, Eric E. Melnick, Ari Golden, Aaron Fazzari, Melissa J. Greally, John M. CG dinucleotide clustering is a species-specific property of the genome |
title | CG dinucleotide clustering is a species-specific property of the genome |
title_full | CG dinucleotide clustering is a species-specific property of the genome |
title_fullStr | CG dinucleotide clustering is a species-specific property of the genome |
title_full_unstemmed | CG dinucleotide clustering is a species-specific property of the genome |
title_short | CG dinucleotide clustering is a species-specific property of the genome |
title_sort | cg dinucleotide clustering is a species-specific property of the genome |
topic | Genomics |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2175314/ https://www.ncbi.nlm.nih.gov/pubmed/17932072 http://dx.doi.org/10.1093/nar/gkm489 |
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