Skip Navigation



Nucleic Acids Research Advance Access published online on October 10, 2007
Nucleic Acids Research, doi:10.1093/nar/gkm489
This Article
Right arrow Full Text Freely available
Right arrow Print PDF (4299K) Freely available
Right arrow Screen PDF (672K) Freely available
Right arrow Supplementary Data
Right arrowOA All Versions of this Article:
35/20/6798    most recent
gkm489v1
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Commercial Re-use Guidelines
for Open Access NAR Content
Google Scholar
Right arrow Articles by Glass, J. L.
Right arrow Articles by Greally, J. M.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Glass, J. L.
Right arrow Articles by Greally, J. M.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© 2007 The Author(s)
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.

Genomics

CG dinucleotide clustering is a species-specific property of the genome

Jacob L. Glass1, Reid F. Thompson1, Batbayar Khulan1, Maria E. Figueroa2, Emmanuel N. Olivier3, Erin J. Oakley4, Gary Van Zant4, Eric E. Bouhassira3,5, Ari Melnick2, Aaron Golden6, Melissa J. Fazzari7 and John M. Greally1,5,*

1Department of Molecular Genetics, 2Department of Developmental and Molecular Biology and 3Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA, 4Division of Hematology/Oncology, University of Kentucky, Markey Cancer Center, 800 Rose Street, Lexington KY 40536, USA, 5Department of Medicine (Hematology), Albert Einstein College of Medicine, Bronx, NY 10461, USA, 6Department of Information Technology, National University of Ireland Galway, Newcastle Road, Galway, Republic of Ireland and 7Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA

*To whom correspondence should be addressed. Tel: +1 718 430 2875; Fax: +1 718 824 3153; Email: jgreally{at}aecom.yu.edu

Received February 9, 2007. Revised May 23, 2007. Accepted June 6, 2007.

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.


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 BioinformaticsHome page
R. F. Thompson, M. Suzuki, K. W. Lau, and J. M. Greally
A pipeline for the quantitative analysis of CG dinucleotide methylation using mass spectrometry
Bioinformatics, September 1, 2009; 25(17): 2164 - 2170.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
M. Oda, J. L. Glass, R. F. Thompson, Y. Mo, E. N. Olivier, M. E. Figueroa, R. R. Selzer, T. A. Richmond, X. Zhang, L. Dannenberg, et al.
High-resolution genome-wide cytosine methylation profiling with simultaneous copy number analysis and optimization for limited cell numbers
Nucleic Acids Res., July 1, 2009; 37(12): 3829 - 3839.
[Abstract] [Full Text] [PDF]

Home page
 BloodHome page
M. E. Figueroa, B. J. Wouters, L. Skrabanek, J. Glass, Y. Li, C. A. J. Erpelinck-Verschueren, A. W. Langerak, B. Lowenberg, M. Fazzari, J. M. Greally, et al.
Genome-wide epigenetic analysis delineates a biologically distinct immature acute leukemia with myeloid/T-lymphoid features
Blood, March 19, 2009; 113(12): 2795 - 2804.
[Abstract] [Full Text] [PDF]

Home page
 Genome ResHome page
V. K. Rakyan, T. A. Down, N. P. Thorne, P. Flicek, E. Kulesha, S. Graf, E. M. Tomazou, L. Backdahl, N. Johnson, M. Herberth, et al.
An integrated resource for genome-wide identification and analysis of human tissue-specific differentially methylated regions (tDMRs)
Genome Res., September 1, 2008; 18(9): 1518 - 1529.
[Abstract] [Full Text] [PDF]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.