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Journal of Virology, April 2009, p. 2930-2940, Vol. 83, No. 7
0022-538X/09/$08.00+0     doi:10.1128/JVI.01974-08
Copyright © 2009, American Society for Microbiology. All Rights Reserved.

Identifying Sites Bound by Epstein-Barr Virus Nuclear Antigen 1 (EBNA1) in the Human Genome: Defining a Position-Weighted Matrix To Predict Sites Bound by EBNA1 in Viral Genomes{triangledown} ,{dagger}

Lindsay R. Dresang, David T. Vereide, and Bill Sugden*

Department of Oncology, McArdle Laboratory for Cancer Research, University of Wisconsin—Madison, Madison, Wisconsin 53706

Received 18 September 2008/ Accepted 2 January 2009

We identified binding sites for Epstein-Barr virus (EBV) nuclear antigen 1 (EBNA1) in the human genome using chromatin immunoprecipitation and microarrays. The sequences for these newly identified sites were used to generate a position-weighted matrix (PWM) for EBNA1's DNA-binding sites. This PWM helped identify additional DNA-binding sites for EBNA1 in the genomes of EBV, Kaposi's sarcoma-associated herpesvirus, and cercopithecine herpesvirus 15 (CeHV-15) (also called herpesvirus papio 15). In particular, a homologue of the Rep* locus in EBV was predicted in the genome of CeHV-15, which is notable because Rep* of EBV was not predicted by the previously developed consensus sequence for EBNA1's binding DNA. The Rep* of CeHV-15 functions as an origin of DNA synthesis in the EBV-positive cell line Raji; this finding thus builds on a set of DNA-binding sites for EBNA1 predicted in silico.

* Corresponding author. Mailing address: Department of Oncology, McArdle Laboratory for Cancer Research, University of Wisconsin—Madison, Rm. 814, 1400 University Ave., Madison, WI 53706. Phone: (608) 262-6697. Fax: (608) 262-2824. E-mail: sugden{at}oncology.wisc.edu

{triangledown} Published ahead of print on 7 January 2009.

{dagger} Supplemental material for this article may be found at http://jvi.asm.org/.

Journal of Virology, April 2009, p. 2930-2940, Vol. 83, No. 7
0022-538X/09/$08.00+0     doi:10.1128/JVI.01974-08
Copyright © 2009, American Society for Microbiology. All Rights Reserved.





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