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Nucleic Acids Research 2004 32(22):6501-6510; doi:10.1093/nar/gkh988
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Published online 14 December 2004

Nucleic Acids Research, Vol. 32 No. 22 © Oxford University Press 2004; all rights reserved

Distributions of Z-DNA and nuclear factor I in human chromosome 22: a model for coupled transcriptional regulation

P. Christoph Champ, Sandor Maurice, Jeffrey M. Vargason, Tracy Camp and P. Shing Ho*

Department of Biochemistry and Biophysics, ALS 2011, Oregon State University, Corvallis, OR 97331, USA

* To whom correspondence should be addressed. Tel: +541 737 2769; Fax: +541 737 0481; Email: hops{at}onid.orst.edu
Present address: Jeffrey M. Vargason, National Institute of Environmental Health Sciences, MD F3-05, PO Box 12233, Research Triangle Park, NC 27709, USA

Received as resubmission July 12, 2004; Revised and Accepted November 22, 2004

An analysis of the human chromosome 22 genomic sequence shows that both Z-DNA forming regions (ZDRs) and promoter sites for nuclear factor-I (NFI) are correlated with the locations of known and predicted genes across the chromosome and accumulate around the transcriptional start sites of the known genes. Thus, the occurrence of Z-DNA across human genomic sequences mirrors that of a known eukaryotic transcription factor. In addition, 43 of the 383 fully annotated chromosomal genes have ZDRs within 2 nucleosomes upstream of strong NFIs. This suggests a distinct class of human genes that may potentially be transcriptionally regulated by a mechanism that couples Z-DNA with NFI activation, similar to the mechanism previously elucidated for the human colony stimulation factor-I promoter [Liu et al. (2001) Cell, 106, 309–318]. The results from this study will facilitate the design of experimental studies to test the generality of this mechanism for other genes in the cell.


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