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.
We have applied a comparative phylogenomic analysis to study the evolutionary relationships between GC content, CpG-dinucleotide content (CpGs), potential nuclear factor I (NFI) binding sites, and potential Z-DNA forming regions (ZDRs) as representative structural and functional GC-rich genomic elements. Our analysis indicates that CpG and NFI sites emerged with a general accretion of GC-rich sequences downstream of the eukaryotic transcription start site (TSS). Two distinct classes of ZDRs are observed at different locations proximal to the eukaryotic TSS. A robust CA/TG class of ZDRs was seen to emerge upstream of the TSS and independently of GC content, CpGs, and NFIs, whereas a second, weaker CG type appears to have evolved along with these downstream GC-rich elements. Taken together, the results provide a model for how GC-rich structural and functional eukaryotic markers emerge relative to each other, and indicate two distinct transition points for their occurrence: the first at the pro/eukaryotic boundary, and the second at or near the amniotic boundary.evolution ͉ genomic analysis ͉ Z-DNA
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