title: Phylogenomic analysis of the emergence of GC-rich transcription elements.
abstract: 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.
authors.affiliation: Department of Biochemistry and Biophysics, ALS 2011, Oregon State University, Corvallis, OR 97331-7305, USA.
authors.forename: Patricia
authors.initials: P
authors.lastname: Khuu
authors.forename: Maurice
authors.initials: M
authors.lastname: Sandor
authors.forename: Jennifer
authors.initials: J
authors.lastname: DeYoung
authors.forename: P Shing
authors.initials: PS
authors.lastname: Ho
mesh_terms: D000818:Animals; D001665:Binding Sites; D043542:DNA, Z-Form / Q000737:chemistry / Q000235:genetics; D019143:Evolution, Molecular; D020862:GC Rich Sequence; D023281:Genomics; D006801:Humans; D051839:NFI Transcription Factors / Q000378:metabolism; D010802:Phylogeny; D050436:Regulatory Elements, Transcriptional; D024363:Transcription Initiation Site; D014158:Transcription, Genetic
chemical_list: D043542:DNA, Z-Form; D051839:NFI Transcription Factors