Non-random distribution and co-localization of purine/pyrimidine-encoded information and transcriptional regulatory domains.
In order to detect sequence-based information predictive for the location of eukaryotic transcriptional regulatory domains, the frequencies and distributions of the 36 possible purine/pyrimidine reverse complement hexamer pairs was determined for test sets of real and random sequences. The distribution of one of the hexamer pairs (RRYYRR/YYRRYY, referred to as M1) was further examined in a larger set of sequences (> 32 genes, 230 kb). Predominant clusters of M1 and the locations of eukaryotic transcriptional regulatory domains were found to be associated and non-randomly distributed along the DNA consistent with a periodicity of approximately 1.2 kb. In the context of higher ordered chromatin this would align promoters, enhancers and the predominant clusters of M1 longitudinally along one face of a 30 nm fiber. Using only information about the distribution of the M1 motif, 50-70% of a sequence could be eliminated as being unlikely to contain transcriptional regulatory domains with an 87% recovery of the regulatory domains present.
Povinelli
C M
CM
Institute for Molecular Genetics, Baylor College of Medicine, Houston, TX 77030.
D000818:Animals; D001483:Base Sequence; D002352:Carrier Proteins; D004742:Enhancer Elements, Genetic; D006801:Humans; D008969:Molecular Sequence Data; D011401:Promoter Regions, Genetic; D011687:Purines; D011743:Pyrimidines; D051381:Rats; D012045:Regulatory Sequences, Nucleic Acid; D017421:Sequence Analysis; D014158:Transcription, Genetic
D002352:Carrier Proteins; D011687:Purines; D011743:Pyrimidines