Statistical information characterization of conserved non-coding elements in vertebrates.
Recently, a set of highly conserved non-coding elements (CNEs) has been derived from a comparison between the genomes of the puffer fish, Takifugu or Fugu rubripes, and man. In order to facilitate the identification of these conserved elements in silico, we characterize them by a number of statistical features. We found a pronounced information pattern around CNE borders; although the CNEs themselves are AT rich and have high entropy (complexity), they are flanked by GC-rich regions of low entropy (complexity). We also identified the most abundant motifs within and around of CNEs, and identified those that group around their borders. Like in human promoter regions, the TBP, NF-Y and some other binding motifs are clustered around CNE boundaries, which may suggest a possible transcription regulatory function of CNEs.
Abnizova
I
I
MRC-BSU, Robinson Way, Cambridge, UK. irina.abnizova@mrc-bsu.cam.ac.uk
Walter
K
K
Te Boekhorst
R
R
Elgar
G
G
Gilks
W R
WR
D000818:Animals; D001482:Base Composition; D001483:Base Sequence; D002874:Chromosome Mapping / Q000379:methods*; D003198:Computer Simulation; D017124:Conserved Sequence / Q000235:genetics*; D003627:Data Interpretation, Statistical; D008957:Models, Genetic; D015233:Models, Statistical; D008969:Molecular Sequence Data; D016366:Open Reading Frames / Q000235:genetics*; D012045:Regulatory Sequences, Nucleic Acid / Q000235:genetics; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D023741:Takifugu / Q000235:genetics*