Biopolymers and cell. 2008; 24 (5): 368 - 376

Comparative analysis of nucleotide composition skew in exons and introns of human genes

D. R. Duplij, V. V. Kalashnikov, M. O. Chaschyn, M. E. Tolstorukov

An analysis of transcription-related bias of base-pair composition was performed in different functional regions of human genes. Four types of the bias (skew indexes) were considered: AT-skew, GC-skew, Purine-skew, and Keto-skew. Our results show the essential differences between base-pair composition of exons and introns. On average, exons are characterized by the following rules: A > T; G і C; A + G > C + T; A + C і G + T, while the rules for introns are: A < T; C Ј G; A + G Ј C + T; A + C < G + T. The indexes reach the highest values in the internal introns and are close to zero in nontranscribed regions of the genome. We also observed that the bias is pronouncedly stronger in the housekeeping genes than in the analyzed groups of tissue-specific genes. Our results suggest that the detailed knowledge of the base-pair compositional bias may help to further our understanding of the overall gene organization.

Keywords: exons, introns, nucleotides, skew.