The occupancy of nucleosomes along chromosome is a key factor for gene 
regulation. However, except promoter regions, genome-wide properties and 
functions of nucleosome organization remain unclear in mammalian genomes. Using 
the computational model of Increment of Diversity with Quadratic Discriminant 
(IDQD) trained from the microarray data, the nucleosome occupancy score 
(NOScore) was defined and applied to splice junction regions of constitutive, 
cassette exon, alternative 3' and 5' splicing events in the human genome. We 
found an interesting relation between NOScore and RNA splicing: exon regions 
have higher NOScores compared with their flanking intron sequences in both 
constitutive and alternative splicing events, indicating the stronger nucleosome 
occupation potential of exon regions. In addition, NOScore valleys present at 
approximately 25 bp upstream of the acceptor site in all splicing events. By 
defining folding diversity-to-energy ratio to describe RNA structural 
flexibility, we demonstrated that primary RNA transcripts from nucleosome 
occupancy regions are relatively rigid and those from nucleosome depleted 
regions are relatively flexible. The negative correlation between nucleosome 
occupation/depletion of DNA sequence and structural flexibility/rigidity of its 
primary transcript around splice junctions may provide clues to the deeper 
understanding of the unexpected role for nucleosome organization in the 
regulation of RNA splicing.