Nucleosome positioning is constrained at eukaryotic transcription start sites 
and implicated in transcriptional regulation. Moreover, recent observations 
indicate that chromatin structure, transcription and splicing are functionally 
intertwined, and that modified nucleosomes with trimethylation of lysine 36 in 
histone subunit 3 (H3K36me3) are enriched at internal exons and the downstream 
flanking intronic regions of highly expressed genes. However, the position of 
nucleosomes in the interior of genes has been thought to be largely random. Here 
we show, by analysis of data sets from human sperm and T cells and medaka 
(Japanese killifish, Oryzias latipes) blastulae, that internal exons of genes 
are characterized by sharply elevated average nucleosome occupancy in comparison 
to flanking intronic sequences. We also show that the preferential positioning 
of nucleosomes at internal exons is independent of their modification status, 
and of the GC content, conservation or the expression level of the exon. These 
findings show that the location of exons is recorded in the chromatin structure 
and may be inherited across generations. Such embedded information may underpin 
transcriptionally coupled exon recognition and splice site selection.