Contributions of DNA mechanics and trans-regulation to nucleosome positioning in Schizosaccharomyces pombe and its role in co-transcriptional splicing

Nucleosome positioning critically regulates chromatin functions, yet species-specific mechanisms remain incompletely understood. This study revisits nucleosome organization in Schizosaccharomyces pombe (S. pombe) using a DNA deformation energy model and a high-resolution nucleosome map. We demonstrate that DNA bending energy—not shearing energy—accurately predicts rotational positioning (72.2–77.4% accuracy) and nucleosome-depleted regions (NDRs) near transcription start sites (TSSs) in S. pombe. Gene-end analyses reveal that NDRs and nucleosome phasing are, at least partly, encoded in DNA sequence. Strikingly, nucleosome enrichment at RNA splice sites is determined primarily by trans-acting factors (e.g., transcription factors Pcr1/Atf1), not by DNA sequence preference for nucleosome positioning, and correlates with splice site usage rates. Highly transcribed genes exhibit reduced nucleosome occupancy upstream of splice sites, while frequently used splice sites show elevated nucleosome occupancy. Furthermore, 3D chromatin architecture analysis indicates that highly transcribed intron-poor genes display enhanced medium-range chromatin looping (10–100 kb), potentially reflecting their preferential aggregation at sub-nuclear environments enriched in transcriptional machinery and splicing factors. Our work identifies DNA bending properties as an important contributor to S. pombe nucleosome organization and reveals the involvement of nucleosome positioning and chromatin architecture in co-transcriptional splicing.