Spn1 Maintains Nucleosome Organization at Transcription End Sites

Background/Objectives: Transcription by RNA polymerase II (RNAPII) occurs within chromatin and requires continuous disassembly and reassembly of nucleosomes. Histone chaperones associate with RNAPII, facilitate transcription, and maintain nucleosome organization. This study investigated the role of the conserved histone chaperone Spn1 in coordinating chromatin organization with transcription termination in Saccharomyces cerevisiae. Methods: Spn1 interacts with elongating RNAPII via Spt6 and its function was examined by reanalyzing published MNase-seq, RNAPII ChIP-seq, NET-seq, and TSS-seq datasets. Results: Mutations that disrupt the Spn1–Spt6 interaction at nonpermissive temperatures caused a pronounced loss of nucleosome array regularity at polyadenylation (pA) sites, whereas nucleosome organization around transcription start sites was less affected. These mutants also showed shorter nucleosome repeat lengths at gene ends. RNAPII accumulated near pA sites and displayed increased termination-proximal stalling, consistent with impaired transcription termination. In addition, transcription of neighboring downstream genes in tandem orientation was preferentially reduced, suggesting interference between termination of the upstream gene and initiation at the neighboring promoter. Conclusions: Together, these results identify Spn1 as an important determinant of chromatin organization at gene ends and suggest that it helps maintain transcriptional fidelity across closely spaced genes.