Chromatin accessibility dynamics and transcriptional regulation in Tetrahymena thermophila

ABSTRACT: Chromatin accessibility dynamics and their relationship to gene expression remain poorly understood in ciliated protozoa. Here, we investigate these dynamics in Tetrahymena thermophila by optimizing ATAC-seq to map chromatin accessibility across its transcriptionally active macronucleus during distinct life cycle stages. We demonstrate that chromatin accessibility at transcription start sites (TSSs) strongly correlates with gene expression levels. Intriguingly, partitioning ATAC-seq signals into nucleosome-free (NFR) and nucleosome-associated (NUC) regions revealed conserved TSS-proximal features: NFR signals peak upstream of TSSs, while phased +1 nucleosome arrays detected via NUC signals align with MNase-seq profiles. Temporal analysis uncovered stage-specific chromatin accessibility patterns, with global accessibility fluctuating dynamically across developmental phases. While most differentially accessible loci mirrored expression changes, subsets exhibited discordant regulation, suggesting context-specific chromatin-transcriptional coupling. Pharmacological inhibition of transcription using flavopiridol (FLV) triggered upstream chromatin compaction, elevated gene body accessibility, and enhanced nucleosome phasing, implicating transcription-coupled processes in shaping chromatin states. Cross-species comparisons of TSS-proximal accessibility across 13 eukaryotes revealed three conserved architectural modes (upstream-biased, symmetric, or upstream-restricted), with divergent spacing of +1 nucleosomes relative to TSSs. Our work establishes Tetrahymena as a model for studying chromatin dynamics in single-celled eukaryotes and provides evolutionary insights into the interplay between nucleosome organization, chromatin accessibility, and transcriptional regulation.

ORGANISM(S): Tetrahymena thermophila

PROVIDER: GSE292857 | GEO | 2026/03/03

REPOSITORIES: GEO