Omics · study · 2026
Chromatin accessibility dynamics and transcriptional regulation in Tetrahymena thermophila
Listed in NCBI GEO
Chromatin accessibility dynamics and their relationship to gene expression remain poorly understood in ciliated protozoa.
Description
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.
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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.
Links
Get the data
- GEO FTP directory ftp.ncbi.nlm.nih.gov/geo/series/GSE292nnn/GSE292857 ↗
download · from NCBI GEO
Where it is published
- GEO accession page ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE292857 ↗
landing page · from NCBI GEO
Documentation and papers
- PRJNA1241763 ncbi.nlm.nih.gov/bioproject/PRJNA1241763 ↗
project · from NCBI GEO
- PubMed 41653370 pubmed.ncbi.nlm.nih.gov/41653370 ↗
publication · from NCBI GEO
Topics
- Stated by source
- Expression profiling by high throughput sequencing · Genome binding/occupancy profiling by high throughput sequencing
- From keywords
- Life Sciences
Provenance · 1 source records, 7 field assertions
| Source | Key | Last seen | Raw |
|---|---|---|---|
| NCBI GEO | GSE292857 | 12 d ago | JSON v1 |
| Field | Assertion | Extractor | Evidence |
|---|---|---|---|
| access_level | source · NCBI GEO | connector:ncbi_geo@1.0.0 | |
| concepts[field].local:field:life-sciences | mapping · NCBI GEO | connector:ncbi_geo@1.0.0 | |
| concepts[method].geo_series_type:expression-profiling-by-high-throughput-sequencing | source · NCBI GEO | connector:ncbi_geo@1.0.0 | /gdstype |
| concepts[method].geo_series_type:genome-binding-occupancy-profiling-by-high-throughput-sequencing | source · NCBI GEO | connector:ncbi_geo@1.0.0 | /gdstype |
| description | source · NCBI GEO | connector:ncbi_geo@1.0.0 | /summary |
| publication_date | source · NCBI GEO | connector:ncbi_geo@1.0.0 | |
| title | source · NCBI GEO | connector:ncbi_geo@1.0.0 | /title |