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Chromatin ends and promoter loops organize chromosome-sized domains in Tetrahymena

ABSTRACT: Three-dimensional genome architecture shapes how regulatory elements controls gene expression, yet how compact unicellular genomes are folded is poorly understood. Ciliates such as Tetrahymena thermophila carry a fragmented, gene-dense somatic macronucleus (MAC) and a silent germline micronucleus (MIC), imposing distinct constraints on chromosome folding. Here we combine nucleosome-resolution Micro-C, ATAC-seq and RNA-seq to map 3D chromatin organization across Tetrahymena life cycle stages and in the related ciliate Tetrahymena pyriformis. We find that MAC chromosomes lack strong mammalian-style compartments and TADs but behave as short interaction units whose telomere-capped ends form accessible, strongly interacting hubs. Within these units, chromatin loops concentrate at promoter-proximal open chromatin and are closely associated with transcription level. During conjugation, long-range internal loops and promoter–promoter contacts are transiently weakened and then rebuilt, while end–end interactions persist. Similar promoter- and end-anchored folding in T. pyriformis points to a conserved ciliate strategy for organizing gene-rich genomes in three dimensions.

ORGANISM(S): Tetrahymena thermophila Tetrahymena pyriformis

PROVIDER: GSE314518 | GEO | 2026/07/02

REPOSITORIES: GEO

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			Action	DRS
		Other
	GSE314518_HiC.tt.log.fa.combined.mcool	Other
	GSE314518_HiC.tt.log.fa.dsg.combined.mcool	Other
	GSE314518_MC.tt.1.5hpm.combined.mcool	Other
	GSE314518_MC.tt.12hpm.combined.mcool	Other

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Distinct 3D Genome Organization in the Two Nuclei of Tetrahymena thermophila

Project description:Somatic macronucleus (MAC) and germline micronucleus (MIC) of Tetrahymena thermophila are different in chromosome numbers, sizes, functions and cohesin complex locations. Loss of cohesin complex resulted in genome-wide disappearance of topologically associating domains (TADs) and chromatin loops in mammalian cells. However, the higher-level chromatin organization in Tetrahymena thermophila which contains both cohesin free MAC and cohesin located MIC are largely unknown. Here, using the Hi-C and HiChIP methods, we reveal that, these two nuclei possess distinct three-dimensional genome structures. In the MAC, each chromosome occupies its own territory and there are no chromatin compartmentalization or chromatin domains. The chromatin loops in MAC are mainly related to chromatin structures rather than transcriptional regulation. The MIC also without chromatin compartmentalization, but with chromatin domains and the domain boundaries are consistent with chromatin breakage sites (CBSs) which indicates that each MIC chromatin domain developed to one MAC chromosome during conjugation. Besides, we found the MIC exhibits unique intra-arm and inter-chromosome interactions at the crescent stage of conjugation, when the MIC undergoes meiotic recombination.

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Tetrahymena thermophila macronucleus chromosomes originate from chromatin breakage sequence defined TAD-like structures in micronucleus chromosomes

Project description:The somatic macronucleus (MAC) and germline micronucleus (MIC) of Tetrahymena thermophila differ in chromosome numbers, sizes, functions, transcriptional activities, and cohesin complex location. However, the higher-order chromatin organization in T. thermophila which contains both cohesin free MAC and cohesin located MIC are largely unknown. Here, we examined the higher-order chromatin organization in the two distinct nuclei of T. thermophila using the Hi-C and HiChIP. Interestingly, we found that the crescent MIC possess specific chromosome interaction pattern. All the telomeres or centromeres on the five MIC chromosomes clustering together, respectively, which could help to identify the midpoints of centromeres in the MIC. We found the transcriptionally active MAC chromosomes lack A/B compartments, topologically associating domains (TADs) and chromatin loops. The transcriptionally inert MIC chromosomes also without A/B compartments and chromatin loops, but have TAD-like structures. The boundaries of the TAD-like structures in the MIC were highly consistent with the chromatin breakage sequence (CBS) sites, suggesting that each TAD-like structure of the MIC chromosomes develops into one MAC chromosome during MAC development during conjugation. Overall, we revealed the higher-order chromatin organization in the T. thermophila and found the chromatin structures might play important roles during the development of the MAC chromosomes.

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MNase-seq of Tetrahymena thermophial macronucleus (MAC) and micronucleus (MIC)

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Project description:We present a comprehensive transcriptome of ciliate T. thermophila using the Illumina RNA-seq platform. The data was generated from the six mRNA samples of growth, starvation and conjugation of Tetrahymena. Despite an AT rich genome, there are about 124.6 million reads mapped to T. thermophila genome. Using these mapped reads, we have significantly improved the previous genome annotation and investigated the gene expression. Besides, our result also provided a comprehensive understanding of the alternative splicing in T. thermophila, and suggested the existence of the regulated unproductive splicing and translation (RUST) in the single-celled eukaryote. RNA-seq for six samples of Tetrahymena growth, starvation and conjugation.

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Investigation of the timing of secondary small RNA biogenesis during programmed DNA elimination in Tetrahymena

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Proteomics analysis of the bromodomain protein IBD2 reveals mechanistic insights into H2A.Z (Hv1) dynamics in Tetrahymena

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