Project description: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.
2026-07-02 | GSE314518 | GEO
Project description:Nanopore sequencing of seven melon genomes
Project description:5-methyl-cytosine DNA methylation regulates gene expression and developmental programming in a broad range of eukaryotes. However, its presence and potential roles in ciliates, complex single-celled eukaryotes with germline-somatic genome specialization via nuclear dimorphism, are largely uncharted. While canonical cytosine methyltransferases have not been discovered in published ciliate genomes, recent studies performed in the stichotrichous ciliate Oxytricha trifallax suggest de novo cytosine methylation during macronuclear development. In this study, we applied bisfulfite genome sequencing, DNA mass spectrometry and antibody-based fluorescence detection to investigate the presence of DNA methylation in Paramecium tetraurelia. While the antibody-based methods suggest cytosine methylation, DNA mass spectrometry and bisulfite sequencing reveal that levels are actually below the limit of detection. Our results suggest that Paramecium does not utilize 5-methyl-cytosine DNA methylation as an integral part of its epigenetic arsenal.
2018-04-01 | GSE111621 | GEO
Project description:Ancient genomes of seven germinated Judean date palms
Project description:Time series microarray analysis on the photosynthetic ciliate was conducted using an oligochip containing 15,654 genes designed from Teleaulax amphioxeia ESTs
