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

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.