Rearrangement of macronucleus chromosomes correspond to TAD-like structures of micronucleus chromosomes in Tetrahymena thermophila

Abstract

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 is still largely unknown. Here, we explored the higher-order chromatin organization in the two distinct nuclei of T. thermophila using the Hi-C and HiChIP methods. We found that the meiotic crescent MIC has a specific chromosome interaction pattern, with all the telomeres or centromeres on the five MIC chromosomes clustering together, respectively, which is also helpful to identify the midpoints of centromeres in the MIC. We revealed that the MAC chromosomes lack A/B compartments, topologically associating domains (TADs), and chromatin loops. The MIC chromosomes have TAD-like structures but not A/B compartments and chromatin loops. The boundaries of the TAD-like structures in the MIC are 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, which provides a mechanism of the formation of MAC chromosomes during conjugation. Overall, we demonstrated the distinct higher-order chromatin organization in the two nuclei of the T. thermophila and suggest that the higher-order chromatin structures may play important roles during the development of the MAC chromosomes.

Comprehensive Chromosome End Remodeling During Programmed DNA Elimination

“…4H). Similar associations have been observed in DNA elimination events in water frogs [6] and the ciliate Tetrahymena [70], and autophagy has been shown to play a role following meiosis in the programmed nuclear death of the old macronucleus in Tetrahymena In the copepod, Cyclops kolensis, eliminated DNA is present in double membrane-bound structures in late interphase and early prophase of an elimination division [54]. We recently observed similar double membrane-bound structures in another copepod, Mesocyclops edax (Zagoskin, M, O'Toole, E., and R.E.…”

Tetrahymena meiosis: Simple yet ingenious

“…However, it has been possible to identify a few meiosis-specific factors that repurpose the microtubule apparatus for meiotic nuclear reorganization [23]. Within the elongated nucleus (often referred to as the crescent), chromosome arms are oriented in parallel, with centromeres and telomeres attached to opposite ends (Fig 3) [27,28]. This arrangement is believed to promote the juxtapositioning of homologous regions, and, thereby, homologous pairing and CO [27,29].…”

“…Thus, whereas in most eukaryotes, cohesin may be involved in the formation of topologically associated domains (TADs), which have been implicated in transcriptional regulation [63,64], this is not the case in Tetrahymena. In fact, Hi-C experiments have confirmed that somatic chromatin lacks TADs [28]. A possible explanation for the absence of this gene regulatory function in Tetrahymena is that the small size of its somatic chromosomes, with each containing only a few genes, may make elaborate regulatory mechanisms dispensable.…”

The 3D architecture of the pepper (Capsicum annum) genome and its relationship to function and evolution

“…The copyright holder for this preprint this version posted December 11, 2021. ; https://doi.org/10.1101/2021.12.10.470457 doi: bioRxiv preprint distinct structural and functional properties 8,[13][14][15] . Thus, clarifying the underlying mechanisms of TADs is necessary for further elucidating their functional specialization.…”

“…Like animals, TAD-like domains have been observed in the Hi-C analyses of many plants; however, the mechanisms by which they form (and whether they are shared with animals) is largely unknown 2,12 . Additionally, TADs organized by different mechanisms may exhibit distinct structural and functional properties 8,13–15 . Thus, clarifying the underlying mechanisms of TADs is necessary for further elucidating their functional specialization.…”