Journal: Genome Research

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

doi: 10.1101/gr.241687.118

Figure Lengend Snippet: The square-shaped interaction patterns in the MAC of T. thermophila are chromosome territories. ( A ) Heatmaps showing the chromosome interactions on the 568 MAC scaffolds (ordered by their locations on the MIC genome) at 3 hpm (whole cells Hi-C data mapped to the MAC scaffolds), and the chromosome interactions of the 83 MAC scaffolds located on the MIC Chromosome 2 at 1.5 hpm, 3 hpm, and 24 hpm. Zoomed-in views of scf_8254803 are shown at the bottom . (hpm) Hours post-mixing. Numbers at the lower left of heatmaps correspond to the maximum signal in the matrix. ( B , C ) The MAC chromosomes (MAC scaffolds with telomere sequences at both ends) and the MAC scaffolds compared to the chromosome interactions on MIC Chromosome 1 at 3 hpm are shown (whole cells Hi-C data mapped to the MIC genome). Regions from 1 Mb to 36.32 Mb ( B ); zoomed in region from 4 Mb to 14 Mb ( C ).

Article Snippet: Then, we centrifuged at 780 g for 10 min at 4°C, transferred the solution which contains MIC to a new tube (the pellet which contains MAC was also collected and washed twice with 1× NEBuffer 2.1), centrifuged the tubes with MIC again at 780 g for 10 min at 4°C, repeated this step 3–4 times and checked by DAPI stain to see if the MIC was pure.

Techniques: Hi-C

Journal: Genome Research

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

doi: 10.1101/gr.241687.118

Figure Lengend Snippet: Boundaries of TAD-like structures in the MIC are consistent with CBS sites. ( A ) The schematic diagram shows the development of MAC and MIC from the same zygotic nuclei during conjugation. ( B ) The location of CBS sites, boundaries, and TAD-like structures compared to the heatmaps on the Chromosome 4 (2.5 Mb to 10.5 Mb) at 3 hpm. ( C ) The bar plot shows percentage of CBS sites localized to the boundaries of the TAD-like structures (10 kb) or 20 kb around the boundaries (total 50 kb). ( D ) Heatmaps showing averaged Hi-C interaction counts (Smc1-HA HiChIP, 1.5 hpm) around the boundaries of TAD-like structures. ( E ) Heatmaps showing averaged Hi-C interaction counts (Smc1-HA HiChIP, 1.5 hpm) around the CBS sites.

Article Snippet: Then, we centrifuged at 780 g for 10 min at 4°C, transferred the solution which contains MIC to a new tube (the pellet which contains MAC was also collected and washed twice with 1× NEBuffer 2.1), centrifuged the tubes with MIC again at 780 g for 10 min at 4°C, repeated this step 3–4 times and checked by DAPI stain to see if the MIC was pure.

Techniques: Conjugation Assay, Hi-C, HiChIP

Journal: Genome Research

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

doi: 10.1101/gr.241687.118

Figure Lengend Snippet: The MAC chromosomes are related to the MIC TAD-like structures during conjugation. ( A ) The heatmap regions (Chromosome 1: 3.2 Mb to 7.2 Mb) of the MIC (Smc1-HA HiChIP at 3 hpm, upper ) and the MAC (whole cells Hi-C at 3 hpm, below ) compared to the CBS sites on the MIC and the MAC scaffolds are plotted. ( B ) The heatmap showing the Hi-C interactions on six of the MAC scaffolds at 3 hpm (whole cells Hi-C data mapped to the MAC scaffolds). ( C ) The heatmap showing the Hi-C interactions on the MIC Chromosome 4 (4.11 Mb to 8.14 Mb) at 3 hpm (whole cells Hi-C data mapped to the MIC genome). ( D ) The heatmap showing the Hi-C interactions on the MIC Chromosome 4 (4.11 Mb to 8.14 Mb) at 3 hpm (Smc1-HA HiChIP data mapped to the MIC genome). ( E ) A model for the MAC chromosomes development during the conjugation of T. thermophila . The TAD-like structures established in the zygotic nuclei were followed by chromosome breakage at CBS sites.

Article Snippet: Then, we centrifuged at 780 g for 10 min at 4°C, transferred the solution which contains MIC to a new tube (the pellet which contains MAC was also collected and washed twice with 1× NEBuffer 2.1), centrifuged the tubes with MIC again at 780 g for 10 min at 4°C, repeated this step 3–4 times and checked by DAPI stain to see if the MIC was pure.

Techniques: Conjugation Assay, HiChIP, Hi-C