Previously we have reported that Hi-C methods did not detect compartment-, TAD-, and loop-like high-order chromatin structures in the transcriptional active macronuclei (MAC) of Tetrahymena thermophila. However, it is still unclear whether there are gene-scale chromatin folding in the MAC beyond the resolution limit of Hi-C. Here, we explored the nucleosome resolution chromatin architecture of the MAC by Micro-C. We found that there are transcription related gene-body associating domains (GADs) in the MAC, which preserved at different stages. In addition, the promoter regions of high expressed genes contact with each other and formed chromatin loop-like and stripe-like structures, suggesting that there is loop extrusion in the MAC. Additionally, our Micro-ChIP results showed that RNA Pol II was associated with loop-like and stripe-like structures. Taken together, these data provide high-resolution chromatin architectures of the MAC, and reveal the present of transcription-associated GADs and loop-like structures in the MAC of T. thermophila.

 

3D genome, Transcription, Tetrahymena