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bioRxiv · 10.1101/2023.09.14.557757

Unique territorial and sub-chromosomal organization revealed in the holocentric moth Bombyx mori

Gil, J.·Rosin, L. F.·Navarrete, E.·Chowdhury, N.·Abraham, S.·Cornilleau, G.·Lei, E. P.·Mozziconacci, J.·Mirny, L. A.·Muller, H.·Drinnenberg, I. A.
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Abstract

Hallmarks of multicellular eukaryotic genome organization are chromosome territories, compartments, and loop-extrusion-mediated structures, including TADs. However, these are mainly observed in model organisms, and most eukaryotes remain unexplored. Using Hi-C in the silkworm Bombyx mori we discover a novel chromatin folding structure, compartment S, which is "secluded" from the rest of the chromosome. This compartment exhibits loop extrusion features and a unique genetic and epigenetic landscape, and it localizes towards the periphery of chromosome territories. While euchromatin and heterochromatin display preferential compartmental contacts, S domains are remarkably devoid of contacts with other regions, including with other S domains. Polymer simulations show that this contact pattern can only be explained by high loop-extrusion activity within compartment S, combined with low extrusion elsewhere through the genome. This unique, targeted extrusion represents a novel phenomenon and underscores how evolutionarily conserved mechanisms--compartmentalization and loop extrusion--can be repurposed to create new 3D genome architectures.

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Gil, J., Rosin, L. F., Navarrete, E., Chowdhury, N., Abraham, S., Cornilleau, G., Lei, E. P., Mozziconacci, J., Mirny, L. A., Muller, H., Drinnenberg, I. A.. 2023-09-16. Unique territorial and sub-chromosomal organization revealed in the holocentric moth Bombyx mori. https://doi.org/10.1101/2023.09.14.557757

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