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bioRxiv · 10.64898/2026.04.25.719469

Kilobase-scale compartments enabled by CRUSH reveal regulatory programs across cell types, single-cells, and ancient mammoths

Kalluchi, A.·Nolan, B.·Reznicek, T. E.·Harris, H. L.·Udupa, D.·Cummings, C. T.·Rowley, J.
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Abstract

How chromatin is spatially organized in the nucleus has long been studied through the lens of large-scale A/B compartments, but whether these sizes reflect true biological units or analytical artifacts has remained unclear. We find that limits imposed by the conventional eigenvector-based compartment calling have required extreme sequencing depth and coarse resolution, obscuring regulatory-scale organization. We developed CRUSH to iteratively refine compartments to 1 kb resolution without the need for extreme sequencing depth, we show that kilobase-scale A/B segregation (micro-compartments) is evident across cell types. Across these maps, we demonstrate that RNA polymerase II pausing contributes to a sub-genic compartment signature at the transcription start site and that active enhancers almost universally occupy the A compartment. We then show that fine-scale compartment maps can resolve cancer subtype-specific regulatory programs, single-cell tissue identity, and cold-adaptation regulomes in a 52,000-year-old woolly mammoth. These findings establish chromatin compartmentalization as a gene-scale regulatory feature with broad implications for development, disease, and genome evolution. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=176 SRC="FIGDIR/small/719469v1_ufig1.gif" ALT="Figure 1"> View larger version (48K): org.highwire.dtl.DTLVardef@15c1992org.highwire.dtl.DTLVardef@192f541org.highwire.dtl.DTLVardef@123a737org.highwire.dtl.DTLVardef@1b7292f_HPS_FORMAT_FIGEXP M_FIG C_FIG CRUSH uses iterative resolution walking to identify and correct A/B compartment measurements. This allows identification of A/B compartments at kilobase resolution with low sequencing depth and consistency across methodologies. Kilobase-scale compartments reveal sub-genic compartment organization, compartment identities in single-cells, and a distinct cold-adapted regulome in mammoths.

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Kalluchi, A., Nolan, B., Reznicek, T. E., Harris, H. L., Udupa, D., Cummings, C. T., Rowley, J.. 2026-04-28. Kilobase-scale compartments enabled by CRUSH reveal regulatory programs across cell types, single-cells, and ancient mammoths. https://doi.org/10.64898/2026.04.25.719469

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