Repeat expansions in C9orf72 rewire the 3D chromatin landscape in ALS

Avila, T. U.; Wang, J.; Adams, L.; Hu, E.; Beltran, A. A.; Kozlenkov, A.; Urhekar, S.; Gonzalez, A. B. M.; Lee, H.-G.; Calabrese, J. M.; Dracheva, S.; Beltran, A. S.; Mah, W.; Won, H.

doi:10.64898/2026.02.09.704902

bioRxiv · 10.64898/2026.02.09.704902

Repeat expansions in C9orf72 rewire the 3D chromatin landscape in ALS

Avila, T. U.·Wang, J.·Adams, L.·Hu, E.·Beltran, A. A.·Kozlenkov, A.·Urhekar, S.·Gonzalez, A. B. M.·Lee, H.-G.·Calabrese, J. M.·Dracheva, S.·Beltran, A. S.·Mah, W.·Won, H.

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Abstract

Amyotrophic lateral sclerosis (ALS) is frequently driven by GGGGCC short tandem repeat (STR) expansions in C9orf72, yet the mechanisms by which these expansions lead to neurodegeneration remain incompletely understood. Here, we propose a novel mechanism involving higher-order chromatin architecture where C9orf72-STR expansions induce widespread, neuron-specific gains in chromatin loops that are closely linked to transcriptomic dysregulation in ALS. These ectopic loops colocalize with the genomic binding sites of C9orf72-STR RNAs and the architectural protein CTCF, supporting a model in which RNA-DNA interactions promote aberrant loop formation. Together, our findings demonstrate how C9orf72-STR expansions remodel the neuronal genome and disrupt gene expression, uncovering an RNA-driven mechanism of chromatin reorganization in C9-ALS that connects altered nuclear topology to gene dysregulation in neurodegeneration.

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Avila, T. U., Wang, J., Adams, L., Hu, E., Beltran, A. A., Kozlenkov, A., Urhekar, S., Gonzalez, A. B. M., Lee, H.-G., Calabrese, J. M., Dracheva, S., Beltran, A. S., Mah, W., Won, H.. 2026-02-11. Repeat expansions in C9orf72 rewire the 3D chromatin landscape in ALS. https://doi.org/10.64898/2026.02.09.704902

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