Nascent transcript O-MAP reveals the molecular architecture of a single-locus subnuclear compartment built by RBM20 and the TTN RNA

Kania, E. E.; Fenix, A.; Marciniak, D. M.; Lin, Q.; Bianchi, S.; Hristov, B.; Li, S.; Camplisson, C. K.; Fields, R.; Beliveau, B. J.; Schweppe, D. K.; Noble, W. S.; Ong, S.-E.; Bertero, A.; Murry, C. E.; Shechner, D. M.

doi:10.1101/2024.11.05.622011

bioRxiv · 10.1101/2024.11.05.622011

Nascent transcript O-MAP reveals the molecular architecture of a single-locus subnuclear compartment built by RBM20 and the TTN RNA

Kania, E. E.·Fenix, A.·Marciniak, D. M.·Lin, Q.·Bianchi, S.·Hristov, B.·Li, S.·Camplisson, C. K.·Fields, R.·Beliveau, B. J.·Schweppe, D. K.·Noble, W. S.·Ong, S.-E.·Bertero, A.·Murry, C. E.·Shechner, D. M.

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Abstract

Eukaryotic nuclei adopt a highly compartmentalized architecture that influences nearly all genomic processes. Understanding how this architecture impacts gene expression has been hindered by a lack of tools for elucidating the molecular interactions at individual genomic loci. Here, we adapt oligonucleotide-mediated proximity-interactome mapping (O-MAP) to biochemically characterize discrete, micron-scale nuclear neighborhoods. By targeting O-MAP to introns within the TTN pre-mRNA, we systematically map the chromatin loci, RNAs, and proteins within a muscle-specific RNA factory organized around the TTN locus. This reveals an unanticipated compartmental architecture that organizes cis- and trans-interacting chromosomal domains, including a hub of transcriptionally silenced chromatin. The factory also recruits dozens of unique RNA-binding and chromatin-scaffolding factors, including QKI and SAFB, along with their target transcripts. Loss of the cardiac-specific splicing factor RBM20--a master regulator of TTN splicing that is mutated in dilated cardiomyopathy--remodels nearly every facet of this architecture. This establishes O-MAP as a pioneering method for probing single-locus, microcompartment-level interactions that are opaque to conventional tools. Our findings suggest new mechanisms by which coding genes can "moonlight" in nuclear-architectural roles.

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Kania, E. E., Fenix, A., Marciniak, D. M., Lin, Q., Bianchi, S., Hristov, B., Li, S., Camplisson, C. K., Fields, R., Beliveau, B. J., Schweppe, D. K., Noble, W. S., Ong, S.-E., Bertero, A., Murry, C. E., Shechner, D. M.. 2024-11-06. Nascent transcript O-MAP reveals the molecular architecture of a single-locus subnuclear compartment built by RBM20 and the TTN RNA. https://doi.org/10.1101/2024.11.05.622011

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