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

ABSTRACT: We here adapt Oligonucleotide-mediated proximity-interactome mapping (O-MAP), a novel RNA-targeted microenvironment-mapping method, to biochemically characterize the molecular neighborhoods near individual genomic loci. By targeting O-MAP to introns within the TTN pre-mRNA, we have systematically mapped the chromatin loci, RNAs, and proteins within a cardiomyocyte-specific "RNA factory" nucleated on these TTN-derived noncoding transcripts. This revealed an unanticipated compartmental architecture that organizes trans-chromosomal domains into a hub of transcriptionally silenced chromatin, and which 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, remodels nearly every facet of factor architecture, suggesting new mechanisms in RBM20-driven dilated cardiomyopathy. This establishes O-MAP as a pioneering method for probing single-locus, microcompartment-level interactions that are opaque to conventional tools, and suggests new mechanisms by which coding genes can "moonlight" as nuclear-architectural noncoding RNAs.

INSTRUMENT(S): Orbitrap Fusion Lumos

ORGANISM(S): Homo Sapiens (ncbitaxon:9606)

SUBMITTER: David Shechner

PROVIDER: MSV000096046 | MassIVE | Tue Oct 08 13:02:00 BST 2024

SECONDARY ACCESSION(S): PXD056627

REPOSITORIES: MassIVE

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