Chromatin topology control by a muscle-specific ribosomal protein

Abstract

Three-dimensional genome organization stabilizes cell-type-specific gene expression, yet the tissue-restricted factors that maintain chromatin insulation remain poorly understood. Here, we identify the muscle-specific ribosomal protein Rpl3l as an unexpected nuclear regulator of genome architecture in atrial cardiomyocytes. Rpl3l is enriched in the nucleus and nucleolus, where it binds its own genomic locus and stabilizes a CTCF-anchored chromatin boundary that represses the T-type calcium channel gene Cacna1h. Loss of Rpl3l weakens local chromatin insulation, increases long-range contacts across the Rpl3l-Cacna1h locus, derepresses Cacna1h, and increases susceptibility to atrial fibrillation (AF), which is suppressed by pharmacological inhibition of T-type calcium channels. Furthermore, AF-associated RPL3L variants exhibit impaired nucleolar localization, reduced rRNA binding, and defective repression of CACNA1H in human iPSC-derived atrial cardiomyocytes. Together, these findings reveal a ribosomal protein-chromatin axis linking genome insulation to ion-channel dosage control and cardiac rhythm stability, expanding the repertoire of cell-type-specific genome architecture regulators. HighlightsThe muscle-specific ribosomal protein Rpl3l exhibits unexpected nuclear and nucleolar enrichment. Rpl3l stabilizes a CTCF-anchored chromatin boundary to maintain atrial-specific local genome insulation. Loss of Rpl3l derepresses Cacna1h which encodes a T-type Ca2+ channel and increases atrial fibrillation susceptibility. Atrial fibrillation-associated RPL3L variants impair nucleolar targeting and CACNA1H repression