An image-based CRISPR screen reveals splicing-mediated control of HP1α condensates

Heterochromatin Protein 1α (HP1α) is a fundamental component of constitutive heterochromatin, forming subnuclear condensates whose regulation and function remain poorly understood. Here, we present an image-based CRISPR screen targeting nuclear factors that identifies splicing as a pivotal pathway regulating HP1α condensates. We discovered that unspliced intronic RNA modulates HP1α condensates by interacting co-transcriptionally with HP1α. By modulating the intron content, RNA processing restricts HP1α-RNA interactions at chromatin, thus enabling heterochromatin organization. Disruption of HP1α condensates due to enhanced interactions with unspliced RNA leads to loss of heterochromatin and the activation of stress response protective genes. We propose that RNA is a central component of heterochromatin that modulates HP1α condensates, and that RNA processing enzymes act as a surveillance mechanism for condensates by dynamically regulating the network of multi-valent interactions between RNA and chromatin factors. This model underscores the crosstalk between chromatin organization, transcription, and RNA processing, potentially governing broader nuclear functions.