Transcriptome profiling identifies the chromatoid body as a dynamic center for RNA surveillance and transcript sorting during spermatogenesis

The chromatoid body (CB) is a hallmark of haploid male germ cells, but how it selects and regulates RNAs has remained unclear. Here we define the RNA landscape of the CB by transcriptome and small RNA profiling of isolated CBs throughout mouse round spermatid differentiation. We find that the CB selectively concentrates pachytene piRNAs, retrotransposon transcripts, specific mRNA isoforms and intron-retaining mRNAs, revealing extensive RNA sorting within this cytoplasmic germline condensate. The enrichment of transposable element transcripts together with PIWI-piRNA complexes identifies the CB as a surveillance center that may safeguard genome integrity in post-meiotic haploid cells. Unexpectedly, mRNA recruitment is not determined by predicted piRNA targeting. Instead, transcript localization is encoded by a combinatorial set of intrinsic sequence and structural features that accurately predict CB enrichment at isoform resolution. These findings establish the CB as a dynamic post-transcriptional regulatory compartment that integrates genome surveillance, RNA quality control and selective transcript sorting, uncovering general principles through which biomolecular condensates shape cell-specific transcriptomes.