Augmented CENH3 loading is accompanied by transcriptional and epigenetic reprogramming at rice centromeres during meiosis.

BACKGROUND: Centromere identity in eukaryotes is defined epigenetically by CENH3 (CENPA), a specialized histone H3 variant essential for kinetochore establishment and faithful chromosome segregation. However, the regulatory mechanisms governing CENH3 loading during meiosis and how they differ from mitotic patterns remain insufficiently elucidated. RESULTS: Here we characterize the dynamics of CENH3 deposition across meiosis and compare them with mitotic loading in rice. Quantitative fluorescence imaging reveals a pronounced increase of CENH3 signal during meiotic prophase I, coinciding with increased accumulation of multiple kinetochore components. Super-resolution stimulated emission depletion microscopy further confirms a distinct peak of CENH3 loading at zygotene. Through low-input ChIP-seq integrated with multi-omics profiling of purified meiocytes, we find that this meiosis-specific enrichment reflects both expanded and intensified CENH3 deposition, predominantly at Ty3-Gypsy retrotransposons. This remodeling is accompanied by reduced transcription of mRNAs and small RNAs, along with a reduction in CHG methylation and H3K9me2 heterochromatin marks. CONCLUSION: Our findings uncover a previously unrecognized, meiotic-specific pattern of CENH3 loading in rice and highlight a coordinated regulatory network linking centromeric chromatin reorganization, transcriptional repression, and epigenetic modification during early meiotic progression.