Constitutive and tissue-specific target site preferences of the maize Mutator transposon

Transposable elements insert non-randomly into host genomes, generating mutations whose consequences depend on the tissue and developmental stage in which transposition occurs. We analyzed 3.2 million de novo Mutator (Mu) insertions across maize leaf, root, pollen, and endosperm to map target site preferences and their tissue specificity at fine-scale resolution. Insertions clustered into 29,408 genomic hotspots near gene 5′ ends, collectively capturing 85% of events while covering just 1.9% of the genome. The vast majority of hotspots were consistently targeted across tissues, indicating that Mu insertion-site preference is largely constitutive rather than tissue-regulated. A minority (∼5%) showed significant tissue-associated variation in Mu activity; this variation was correlated with tissue-specific gene expression, but the relationship was imperfect: some tissue-associated hotspots overlapped broadly expressed genes, while other constitutively active hotspots overlapped genes with tissue-specific expression. These discrepancies indicate that gene expression alone is insufficient to predict Mu insertion-site preference, pointing to additional genomic or chromatin determinants. Together, our results provide a genome-wide, locus-level map of Mu targeting and a quantitative framework for understanding how developmental and genomic context shapes transposon target site preference.