Genomic characterization and evolutionary path of human satellite 1B in primates highlight a dynamic relationship with transposable elements
Human Satellite 1B (HSat1B) remains one of the least characterized classical human satellite DNAs, despite its massive abundance on the human Y chromosome. Its tripartite ~2.5 kb monomer - comprising an AluY fragment, a GC-rich unit (here named H1B) and an AT-rich block - points to an evolutionary origin tightly linked to transposable elements (TEs). Here, we present the first comprehensive comparative genomic, phylogenetic and transcriptional characterization of HSat1B across 10 primate species using Telomere-to-Telomere (T2T) and chromosome-scale long-read assemblies, combined with DNA-FISH, RNA-FISH and long-read transcriptomic analyses. We demonstrate that while canonical tandem HSat1B arrays are restricted to Homininae (human, chimpanzee, bonobo and gorilla), the core H1B unit and its structural variants (H1Bsv1 and H1Bsv2) occur across all 10 primate genomes, including strepsirrhines (lemur). This indicates that the H1B sequence predates the assembly of the composite HSat1B monomer by at least 60 million years. H1B variants consistently map within TE-rich genomic contexts, supporting a stepwise, TE-mediated model of satellite diversification and mobilization. Within Homininae, humans exhibit a dramatic lineage-specific expansion driven by Yq12 amplification (~14.2 Mb; 92% of total genomic content), whereas non-human great apes carry smaller, highly polymorphic autosomal and Y-linked arrays. Finally, we show that H1B-containing sequences are transcriptionally active in human and gorilla nuclei via RNA-FISH and characterize heterogeneous H1B/Alu chimeric non-coding transcripts in the human male germline. Collectively, our findings uncover the birth and Homininae-specific expansion of a composite satellite DNA seeded by an ancient primate sequence module and sculpted by transposable elements.