To determine the mechanisms of spermatogenesis, it is essential to identify and characterize germ cell-specific genes. Here we describe a protein encoded by a novel germ cell-specific gene, Mm.290718/ZFP541, identified from the mouse spermatocyte UniGene library. The protein contains specific motifs and domains potentially involved in DNA binding and chromatin reorganization. An antibody against Mm.290718/ZFP541 revealed the existence of the protein in testicular spermatogenic cells (159 kDa) but not testicular and mature sperm. Immunostaining analysis of cells at various stages of spermatogenesis consistently showed that the protein is present in spermatocytes and round spermatids only. Transfection assays and immunofluorescence studies indicate that the protein is localized specifically in the nucleus. Proteomic analyses performed to explore the functional characteristics of Mm.290718/ZFP541 showed that the protein forms a unique complex. Other major components of the complex included histone deacetylase 1 (HDAC1) and heat-shock protein A2. Disappearance of Mm.290718/ZFP541 was highly correlated with hyperacetylation in spermatids during spermatogenesis, and specific domains of the protein were involved in the regulation of interactions and nuclear localization of HDAC1. Furthermore, we found that premature hyperacetylation, induced by an HDAC inhibitor, is associated with an alteration in the integrity of Mm.290718/ZFP541 in spermatogenic cells. Our results collectively suggest that the Mm.290718/ZFP541 complex is implicated in chromatin remodeling during spermatogenesis, and we provide further information on the previously unknown molecular mechanism. Consequently, we re-designate Mm.290718/ZFP541 as "SHIP1" representing spermatogenic cell HDAC-interacting protein 1.During spermatogenesis, primary spermatocytes undergo meiotic division to produce spermatids. Early round spermatids undergo differentiation through elongation and condensation to develop into spermatozoa, a process termed spermiogenesis. Major events during this post-meiotic phase of male germ cell development include nuclear condensation and morphogenesis. In particular, spermatid chromatin undergoes reorganization to substitute histones with specific basic proteins (transition proteins). Subsequently, small arginine-rich proteins (protamines) replace transition proteins. As a result, the sperm head is condensed, and DNA is stabilized (1-3). This tightly regulated process indicates the presence of a highly organized, intrinsic genetic program involving genes unique to germ cells.Previously, we investigated mouse spermatocyte and round spermatid UniGene libraries containing 2124 and 2155 geneoriented transcript clusters (4, 5). Based on these studies, the proportions of germ cell-specific genes in the spermatocyte and round spermatid libraries were predicted as 11% (230 genes) and 22% (467 genes), respectively. Remarkably, more than half of these unique genes are currently unknown or uncharacterized. With the aid of systematic in silico and in v...