Chromatin remodeling is a major event that occurs during mammalian spermiogenesis, the process of spermatid maturation into spermatozoa. Nuclear condensation during spermiogenesis is accomplished by replacing somatic histones (linker histone H1 and core histones) and the testis-specific linker histone, H1t, with transition proteins and protamines. It has long been thought that H1t is the only testis-specific linker histone, and that all linker histones are replaced by transition proteins, and subsequently by protamines during spermiogenesis. Here, we report the identification and characterization of a spermatid-specific linker histone H1-like protein (termed HILS1) in the mouse and human. Both mouse and human HILS1 genes are located in intron 8 of the ␣-sarcoglycan genes. HILS1 is highly expressed in nuclei of elongating and elongated spermatids (steps 9 -15). HILS1 displays several biochemical properties that are similar to those of linker histones, including the abilities to bind reconstituted mononucleosomes, produce a chromatosome stop during micrococcal nuclease digestion, and aggregate chromatin. Because HILS1 is expressed in late spermatids that do not contain core histones, HILS1 may participate in spermatid nuclear condensation through a mechanism distinct from that of linker histones. Because HILS1 also belongs to the large winged helix͞forkhead protein superfamily, HILS1 may also regulate gene transcription, DNA repair, and͞or other chromosome processes during mammalian spermiogenesis.spermatogenesis ͉ transition nuclear proteins ͉ in silico subtraction ͉ genome database mining H istones are a family of basic proteins that organize eukaryotic DNA into a compact chromatin. There are five major classes of histones, the core histones H2A, H2B, H3, and H4, and the linker histones, H1. Two of each of the four core histones constitute an octamer unit of the nucleosome particle. H1 histones bind to DNA in the nucleosome and to the linker DNA between nucleosomes, thereby facilitating the compaction of nucleosomes into a 30-nm chromatin fiber and higher-order chromatin structures (1). These interactions between histones and DNA modulate gene activity, and both core and H1 histones have profound effects on transcription (2, 3). Among the five histone classes, H1 histones exhibit the most diversity. In mice and humans, there are eight previously described H1 subtypes, including the five somatic subtypes H1a-H1e, the replacement subtype H1o, the testis-specific linker-histone H1t (4-6), and the oocyte-specific H1 linker histone, H1foo (7). The genomic organizations of these histone H1 genes are conserved (8,9).Spermatogenesis is the process of development of male germ cells from spermatogonia to highly differentiated spermatozoa. During spermatogenesis, chromatin is restructured, and dramatic changes in histone gene expression are observed (10). In spermatogonia and preleptotene spermatocytes (cells undergoing DNA replication), the H1a and H1b linker histones are expressed (11). During meiotic prophase, striking ...