We report the identification and cloning of a nuclear matrix protein termed matrin cyclophilin or matrin CYP. The derived sequence of matrin cyp encodes a protein of 752 amino acids with a predicted mass of 88 kDa. A 172-residue stretch at the amino terminus shows high identity with the ubiquitous family of cyclophilins. Clustered throughout the carboxyl half of the protein are a series of serine-arginine (SR) repeats that are a characteristic feature of many RNA splicing factors. Antibodies raised against matrin CYP recognize a 106-kDa antigen that is detected in isolated nuclei and quantitatively subfractionates in the nuclear matrix. Laser scanning confocal microscopy localizes most of the anti-matrin CYP-specific antigen within the nucleus in a pattern of large bright speckles that co-localize with splicing factors and diffuse nucleoplasmic staining. A strikingly similar pattern of staining is observed in cells extracted for in situ nuclear matrices. A fusion protein containing the cyclophilin domain of matrin CYP exhibits cyclosporin A (CsA)-sensitive, peptidylprolyl cis-trans-isomerase activity that is characteristic of native cyclophilins. Although total rat liver nuclei contains predominantly CsA-resistant PPIase activity, the corresponding activity in the nuclear matrix is largely CsA-sensitive.The many functions associated with the cell nucleus are temporally and spatially regulated. Nuclear proteins and nucleic acids are often partitioned into functional domains (1). Examples include the nucleoli, heterochromatin, DNA replication sites (2, 3), and transcription domains (4, 5). In addition, a number of other domains have been identified that may also perform specific functions, such as the nuclear speckles (1, 6) and coiled (7) and promyelocytic leukemia (8 -10) bodies. Determining which molecules comprise these structures and how these molecules interact will lead to a greater understanding of the mechanisms responsible for their diverse functions and the role of nuclear architecture in these processes.The proteins and nucleic acids in the cell nucleus that resist solubilization by high salt extraction, nuclease digestion, and detergent solubilization constitute a structure termed the nuclear matrix (11,12). The isolated nuclear matrix has been shown to maintain a structure similar to and containing many of the functional properties associated with the nucleus (13).Several major proteins of the internal nuclear matrix have been identified by immunological methods and termed the nuclear matrins (14). The nuclear matrins include previously characterized proteins such as human RNP 1 A, human nRNP B (15), the nucleolar protein, B23/numatrin (14, 16), the hyperphosphorylated form of RNA pol II LS (17, 18), numerous SR-related proteins (19), and a 125-kDa acidic protein, termed matrin 3 (20). A recent study has confirmed the RNP nature of many of the major nuclear matrix proteins (21).Here we present results on the isolation of a cDNA that encodes an 88-kDa protein with a cyclophilin domain at the amino ter...