DNA-protein complexes have been isolated from HeLa cell nuclei and nuclear matrix preparations. Two proteins, 55 and 66 kilodaltons in size, remain bound to HeLa DNA after treatment at 80°C in 2% sodium dodecyl sulfate and purification by exclusion chromatography on Sepharose 2B-CL in the presence of 0.3% sodium dodecyl sulfate. These proteins appear to be tightly bound but not covalently linked to the DNA, and they are distributed over the DNA with an average spacing of 40 kilobase pairs. This spacing distribution remains essentially constant throughout the cell cycle. The proteins are bound to the residual 2% of HeLa cell DNA which remains attached to the nuclear matrix after extensive nuclease digestion, a condition which reduces the average size of the DNA to -150 base pairs. Our results suggest that these tightly bound proteins are involved in anchoring cellular DNA to the nuclear matrix. These tightly bound proteins are identical by partial peptide mapping to proteins found tightly bound to the DNA of mammalian, plant, and bacterial cells (D. Werner and C. Petzelt, J. Mol. Biol. 150:297-302, 1981), implying that these proteins are involved in the organization of chromosomal domains and are highly conserved in both procaryotic and eucaryotic cells.The DNA of eucaryotic cells is organized into structural domains 30 to 90 kilobases (kb) in size. These domains are seen in metaphase chromosomes as loops or rosettes of DNA bound to a protein scaffold (10,40,43). In interphase nuclei the DNA is organized in domains of supercoiling measured at 84 to 94 kb (4,22,57), and the DNA is attached to the nuclear matrix with an average spacing of between 35 and 60 kb (25,48). Cellular DNA replication also takes place in association with the nuclear matrix (16,34,42,58), and eucaryotic DNA replicons have a size distribution similar to that of the structural domains described above (18). Several proteins that are tightly bound to cellular DNA have been implicated in maintaining supercoiled domains, binding DNA to chromosome and nuclear scaffolds, or binding to transcriptionally active genes (3,24,28,37,46,47 1981). However, proteins that mediate the interaction between cellular DNA and the nuclear matrix have not been defined.Using methods initially developed to study the adenovirus terminal protein-DNA complex (14, 21, 50), we isolated a stable DNA-protein complex from HeLa cells that contains two proteins, 55 and 66 kilodaltons (kd) in size. These proteins are tightly bound to cellular DNA and exhibit a constant average spacing of about 40 kb throughout the cell cycle. They are specifically enriched in the nuclear matrix fraction, even after 98% of the cellular DNA is removed by nuclease digestion and the size of the bulk DNA is reduced to approximately 150 base pairs (bp). These proteins also possess peptide map homology to proteins previously reported to be bound to a wide variety of procaryotic, eucaryotic, and plant cells DNAs, even after alkali treatment, pronase digestion, and phenol extraction (7,28,(60)(61)(62)(63...
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