Metabolic behaviour of a stable DNA-protein complex

Stably DNA-bound chromosomal proteins

DNA accomplishes its biological function in a complex with nuclear proteins. A minor protein fraction has been found in chromatin which could not be dissociated from DNA by reagents abolishing non-covalent type of interactions. The controversy surrounding the nature of the protein moiety and the nature of the bond linking the two components on the one hand, and the fact pointing to its evolutionary conservatism and metabolic stability on the other, make it necessary to critically evaluate the data in view of the possible biological function for such proteins.

DNA sequences tightly bound to proteins in mouse chromatin: identification of murine MER sequences

The finding of stably (tightly) associated DNA-protein complexes in eukaryotic chromatin has provoked many hypotheses and speculations concerning their possible role. While the answer of this question is not envisaged yet, it is clear that elucidation of the nature of the individual components involved in such complexes is a necessary step in this direction. Here, the nature of several mouse DNA sequences in the vicinity of a putative stably attached protein is studied. Eight independently isolated clones containing such sequences were compared to known sequences in GenBank. Two clones were found to belong to different subfamilies of repetitive sequences, organized into a larger family--the L1md family. One clone harbors a sequence that is a member of the Alu-type family. Four of the cloned sequences are preset in low copy numbers, but the computer search found similar sequences in various genomic regions of different rodents. These facts, together with the finding that regions homologous to the above clones often flank other repetitive elements in the genome, suggest that the cloned sequences belong to new, not yet described families of repeats in the murine genome. It is possible that they correspond to the medium reiteration frequency sequences, MER-sequences, discovered recently in the human genome (Jurka, 1990; Kaplan and Duncan, 1990). Particularly intriguing is the homology found at the integration sites of polyoma virus in two transformed cell lines with two of these clones.

Binding of sequences from the 5'- and 3'-nontranscribed spacers of the rat rDNA locus to the nucleolar matrix

Nucleolar matrix structures were obtained under different extraction conditions from highly purified isolated nucleoli. Their ultrastructural appearance, protein composition and capacity to bind rDNA preferentially were studied in a model binding system. A region spanning approximately 25 kb in the rat ribosomal gene locus was screened for DNA sites capable of specifically interacting with the proteins of the nucleolar matrix (MARs). Two such sites were identified: one is located on an EcoRV-KpnI fragment in the 5'-nontranscribed spacer region, between two repetitive elements and close to the transcription initiation site; the other MAR is on a PvuII-BamHI fragment located in the 3'-nontranscribed region, encompassing an element 85% homologous to a B2-sequence. The two MARs are located in regions rich in polypyrimidine/polypurine tracks and contain a few elements homologous to the consensus sequence for topoisomerase II. This indicates that the "attachment sites" for the ribosomal genes belong to the same class of sequences as the MARs attaching the chromosomal DNA to the nuclear matrix.

An evolutionarily conserved protein fraction stably linked to DNA

Chromatins from four evolutionarily remote species (insect, fish, amphibian and bird) were isolated, high-salt-extracted and extensively deproteinized to remove noncovalently associated proteins. A protein fraction resisting the extraction procedures was found firmly linked to DNA in all four chromatins. Two-dimensional tryptic peptide mapping revealed a remarkable evolutionary conservativeness of this protein component, suggesting an indispensable function for it in the nucleus.

A protein fraction stably linked to DNA in plant chromatin

DNA from the chromatin of roots and shoots of maize seedlings was isolated and extensively deproteinized by repeated high-salt extractions, by subsequent deproteinizations eliminating noncovalently associated proteins and by CsC1 density gradient centrifugation. Nevertheless, a protein component resisting all extraction procedures was found firmly associated to plant nuclear DNA. This component was responsible for the (125)I uptake when a DNA preparation had been labeled by the chloramine-T method.A residual oligodeoxynucleotide-oligopeptide complex was obtained after extensive digestions of the initial DNA-protein complex with proteases and nucleases. The stability of this complex to different chemical treatments suggested a phosphoester type of a linkage. The hydrolysis of this complex by phosphodiesterases indicated that the protein component was linked to plant chromosomal DNA through a phosphodiester bond formed by a hydroxyaminoacid and a 5'-end DNA phosphate. Two-dimensional tryptic peptide mapping of the proteins isolated from the two maize chromatins revealed a high degree of similarity to the corresponding proteins of animal origin. Its conservative structure suggests an important role for this protein component in the functioning of the eukaryotic genome.