Intermediate filaments reconstituted from vimentin, desmin, and glial fibrillary acidic protein selectively bind repetitive and mobile DNA sequences from a mixture of mouse genomic DNA fragments

Employing the whole-genome PCR technique, intermediate filaments (IFs) reco nstituted from vimentin, desmin, and glial fibrillary acidic protein were s hown to select repetitive and mobile DNA sequence elements from a mixture o f mouse genomic DNA fragments. The bound fragments included major and minor satellite DNA, telomere DNA, minisatellites, microsatellites, short and lo ng interspersed nucleotide elements (SINEs and LINEs), A-type particle elem ents, members of the mammalian retrotransposon-like (MaLR) family, and a se ries of repeats not assignable to major repetitive DNA families. The latter sequences were either similar to flanking regions of genes; possessed reco mbinogenic elements such as polypurine/polypyrimidine stretches, GT-rich ar rays, or GGNNGG signals; or were characterized by the distribution of oligo purine and pyrimidine motifs whose sequential and vertical alignment result ed in patterns indicative of high recombination potentials of the respectiv e sequences. The different IF species exhibited distinct quantitative diffe rences in DNA selectivities. Complexes consisting of vimentin IFs and DNA f ragments containing LINE, (GT)(n) microsatellite, and major satellite DNA s equences were saturable and dynamic and were formed with high efficiency on ly when the DNAs were partially denatured. The major-groove binder methyl g reen exerted a stronger inhibitory effect on the binding reaction than did the minor-groove binder distamycin A; the effects of the two compounds were additive. In addition, DNA footprinting studies revealed significant confi gurational changes in the DNA fragments on interaction with vimentin IFs. I n the case of major satellite DNA, vimentin IFs provided protection of the T-rich strand from cleavage by DNase I, whereas the A-rich strand was total ly degraded. Taken together, these observations suggest that IF protein(s) bind to double-stranded DNAs at existing single-stranded sites and, taking advantage of their helix-destabilizing potential, further unwind them via a cooperative effort of their N-terminal DNA-binding regions. A comparison o f the present results with literature data, as well as a search in the NCBI database, showed that IF proteins are related to nuclear matrix attachment region (MAR)-binding proteins, and the DNA sequences they interact with ar e very similar or even identical to those involved in a plethora of DNA rec ombination and related repair events. On the basis of these comparisons, IF proteins are proposed to contribute in a global fashion, not only to genet ic diversity, but also to genomic integrity, in addition to their role in g ene expression.