Nuclease digestion in between and within nucleosomes

Abstract

In the course of digestions of rat liver nuclei with micrococcal nuclease the size of the nucleosomal DNA is shortened by 50-60 nucleotide pairs from starting lengths of about 200, 400, 600, 800, etc. nucleotide pairs in the monomeric and oligomeric nucleosomes, respectively. Acid soluble DNA material is created relatively slowly as compared to the rate of formation of subnucleosomal material. More DNA with lengths in between the 200, 400, etc. nucleotide pairs of nucleosomal DNA is formed when digestions with micrococcal nuclease are carried out at 0 to 10 degrees C compared to 40 degrees C. With DNAase II, on the other hand, formation of a 200 nucleotide pair pattern is favoured at the low temperatures. Apparently, the accessibility of potential cleavage sites in between and within nucleosomes depends strongly on the conditions of digestion. Possible reasons for this dependence are discussed.

On the mechanism of nucleodisome splitting off by nucleases

“…In agreement with [6,7] our results indicate that DNase II initially cleaves erythrocyte nuclear DNA at 210 bp intervals ( fig.lB) and that, as digestion proceeds, the 100 bp periodicity of DNA fragmentation is revealed ( fig. 1C).…”

“…To analyze the mechanism of dinucleosomal periodicity of chromatin fragmentation we used DNase II -a nuclease which is able to cleave chromatin not only in the linker DNA region (just like micrococcal nuclease), but also within nucleosome core giving rise to a 100 bp repeat [5][6][7]. We have demonstrated that formation of a double-nucleosome repeat generated by DNase II is the result of DNA cleavage at the sites identified within nucleosome core [7].…”

Nuclease digestion patterns as a criterion for nucleosome orientation in the higher order structure of chromatin

“…These data suggest that the 'double nucleosome' and the 'half nucleosome' repeat patterns have a common origin determined by the higher order structure of chromatin and not by the mode of digestion of the nucleases. Indeed when nuclei were digested with micrococcal nuclease at O"C, two distinct shoulders were seen between mono-and dinucleosome peaks with lengths of 260 and 320 bp [18] corresponding to N + 50 and to 2N-1OOn.…”

Herpes Simplex Virus 1 DNA Is in Unstable Nucleosomes throughout the Lytic Infection Cycle, and the Instability of the Nucleosomes Is Independent of DNA Replication

“…The chromatin structure is classically probed with nucleases (61). The endonuclease micrococcal nuclease (MCN), for example, preferentially cleaves linker DNA between nucleosomes (2,19). Mild MCN digestions first cleave linker DNA sparsely, releasing polynucleosomes, which are eventually cleaved to mononucleosomes.…”