The Structure of Chromatin

Abstract

The DNA in chromatin of isolated thymus nuclei, and in two different preparations of deoxyribonucleoprotein extracted from chromatin, has been digested with DNase. Chromatin is the term coined by Flemming to designate the material in the cell nucleus that takes basic stains. Flemming, on the basis of experiments by Zacharias, recognized that DNA is the substance in chromatin that takes basic stains (1). Kossel discovered histones and was aware that these basic proteins are combined with DNA in chromatin (2). Proteins other than histones are also combined with DNA in chromatin (3). Chromatin is a deoxyribonucleoprotein complex containing a large number of protein components and some RNA; the structure of this complex is not well understood. In the present study, the enzyme DNase is used to probe the structure of chromatin. Experiments are reported concerning the action of DNase on chromatin in isolated cell nuclei and on two different preparations of deoxyribonucleoprotein (DNP) extracted from nuclei. The action of DNase on preparations of DNP has been the subject of some recent investigations (4-6).Although DNP has been extracted from chromatin for 79 years, it was only about 10 years ago that some investigators began referring to the extracted material as chromatin (7). This practice seems reasonable, because the composition of the extracted DNP and some of its properties resemble those of chromatin in the nucleus. Even so, just how far this resemblance goes is not known, and it is unlikely that material as complex as chromatin is not significantly changed when extracted by any of the methods presently used. The likelihood of change is shown by the observations reported here on two preparations of DNP, both of which have been termed "chromatin" by different investigators, but which differ considerably from each other when treated with DNase. I would suggest that the term chromatin be reserved to designate the material in the cell nucleus for which Flemming first used the word, and that each DNP preparation have a subscript referring to those who devised the method by which that particular preparation was made. In this way we shall be reminded continually that the purpose of these investigations is to understand the chromatin of the cell nucleus-surely a highly significant material.Materials. Nuclei were isolated from calf thymus in a 0.25 M sucrose-mM CaCl2 medium (8). In some experiments nuclei were freshly prepared; in other experiments preparations stored at -60'C were used, for it was found that DNase acted on freshly prepared and on nuclei stored frozen in much the same way. DNP was prepared by two different methods. One preparation, beginning with thymus nuclei isolated in sucrose, was that recently described by Clark and Felsenfeld (6). It was stored at -60'C in 0.2 mM EDTA, pH 7.0, and was a clear solution at a concentration of 0.01 mg of DNA phosphorus per ml. It should be noted that this preparation of DNP, as are some others described in recent years, is similar to that described by Zubay an...

Identification of nonhistone chromatin proteins in chromatin subunits.

“…Hewish and Burgoyne (5) demonstrated that a uniform size of chromatin DNA could be obtained by Ca++-Mg++-dependent endonuclease digestion. The electron microscopic observations made by Olins and Olins (6,7) and Woodcock et al (8,9) indicate that chromatin structure resembles beads on a string, greatly substantiating the biochemical investigations (1)(2)(3)(4)(5).…”

“…Clark and Felsenfeld (2) used chemical probes to measure the accessibility of the DNA in chromatin and reported that about half of the DNA could be titrated with divalent cations, polylysine, or histones and could be subjected to staphylococcal nuclease or deoxyribonuclease I digestion. Others also used nucleases as probes to study the interaction of DNA and histones, as well as to isolate an active and inactive chromatin fraction (3,4). Hewish and Burgoyne (5) demonstrated that a uniform size of chromatin DNA could be obtained by Ca++-Mg++-dependent endonuclease digestion.…”

The Dynamics of DNA Methylation in Schizophrenia and Related Psychiatric Disorders

“…In more recent times, biochemical studies on the structure and function of histone proteins began to appear in the literature during the 1950's. It soon became clear that deoxyribonucleoprotein is complex and exists in different forms as probed by deoxyribonuclease I (Mirsky, 1971). Transitions between euchromatin and heterochromatin are associated with active and inactive transcription, respectively, and are mediated by modifications in the structures of histone proteins comprising the nucleosome (Figure 1).…”

The Mechanisms of Action of the Carcinogenic Nitroso and Related Compounds

“…2 conditions under which such interactions could take place: the relevant part of the nucleic acid base must be accessible and the particular sulphur containing nucleohistones, or other specific protein, must be in reduced form at the time of encounter with the activated molecule of the carcinogen. The spatial distribution of the specific reactive centres in chromatin and their accessibility (Mirsky, 1971) probably determine that only compounds of appropriate size and geometry, and having apposite functional groups, could fit and interact with it in a concerted manner. When bulky substituents are present, e.g.…”