BIOCHEMISTRY
A Study of the Structure of Isolated Chromatin* R. Chalkleyt and R. H. JensenT
ABSTWCT: Calf thymus chromatin, isolated by chemically gentle means, can be partially disrupted by shear. The resulting nucleohistone is highly heterogeneous with respect to molecular size and can be fractionated by sedimentation into nucleohistones of increasingly complex structure. The large molecules are made up of smaller nucleohistone molecules linked together noncovalently by protein cross-links. Lysine-rich histone appears to play a role in maintaining the structure of such complexes. The chemical and physical properties of large and small nucleohistones are of two classes. First, the properties in common are the general chemical composition, ultraviolet absorption spectrum, melt-
I
n the nuclei of higher organisms, chromosomal DNA exists in close association with specific proteins, both histone and non-histone (Bonner and Ts'o, 1964). When isolated nuclei are disrupted, most of the chromosomal complement can be separated from the nuclear sap by differential centrifugation. The rapid sedimentation of isolated chromatin is not simply due to the presence of DNA of high molecular weight, but is a result of the complex structural nature of the chromatin itself which is subsequently isolated as a gel (Zubay and Doty, 1959). Chemically, the preparation of chromatin gels is a gentle procedure, and inherent in work in this field is the concept that these gels may serve as worthwhile models for nuclear chromatin. We have been concerned with the physicochemical and biological properties of calf thymus chromatin (itself a gel). Because of the difficulty of studying a gel directly, we have partially disrupted chromatin by high-speed mixing and obtained nucleohistone (Bonner et ai., 1968) which has proved more amenable to physicochemical analysis. Nucleohistone prepared in this manner is heterogeneous in molecular size, and it can be fractionated by sedimentation. We have studied the properties of fractions of increasing molecular complexity in order to gain information concerning the nature of chromatin which is even more complex.
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* From the Division of Biology, California Institute of Technology, Pasadena, California. Receiaed July 19, 1968. This work was supported by U. S. Public Health Service Grant GM-13762 and by the Herman Frasch Foundation. R. H. J. was supported by International Minerals and Chemical Corp. t Present address: Department of Biochemistry, School of Medicine, University of Iowa, Iowa City, Iowa 52240. 3 Present address : International Minerals and Chemical Corp., Libertyville, Ill.
CHALKLEY
AND
JENSEN
ing profile, and a compact conformation in low ionic strength buffers ; second, those properties which are solely dependent upon the presence of a complex structure and are found only in large nucleohistones. This includes sensitivity to 4 M urea and to NaCl of concentration high enough to remove only a small amount of protein. Treatment with these materials invariably destroys the cross-linked structure of more complex nucleohistones. Fractionation of nucleohistone on the basis of sedimentation velocity also fractionates it with respect to in vitro template activity for ribonucleic acid synthesis. More complex nucleohistones direct ribonucleic acid synthesis at a reduced rate; destruction of the structure gives rise to an increased template activity.
The results with nucleohistone suggest that isolated chromatin is composed of complexes of DNA and histone forming units which are linked together by protein. The nature of this linkage has been examined and is described. A relationship has been observed between the extent of cross-linking in nucleohistone and its ability to act as a template for in vitro RNA synthesis; the more extensively cross-linked the nucleohistone, the lower its template activity. Materials and Methods Preparation of Calf Thymus Chromatin. Calf thymus tissue was obtained within minutes of slaughter, and transported to the laboratory in ice. The tissue was cleared from surrounding fat, divided into ca. 15-g pieces, and stored at -60". The isolation of thymus chromatin followed the method described by Maurer and Chalkley (1967) for calf endometrium chromatin. The calf thymus chromatin was homogenized in a final volume of 40 ml of 0.01 M Tris (pH 8.0) and dialyzed against the same overnight. The dialyzed chromatin which appears as an opalescent gel was diluted with 0.01 M Tris (pH 8.0) to a final A260 of 20 and sheared in a Virtis homogenizer at 40 V for 2 min. The homogenate was clarified by centrifuging at 18,000 rpm for 30 min. More than 95% of the DNA in the homogenate was recovered in the supernatant fractions. In order to isolate nucleohistones of differing sedimentation coefficient, unfractionated nucleohistone (7 ml) was layered onto 45 ml of a 5-30z (w/v) linear sucrose density gradient in 0.01 M Tris (pH 8.0) and centrifuged for 4.7 hr at 25,000 rpm in a Spinco SW-25.2 rotor. A glass tube (2-mm i.d.) was inserted, penetrating about five-sixths of the gradient, and the solution was pumped out (suction) using a polystaltic pump (Buchler
VOL.
7,
TABLE I :
NO.
12,
DECEMBER
1968
Sedimentation Characteristics of Nucleohistone and DNA Isolated from Nucleohistone. (S) at Half-Peak Height
Material
Bulk Solvent (M)
s;o,w6)
Rear
Front
30s nucleohistone (a).
NaCl(O,Ol)-50% D20, Tris (0.001), pH 8 Same Same Same NaCl (3)-Tris (0. l), pH 8 Same Same Same
27.0
18.2
43.5
32.2 128 132 25.2 26.0 14.0 14.5
25,l 92.2 99.7 9.6 6.4 9.7 11.5
49.4 168 159 39.6 44.0 17.7 17.8
30s nucleohistone (b) 130s nucleohistone (a) 130s nucleohistone (b) Chromatin* DNA from chromatin' 30s nucleohistone 130s nucleohistone
a The letters a and b in parentheses are two separate preparations of nucleohistone from different samples of calf thymus tissue. * Nucleoproteins dissociate fully into DNA and protein in 3 M NaCl; the s:o,w recorded is therefore that of the DNA of the nucleoprotein. c The DNA from chromatin was prepared by the Marmur (1961) procedure followed by two phenol extractions and ether extraction. DNA was prepared from the other fractions in an identical was the same as the material directly layered onto 3 M NaCl. manner, and in all cases
Instruments), and collected in 1 -ml fractions. Desired fractions were pooled and dialyzed overnight against 0.01 M Tris (pH 8.0). That this technique gives samples of moderately homogeneous S-value range is shown by the data of Tables I and 111. Preparation uf DNA. DNA was isolated from calf thymus nucleohistone by a modified Marmur procedure (Marmur, 1961), followed by two phenol extractions and subsequent removal of phenol with ether. Preparation uf R N A Pulymerase. RNA polymerase was isolated from early log-phase cells of Escherichia coli strain D-10 (a ribonuclease-minus strain) following the method of Chamberlin and Berg (1962) up to their fraction 4 (F4). Chemical Analyses. DNA and RNA were analyzed after separation using a modified Schmidt-Tannhauser procedure (Ts'o and Sato, 1959). DNA was determined by the diphenylamine assay of Burton (1956), and RNA was determined by the orcinol reaction (Dische and Schwarz, 1937). Purified calf thymus DNA (Worthington Biochemical Corp.) and yeast RNA (Sigma) were used as standards. Protein was analyzed by the Lowry procedure (Lowry et al., 1951) following separation into histone and nonhistone components. Histone was first extracted into 0.4 N HLSOl (30 min at 2'), then precipitated with 25% trichloroacetic acid and finally redissolved in 1 N NaOH for analysis. Acid-insoluble material was treated with 10% trichloroacetric acid (100' for 10 min) and the residue of nonhistone protein was dissolved in 1 N NaOH for analysis. Calf thymus histones and bovine serum albumin (Sigma) were used as standards. Ultraijiolef Absorption and Thermal Denaturufion. Ultraviolet absorption spectra were determined with a Cary 12M recording spectrophotometer. Thermal melting profiles were recorded using a Gilford Model 2000
spectrophotometer with a jacketed cuvet compartment and a linear temperature programmer. The rate of temperature increase was 0.5 "/min. Assay fur R N A Synthesis. The incubation and assay systems were those described by Marushige and Bonner (1966) with the exception that spermidine phosphate was omitted from the incubation medium. After incubation, the sample was chilled in ice, and 0.5 ml of sheared calf thymus DNA (200 pg/ml) was added as coprecipitant followed immediately by 2 ml of cold 20% trichloroacetic acid. When using RNA polymerase fraction 4 and low levels of template, the addition of a coprecipitant is strongly recommended. Sedimentation Analysis. Sedimentation velocity was studied using band-sedimentation techniques either on preformed sucrose gradients in a Spinco Model L ultracentrifuge or on self-generating density gradients in a Spinco Model E ultracentrifuge (Vinograd et al., 1963). All sedimentation coefficients were calculated from the results of analytical ultracentrifugation. Distribution of sedimentation coefficients was calculated by the method of Vinograd and Bruner (1966). Results Carf Thymus Chromatin. Calf thymus chromatin, isolated by chemically gentle methods (see Materials and Methods), exists as a gel. It has a high sedimentation velocity and is completely sedimented at 2000g in 20 min. However, DNA isolated from calf thymus chromatin has = 25, which corresponds to mol wt 12 X lo6(Studier, 1965), and the chemical composition of calf thymus chromatin by mass is DNA 1.0, histone 0.97, and nonhistone protein 0.52. It is unlikely that a simple complex of 25s DNA and protein could account for the rapid sedimentation of chromatin and we sus-
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STRUCTURE OF CHROMATIN
BIOCHEMISTRY
TABLE 11: Chemical Composition
of Calf Thymus Nucleohistones..
Nucleohistone
DNA
Histone
Nonhistone Protein
RNA
30s 130s Unfractionated nucleohistone Chromatin
1.03
0.91 =t0.02
1.03 1 0 . 0 3
0.32 =t0.03 0.31 =t0.03 0.33 0.52
