On the Structure of Eukaryotic, Prokaryotic, and Viral Chromatin

Varshavsky, Alexander; Bakayev, Valery V.; Nedospasov, Sergei A.; Georgiev, G.P.

doi:10.1101/sqb.1978.042.01.049

Cited by 54 publications

(18 citation statements)

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“…(16,17). Secondly, electron micrographs of SV40 chromatin (18,19) show the same kind of zigzag structure which has been found in systematic electron microscope studies on cellular chromatin, and which has been attributed to the presence of HI on the side of the nucleosome at the entry and exit points of the DNA (20 (20)).…”

Section: Is There a Linkage Number Problem?mentioning

confidence: 72%

The helical periodicity of DNA on the nucleosome

Klug¹,

Lutter²

1981

Nucl Acids Res

164

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Section: Is There a Linkage Number Problem?mentioning

confidence: 72%

The helical periodicity of DNA on the nucleosome

Klug¹,

Lutter²

1981

Nucl Acids Res

164

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“…Yet even in the worst case, where only 40% of the Poisson distribution with the smallest hit number were repaired, the average number of hits per repaired molecule would be about 4.1 at the highest dose. The near independence of superhelical density on the number of breaks indicates that the supercoils retained in the repaired DNA are not attributable to a segregation of the F DNA into a few domains in which supercoiling is independently relaxed, as can occur in the E. coli chromosome (17,24 (25), transcription (26), and some forms of DNA repair (27) (7)(8)(9) and that the nucleosome-like structures are relatively unstable (10 …”

Section: Resultsmentioning

confidence: 99%

“…Prokaryotic DNA has superhelical densities similar to those found in eukaryotes (5,6), but thereis no clear evidence for restraint of the supercoils in structures analogous to the nucleosome. Histone-like proteins are found in prokaryotes (7,8), and their mode of interaction with DNA in prokaryotic chromosomes may have some similarity with nucleosomic histones (8,9). Also, beaded structures having the appearance of nucleosomes have been seen in an electron microscope study of DNA from partially lysed bacteria (10).…”

mentioning

confidence: 99%

Supercoils in prokaryotic DNA restrained in vivo.

Pettijohn¹,

Pfenninger²

1980

Proc. Natl. Acad. Sci. U.S.A.

128

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Cells of Escherichia coli containing the plasmid F were 7-irradiated with various doses to introduce determined numbers of single-strand breaks in the F DNA. The cells were then incubated to permit repair of the breaks while DNA gyrase was inhibited with coumermycin to limit restoration of any relaxed supercoils. Repaired, covalently continuous F DNA was isolated and its superhelical density was measured by two different methods. Both indicated that a major part (50-60%) of the negative superhelical turn's were maintained in the repaired molecules, suggesting that the supercoils are restrained in vivo.In eukaryotic chromatin and chromosomes, the first order of DNA packaging seems to be attained via the nucleosome structure (for reviews, see refs. 1 and 2). The double-helical DNA in this particle is coiled through its interaction with the core histones into about 13/4 toroidal superhelical turns per core nucleosome (3, 4). Prokaryotic DNA has superhelical densities similar to those found in eukaryotes (5, 6), but thereis no clear evidence for restraint of the supercoils in structures analogous to the nucleosome. Histone-like proteins are found in prokaryotes (7,8), and their mode of interaction with DNA in prokaryotic chromosomes may have some similarity with nucleosomic histones (8, 9). Also, beaded structures having the appearance of nucleosomes have been seen in an electron microscope study of DNA from partially lysed bacteria (10).However, pure DNA can spontaneously form beaded structures in certain solvents (11), and electron microscopic evidence alone cannot be considered sufficient to establish the existence of the prokaryotic equivalent of a nucleosome.DNA gyrase seems to play a vital role in forming DNA supercoils in prokaryotic chromosomes. This enzyme can catalyze an ATP-driven reaction that has the topological effect of decreasing the linking number between the two continuous strands of a DNA double helix, thereby introducing negative superhelical turns into the DNA (12). When the DNA gyrase is inhibited by coumermycin (or oxolinic acid) in intact Escherichia coli cells, X DNA molecules, which are converted in vivo to the covalently circular form, attain only a small fraction of their normal superhelical density (13,14). This result indicates that the DNA gyrase activity is necessary for the formation (or the maintenance or both) of at least part of the DNA supercoils in prokaryotic cells. Thus, it seems possible that, in viwo, supercoils in prokaryotic DNA may not be stabilized by a nucleosome-like structure and that the Major reason for both the formation and maintenance (15) of DNA supercoils is the activity of DNA gyrase. Other alternatives include the possibility that DNA supercoils catalyzed by the DNA gyrase are subsequently restrained in a nucleosome-like structure by interactions involving molecules other than DNA gyrase (9). These two alternatives differ in that in the former case the double helix (17). After irradiation, the 32p-labeled cells kept at 0C were divided into several p...

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“…Reconstitution studies with the four intranucleosomal histones and small circular DNAs in the presence of nicking-closing enzyme have revealed that the DNA coiling around a nucleosome changes the DNA linking number by -1 (14). The histone Hl-induced compaction of the "beads on a string" into a 250-A-diameter supranucleosomal structure (15) does not cause further changes in the linking number (16). Because the nicking-closing enzyme relaxes the spacer DNA (16), the observed change in the linking number must be due to the particular DNA structure in the nucleosome.…”

mentioning

confidence: 99%

Structure of chromatin and the linking number of DNA.

Worcel¹,

Strogatz²,

Riley³

1981

Proc. Natl. Acad. Sci. U.S.A.

200

118

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Recent observations suggest that the basic supranucleosomal structure of chromatin is a zigzag helical ribbon with a repeat unit made of two nucleosomes connected by a relaxed spacer DNA. A remarkable feature of one particular ribbon is that it solves the apparent paradox between the number of DNA turns per nucleosome and the total linking number of a nucleosome-containing closed circular DNA molecule. We show here that the repeat unit of the proposed structure, which contains two nucleosomes with -13/4 DNA turns per nucleosome and one spacer crossover per repeat, contributes -2 to the linking number of closed circular DNA. Space-filling models show that the cylindrical 250-A chromatin fiber can be generated by twisting the ribbon.It is now well-established that the unit structure of chromatin, the nucleosome (1-3), is a flat cylindrical particle (110 X 110 x 57 A) with DNA wrapped around a histone octamer in a lefthanded toroidal supercoil of approximately 80 base pairs (bp) per turn (4). There are 146 bp of DNA in the nucleosome core describing -13/4 superhelical turns (5) and 20-95 bp of spacer DNA between neighboring nucleosome cores (6).The nature of the supranucleosomal structure of chromatin is less clear. Electron microscopic studies of eukaryotic nuclei have revealed a "thin" 100-A chromatin fiber and a "thick" 250-A fiber (7-9). Many past models have assumed that neighboring nucleosomes are stacked side by side to generate a 100-A nucleofilament, which is further coiled into a 250-A "solenoid" (10, 11). The unstacked 100-A fiber ("beads on a string") can be readily observed in nuclei and chromatin preparations spread under isotonic conditions (1, 2, 12). A stacked 100-A nucleofilament also has been detected, but only at high salt concentrations (11). Although the 100-A fiber is present in histone Hi-depleted chromatin, the 250-A fiber is never observed under these conditions (11, 12). Thus, histone HI must play a role in the further compaction of the linear chain of beads (12, 13). Reconstitution studies with the four intranucleosomal histones and small circular DNAs in the presence of nicking-closing enzyme have revealed that the DNA coiling around a nucleosome changes the DNA linking number by -1 (14). The histone Hl-induced compaction of the "beads on a string" into a 250-A-diameter supranucleosomal structure (15) does not cause further changes in the linking number (16). Because the nicking-closing enzyme relaxes the spacer DNA (16), the observed change in the linking number must be due to the particular DNA structure in the nucleosome.The linking number L of a closed circular DNA (ccDNA) molecule is the number of topological revolutions made by one strand about the other [counted after the molecule is constrained to lie in a plane (17)]. L is a topological invariant (i.e., an integer which is unchanged by all deformations that leave the strands intact). Moreover, it is related to the writhing number W and the twist number T by the equation (18-21)W is a real number that measures the shape...

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On the Structure of Eukaryotic, Prokaryotic, and Viral Chromatin

Cited by 54 publications

References 0 publications

The helical periodicity of DNA on the nucleosome

The helical periodicity of DNA on the nucleosome

Supercoils in prokaryotic DNA restrained in vivo.

Structure of chromatin and the linking number of DNA.

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