Chromatin architecture: investigation of a subunit of chromatin by dark field electron microscopy

Chromosomal subunits in active genes have an altered conformation

Ten percent digestion of isolated nuclei by pancreatic deoxyribonuclease I preferentially removes globin DNA sequences from nuclei obtained from chick red blood cells but not from nuclei obtained from fibroblasts, from brain, or from a population of red blood cell precursors. Moreover, the nontranscribed ovalbumin sequences in nuclei isolated from red blood cells and fibroblasts are retained after mild deoxyribonuclease I digestion. This suggests that active genes are preferentially digested by deoxyribonuclease I. In contrast, treatment of red cell nuclei with staphylococcal nuclease results in no preferential digestion of active globin genes. When the 11S monomers obtained after staphylococcal nuclease digestion of nuclei are then digested with deoxyribonuclease I, the active globin genes are again preferentially digested. The results indicate that active genes are probably associated with histones in a subunit conformation in which the associated DNA is particularly sensitive to digestion by deoxyribonuclease I.

Chromatin and nucleosome structure

Chromatin nucleosomes (mononucleosomes through pentanucleosomes) have been isolated by staphylococcal nuclease digestion of calf thymus nuclei. The peak value ellipticity is the same for all oligomers, 1900 deg cm2, mol-1 at 280-nm, 23 degrees C. The dh280/dT vs T show a progressive increase in Tm of the main thermal band (73.5 degrees C, monomer; 79 degrees C, pentamer). Very small amounts of free DNA can be observed in the melting profiles, and shoulders at 60 degrees C and 93 degrees C appear and increase in magnitude as the particle size increases. The magnitude of the change, delta[theta]280, increases with oligomer size. This pattern could result from an initial unfolding of an asymmetric assembly of nucleosomes (polynucleosome superhelix) in addition to the denaturation of the internal nucleosome structure, and a subsequent or simultaneous denaturation of the double strand DNA. The extent of this unfolding appears to depend upon the size of the oligomer and therefore implies interactions between asymmetrically assembled neighboring nucleosomes.

Minichromosome of simian virus 40: presence of histone HI

In contrast to conclusions of previous studies /I-3/ claiming the absence of histone HI from the SV40 and polyoma viral minichromosomes we have found that a preparation of purified SV40 minichromosomes does contain histone HI. The content of HI in relation to other four histones in the SV40 minichromosomes is close to that in the cellular chromatin. Histone HI in the isolated SV40 minichromosomes is bound apparently to internucleosomal DNA stretches as was shown already for HI in the cellular chromatin /4/. In addition it was found that more than 90% of the purified SV40 minichromosomes migrated as a single discrete deoxyribonucleoprotein band upon agarose gel electrophoresis.

Removal of histone H1 exposes a fifty base pair DNA segment between nucleosomes

Micrococcal nuclease has been used to prepare chromatin from HeLa cells and to probe the structure of HeLa chromatin under various ionic conditions and after the removal of chromatin proteins by salt extraction. The results suggest that (1) HeLa chromatin DNA exists as 150-160 base pair beads interspersed with 40-50 base pair bridges;(2) the bead and bridge conformation exists at physiologic salt concentrations; and (3) removal of histone H1 renders the 40-50 base pair bridge, but not the 150-160 base pair bead, more nuclease susceptible.

Cross-linking of DNA in situ as a probe for chromatin structure

The photochemical cross-linking of DNA in situ in chromatin is blocked over short intervals. Electron microscopy of DNA cross-linked in chromatin reveals the lengths of protected regions and provides a map of their sites along the DNA. Protected regions occur most frequently in tandem and have a basic length of 160 to 200 base pairs.

Stimulation of transcription on chromatin by polar organic compounds

Polar organic compounds, including DMSO, increase RNA synthesis on isolated chromatin by E. coli RNA polymerase and RNA polymerase II from calf thymus. Transcription is stimulated on chromatin from Friend-virus-infected erythroleukemia cells and from various other sources. Using procedures which inhibit specifically the formation of a stable initiation complex, it is shown that the stimulation does not result from an increase in initiation of both E. coli and the eukaryotic RNA polymerase. After separation of chromatin into template active and inactive fractions, DMSO increases RNA synthesis by a factor of about 1.5 using the template inactive fraction, while stimulation of transcription on the template active portion is lower (factor of 1.2). It is suggested that the effect on RNA synthesis is mediated by a weakening of the apolar interactions between histones in chromatin subunits, releasing transcription partially from the constraints imposed by histones.

Genomic transcriptional activity and the structure of chromatin

Nucleic acid hybridisation has shown that micrococcal nuclease-derived chromatin subunits from the cells of Xenopus laevis contain fragments of ribosomal 28S, 18S and 5S RNAS within the population of 200 base-pair pieces of DNA. Subunits from cultured embryonic cells actively transcribing ribosomal RNA contain only 70-74% of the cistrons present in undigested wild-type DNA, while subunits from adult erythrocytes not active in RNA transcription contain close to 90% of the ribosomal cistrons in native chromatin.

Heterogeneity of chromatin subunits in vitro and location of histone H1

Chromatin subunits ("nucleosomes") which were purified by sucrose gradient centrifugation of a staphylococcal nuclease digest of chromatin have been studied. We found that such a preparation contains nucleosomes of two discrete types which can be separated from each other by polyacrylamide gel electrophoresis. Nucleosome of the first type contains all five histones and a DNA segment of approximately 200 base pairs long, whereas nucleosome of the second type lacks histone H1 and its DNA segment is approximately 170 base pairs long, i.e., about 30 base pairs shorter than the DNA segment of the nucleosome of the first type. Purified dimer of the nucleosome also can be fractionated by gel electrophoresis into three discrete bands which correspond to dinucleosomes containing two molecules of histone H1, one and no H1. These and related findings strongly suggest that the H1 molecule is bound to a short (approximately 30 base pairs) terminal stretch of the nucleosomal DNA segment which can be removed by nuclease (possibly in the form of H1-DNA complex) without any significant disturbance of main structural features of the nucleosome.

Analysis of subunit organization in chicken erythrocyte chromatin

Micrococcal nuclease digestion of intact chicken erythrocyte nuclei is shown to result in the formation of core nucleoprotein particles containing about 140 base pairs of DNA. These core particles, which are almost entirely devoid of histones f1 and f2c, are derived from transient nucleoprotein particles containing an average of approximately 180 base pairs of DNA. Oligomers of these latter particles may be isolated after brief nuclease digestion. The time course of digestion of these oligomers demonstrates the existence of "spacer" regions of more accessible DNA between core particles. Redigestion of purified monomer core nucleoprotein particles gives rise to both single-strand and double-strand DNA fragment patterns similar to those resulting from digestions of chromatin in situ. This observation indicates that the core particles we isolate are representative of nucleoprotein structures existing within the nucleus.

Low-angle neutron scattering from chromatin subunit particles

Monomer chromatin particles containing 140 base pairs of DNA and eight histone molecules have been studied by neutron scattering. From measurements in various H2O/D2O mixtures, radii of gyration and the average scattering density of the particle were determined. The radius of gyration under conditions when scattering from the DNA dominates is 50A, and when scattering from the protein dominates, 30A. Consequently the core of the particle is largely occupied by the histones while the outer shell consists of DNA together with some of the histone.