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G Felsenfeld

Publications and source records attributed to G Felsenfeld.

At least 91 records · Page 5Linked to original sources
PubMed1987

Protein-binding sites within the 5' DNase I-hypersensitive region of the chicken alpha D-globin gene.

We mapped at high resolution and as a function of development the hypersensitive domain in the 5'-flanking region of the chicken alpha D-globin gene and determined the specific protein-binding sites within the domain. The domain extends from -130 to +80 nucleotides (nt) relative to the cap site. DNase I footprinting within intact embryonic erythrocyte nuclei revealed a strongly protected area from -71 to -52 nt. The same area was weakly protected in adult nuclei. A factor was present in extracts of erythrocyte nuclei from both embryos and adults that protected the sequence AAGATAAGG (-63 to -55 nt) in DNase I footprinting experiments; at higher concentrations of extract, sequences immediately adjacent (-73 to -64 and -53 to -38) were also protected. The same pattern of binding was revealed by gel mobility shift assays. The identical AAGATAAGG sequence is found in the 5'-flanking region of the beta rho gene; it competed for binding of the alpha D-specific factor, suggesting that regulatory elements are shared.

Animals↗
PubMed1986

Comparison of the folding of beta-globin and ovalbumin gene containing chromatin isolated from chicken oviduct and erythrocytes.

The dependence of chromatin conformation upon salt concentration has been studied for chicken ovalbumin and beta-globin genes isolated from oviduct and adult erythrocytes. At NaCl concentrations of 25 or 50 mM, the sedimentation properties, as a function of DNA size, of ovalbumin and globin chromatin are similar regardless of the source of the chromatin. In 100 mM NaCl, however, beta-globin chromatin isolated from erythrocytes sediments more slowly than an ovalbumin chromatin fraction from erythrocytes containing DNA of the same size. When the same experiment is carried out with material isolated from oviduct nuclei, the relative sedimentation rates are reversed, so that the ovalbumin chromatin sediments more slowly. This behavior cannot be accounted for by differences in binding of RNA polymerase or other molecules associated with transcription, or by partial aggregation of the chromatin. The most reasonable explanation is that transcriptionally active chromatin with a history of transcriptional activity, although largely covered with histones and capable of considerable compaction, is not able to form a fully compact structure as the ionic strength is raised. This behavior is consistent with a slight depletion in active chromatin of core histones or histone H1/H5 or both.

Animals↗
PubMed1986

Regulated gene expression in transfected primary chicken erythrocytes.

We describe a method for studying transient gene expression in primary avian erythroid cells that involves controlled osmotic shock, followed by DNA transfection using DEAE-dextran. Cells treated in this way reproducibly express high levels of chloramphenicol acetyltransferase (CAT) when transfected with a plasmid having the cat gene coupled to an appropriate viral promoter. An observed correlation between levels of CAT expression and extent of hemoglobin release during controlled shock makes it possible to choose optimum conditions for expression in erythroid cells at various stages of embryonic development. Using these techniques, we have investigated the effect on CAT expression of fusing to the cat gene various portions of the chicken adult beta-globin (beta A) gene. We show that in 9-day or 12-day embryonic erythrocytes, the promoter activity of the 5' flanking region of the beta A gene (in the absence of any viral promoters) is strongly stimulated by a downstream sequence, located in the region 110-588 base pairs on the 3' side of the poly(A) signal, that acts as an enhancer. Its activity is reduced in 5-day embryonic cells and absent in primary chicken fibroblasts and mouse L cells, suggesting that this transient expression system will be useful in studying developmentally regulated globin gene expression.

Acetyltransferases↗
PubMed1985

Solubility and structure of domains of chicken erythrocyte chromatin containing transcriptionally competent and inactive genes.

Chromatin generated by micrococcal nuclease digestion of erythrocyte nuclei can be fractionated into two pools of differing solubility in solvents containing 0.15-0.25 M NaCl. A fixed percentage of the chromatin is soluble under these conditions, independent of the average size of the DNA in the unfractionated chromatin. Chromatin containing particular gene sequences is also distributed between soluble and insoluble fractions in a way that is independent of the average size of the starting material. However, the actual percentage of gene copies present in each fraction is not necessarily the same as for bulk chromatin. The transcriptionally active chicken erythrocyte adult beta-globin gene is more soluble than the bulk, while the ovalbumin gene in the same tissue is less soluble. These differences do not appear to be related to variations in content of RNA, core histones, or two classes of non-histone proteins. Instead, we find that the soluble chromatin pool is somewhat depleted in histones H1 and H5 and contains lower molecular weight DNA than precipitable chromatin. The soluble fraction can be made insoluble by addition of H1. If the precipitable chromatin fraction is redigested to reduce its size and then recombined with the soluble fraction and reprecipitated, the distribution of globin gene is randomized. The results suggest that the partitioning of chromatin into soluble and insoluble pools in 0.15-0.25 M NaCl arises from redistribution of a limiting amount of histones H1 and H5 to the chromatin fractions containing the longest DNA.

Animals↗
PubMed1985

Interaction of specific nuclear factors with the nuclease-hypersensitive region of the chicken adult beta-globin gene: nature of the binding domain.

We have studied the properties of a factor or factors that bind selectively to the 5' flanking region of the chicken adult beta-globin (beta A-globin) gene. We previously showed that these components, when bound with histones on plasmids containing the region, confer on the complex a pattern of hypersensitivity to nuclease digestion similar to that in the nucleus. We have now measured the abundance of the factor(s) in partially purified preparations, and the affinity constants for binding to specific and nonspecific DNA sequences. Footprinting studies of the specific complex with DNAase I and II reveal two discrete protected regions within the hypersensitive domain. When these regions are physically separated, they interact with the factor(s) independently, suggesting that each region binds one or more distinct components. The footprint patterns of our complexes in vitro agree with the patterns observed in intact chicken erythrocyte nuclei. These complexes thus are on the transcriptionally active beta A-globin gene in vivo.

Animals↗
PubMed1985

DNA.

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Animals↗
PubMed1985

A method for mapping intranuclear protein-DNA interactions and its application to a nuclease hypersensitive site.

We have devised a method for mapping sites on DNA within the nucleus that are protected against nuclease attack by interaction with bound protein or other factors. This "footprinting" method uses an end-labeled sequence-specific DNA probe, which is annealed to the DNA from nuclear digests under carefully controlled conditions. The annealed complexes are treated with single-strand-specific nuclease, the resulting duplex molecules are electrophoresed on gels, and the gels are autoradiographed. The high sensitivity and resolution of the method have made it possible to obtain a detailed map of DNase I cutting patterns in the 5' flanking sequence of the chicken adult beta (beta A)-globin gene within nuclei from various tissues. In nuclei from adult erythrocytes, this domain is hypersensitive to nucleases. However, we detect within the domain two well-defined regions that are protected against attack, indicating the presence of one or more bound factors. Nuclei from oviduct or 5-day-old embryonic erythrocytes, in which the domain is not hypersensitive, show limited and different patterns of protection.

Animals↗
PubMed1984

A 145-base pair DNA sequence that positions itself precisely and asymmetrically on the nucleosome core.

A 145-bp DNA sequence, cloned from Escherichia coli, was reconstituted into nucleosome core particles by a number of methods. The behaviour of the resulting complex upon sucrose gradient sedimentation and nucleoprotein gel electrophoresis closely resembled that of control bulk nucleosome core particles. DNase I digestion of the 32P-end-labelled complex revealed the 10-bp periodicity of cleavages expected for DNA bound on a histone surface. The narrow cleavage sites observed (1 bp wide) imply that the sequence occupies a single preferred position on the nucleosome core, accurate to the level of single base pairs. By relating the digestion pattern observed to the pattern of site protection found for random sequence nucleosomes, the DNA position was found to be offset by 17 bp from that in the normal core particle. A number of experiments argue against the involvement of length or end effects and suggest that it is some feature of the DNA sequence itself that determines this precise positioning of DNA on the nucleosome.

Animals↗
PubMed1984

Specific factor conferring nuclease hypersensitivity at the 5' end of the chicken adult beta-globin gene.

Chromatin in the 5' flanking region of the transcriptionally active chicken adult beta(beta A) globin gene is hypersensitive to nuclease digestion. When plasmids carrying this gene are combined with histones in the presence of extracts from 9-day-old chicken erythrocyte nuclei, the resultant complex displays hypersensitive behavior in the same region. No such behavior is observed with extracts from cells in which the beta A-globin gene is not expressed. Partially purified preparations of the factor conferring hypersensitivity bind preferentially to DNA fragments containing the hypersensitive region.

Animals↗
PubMed1983

Histone hyperacetylation has little effect on the higher order folding of chromatin.

HeLa cells were grown in the presence of 10 mM sodium butyrate and soluble chromatin containing hyperacetylated histones was prepared by mild micrococcal nuclease digestion and sucrose gradient fractionation. Sedimentation and electric dichroism were used to study the cation-induced folding of this acetylated chromatin from the 10 nm filament to the 30 nm solenoid conformation. Although under some conditions acetylated chromatin appears slightly less condensed than control chromatin, the major conclusion is that hyperacetylation of histones does not in itself prevent the formation of the higher order chromatin solenoid.

Centrifugation, Density Gradient↗
PubMed1983

Higher order structure of chromatin: orientation of nucleosomes within the 30 nm chromatin solenoid is independent of species and spacer length.

We have used electric dichroism to study the arrangement of nucleosomes in 30 nm chromatin solenoidal fibers prepared from a variety of sources (CHO cells, HeLa cells, rat liver, chicken erythrocytes, and sea urchin sperm) in which the nucleosome spacer length varies from approximately 10 to approximately 80 bp. Field-free relaxation times are consistent only with structures containing 6 +/- 1 nucleosomes for every 11 nm of solenoidal length. With very few assumptions about the arrangement of the spacer DNA, our dichroism data are consistent with the same orientation of the chromatosomes for every chromatin sample examined. This orientation, which maintains the faces of the radially arranged chromatosomes inclined at an angle between 20 degrees-33 degrees to the solenoid axis, thus appears to be a general structural feature of the higher order chromatin fiber.

Animals↗
PubMed1983

DNA conformation at the 5' end of the chicken adult beta-globin gene.

We have examined the conformation of DNA cloned from the hypersensitive region 5' of the chicken adult beta-globin gene, in order to determine whether the unusual sensitivity to nucleases is related to altered secondary structure of the DNA. The region contains a large number of sites for methylation; we have studied the effect of methylation at HpaII sites on the topological properties of a small plasmid containing the region. We find that methylation does not alter the supercoiling properties of the plasmid under a wide variety of conditions; we find no evidence for conversion of any measurable segment of DNA to the Z conformation, even at high superhelix densities. We have also devised a protocol for mapping precisely the sites sensitive to S1 nuclease. The data are not consistent with the presence of cruciform structures. They reveal, however, a major cutting site located within a tract of 16 consecutive deoxyguanosine residues in the center of the hypersensitive region. Susceptibility to cutting is dependent upon supercoiling, but methylation at HpaII sequences has no effect on the S1 cutting pattern.

Animals↗
PubMed1983

Another potential artifact in the study of nucleosome phasing by chromatin digestion with micrococcal nuclease.

We show that, contrary to expectations, restriction enzyme cleavage of chicken erythrocyte nucleosome core particle DNA generates a series of distinct subnucleosome fragments. These fragments do not result from bulk nucleosome phasing in vivo, but arise from micrococcal nuclease cleavages internal to the core particle, at roughly 10-base pair intervals and at AT-rich sequences. Those 145-base pair DNA fragments remaining intact are a biased population in which the guanine content can fluctuate by as much as 10%, with a 10-base pair period. We suggest that these same considerations, when applied to a unique DNA sequence, are the true explanation for several previous claims for nucleosome phasing.

Adenine↗
PubMed1983

Chromatin structure of the chicken adult beta-globin gene: is gene activity associated with local or long-range perturbations in chromatin structure?

We review our physical studies on the higher-order structure of bulk chromatin. Using the method of electric dichroism, we determine the arrangement of DNA in the 30-nm solenoid or thick chromatin fiber. With few assumptions, our results lead to a detailed model, in which the chromatosomes are arranged radially but tilted approximately 25 degrees from the solenoid axis. We then attempt to determine if the chromatin of the adult beta-globin gene in embryonic chicken red cells normally exists in a solenoidal configuration. We conclude that it does and that the stability of this globin gene-containing solenoid is similar to that of bulk DNA. Furthermore, the solenoid stability is not measurably perturbed by the binding of the nonhistone chromosomal proteins HMG 14 and 17. We describe the nature of a hypersensitive site close to the 5' end of the adult beta-globin gene. Approximately 200 bp of DNA appear accessible to nuclease digestion and moreover a substantial portion of this region can be excised as naked DNA. Overall there is strong evidence that gene activity is associated with local perturbations in chromatin structure but much weaker evidence that gene activity is associated with a perturbation in chromatin higher-order structure.

Animals↗