A major nucleolar protein, nucleolin, induces chromatin decondensation by binding to histone H1

Using circular dichroism to probe the extent of DNA condensation in chromatin, we have demonstrated that a major nucleolar protein, nucleolin can decondense chromatin. By means of various binding assays we show that nucleolin has a strong affinity for histone H1 and that the phosphorylated N-terminal domain, rich in lengthy stretches of acidic amino acids, is responsible for this ionic interaction. Additional experiments clearly demonstrate that nucleolin is unable to act as a nucleosome core assembly or disassembly factor and hence has little affinity for the core histone octamer. We propose that this nucleolar protein induces chromatin decondensation by binding to histone H1, and that nucleolin can therefore be regarded as a protein of the high-mobility-group type.     

Fractionation of L-cell chromatin into DNA, RNA, and protein fractions on Cs2SO4 equilibruim density gradients

A new procedure is described for fractionation of chromatin into DNA, RNA, and total chromatin protein. By isopycnic gradient centrifugation of chromatin preparations in Cs₂SO₄ solutions containing dimethylsulfoxide and sodium sarcosyl it is possible to obtain highly purified fractions of these components. The method gives a very high yield of these chromatin fractions unlike some other methods, where irreversible binding to columns occurs. Also with this method it is possible to obtain highly concentrated fractions, which after a simple dialysis step, can be conveniently analyzed by polyacrylamide gel electrophoresis.Nuclei from L-929 cells were isolated by a method involving citric acid or by a method using a nonionic detergent. The yields of DNA obtained by both methods was compared. Chromatin was isolated from purified nuclei (prepared in either of the above ways) in two different ways also. In one method, chromatin was extracted from nuclei with 1 m NaCl. A second method involving fractionation of lysed nuclei in sucrose and metrizamide solutions was also used. The yields of DNA obtained by both methods was compared. There appears to be little nuclear membrane contamination of any of these chromatin preparations.A preliminary analysis of L-929 cell chromatin total RNA and protein fractions on polyacrylamide and agarose gels has been made. Both fractions appear to be quite complex with a wide spectrum of subcomponents of differing S values.     

Phosphorylation of chromatin- and ribosome-associated proteins in cells transformed by adenovirus, murine sarcoma virus, and methylcholanthrene.

Endogenous protein phosphorylation in chromatin and ribosomes of monkey, mouse, and rat cells transformed by DNA, RNA tumor viruses, and a chemical carcinogen revealed the association of a protein of approximately 90,000 daltons (90K), which is highly phosphorylated in vitro. Peptide map analysis showed that the 90K proteins associated with these organelles of various transformed cells are similar irrespective of the species of cells and transforming agents. This species of protein could not be detected, or was scarcely detected, by phosphorylation in chromatin and ribosomes of untransformed cells and in revertants of transformed cells. These results suggest that the alteration in the pattern of endogenous protein phosphorylation in these organelles is closely related to the transformed state of cells.     

The effects of alcohols, procaine and hyperthermia on the protein content of nuclei and chromatin

Since previous studies suggest that heat-induced nuclear changes correlate with cell killing we have extended these observations by measuring nuclear and chromatin protein content in HeLa cells heat sensitized by agents which are believed to cause membrane damage. Specifically, we have investigated the effects of alcohol (C2-C5) and procaine. Exposure of HeLa cells to alcohol concentrations greater than 1 M ethanol or 0.2 M butanol for 30 min causes a measurable increase in the protein content of both nuclei and chromatin. When cells were heated (45 degrees C) in the presence of alcohol, the increase in nuclear and chromatin protein content was significantly greater than that for heat alone at concentrations above 0.25 M ethanol and 0.07 M butanol. In addition, the presence of 0.41 M ethanol causes a two-fold increase, over heat alone, in the amount of protein absorbed to chromatin when cells are heated at 45 degrees C from 0 to 60 min. Similar effects were observed with procaine. Thus, alcohol or procaine alone can cause an increase in chromatin protein content and can act synergistically with heat to cause a larger increase. These results suggest that membrane damage may cause a larger increased protein content of chromatin and thereby lead to cell death.     

The nonhistone chromosomal protein, H2A-specific protease, is selectively associated with nucleosomes containing histone H1

We have determined the distribution of the nucleosomal bound nonhistone chromosomal protein, H2A-specific protease, in calf thymus and liver chromatin. The protease was unevenly distributed in chromatin with domains containing histone H1 being selectively complexed with the enzyme. Moreover, the protease had a preference for the less compact chromatin domains enriched in the H1 subtypes H1a and -c. We have demonstrated that ubiquitinated H2A is a substrate of the H2A-specific protease and that the enzyme is a serine protease which can be inactivated with protease inhibitors only after it is released from the nucleosome. Possible functions of the protease in modulating chromatin structure are discussed.     

CC1, a novel crenarchaeal DNA binding protein

The genomes of the related crenarchaea Pyrobaculum aerophilum and Thermoproteus tenax lack any obvious gene encoding a single-stranded DNA binding protein (SSB). SSBs are essential for DNA replication, recombination, and repair and are found in all other genomes across the three domains of life. These two archaeal genomes also have only one identifiable gene encoding a chromatin protein (the Alba protein), while most other archaea have at least two different abundant chromatin proteins. We performed a biochemical screen for novel nucleic acid binding proteins present in cell extracts of T. tenax. An assay for proteins capable of binding to a single-stranded DNA oligonucleotide resulted in identification of three proteins. The first protein, Alba, has been shown previously to bind single-stranded DNA as well as duplex DNA. The two other proteins, which we designated CC1 (for crenarchaeal chromatin protein 1), are very closely related to one another, and homologs are restricted to the P. aerophilum and Aeropyrum pernix genomes. CC1 is a 6-kDa, monomeric, basic protein that is expressed at a high level in T. tenax. This protein binds single- and double-stranded DNAs with similar affinities. These properties are consistent with a role for CC1 as a crenarchaeal chromatin protein.     

Easy detection of chromatin binding proteins by the histone association assay

The Histone Association Assay provides an easy approach for detecting proteins that bind chromatin in vivo. This technique is based on a chromatin immunoprecipitation protocol using histone H3-specific antibodies to precipitate bulk chromatin from crosslinked whole cell extracts. Proteins that co-precipitate with chromatin are subsequently detected by conventional SDS-PAGE and Western blot analysis. Unlike techniques that separate chromatin and nonchromatin interacting proteins by centrifugation, this method can be used to delineate whether a protein is chromatin associated regardless of its innate solubility. Moreover, the relative amount of protein bound to DNA can be ascertained under quantitative conditions. Therefore, this technique may be utilized for analyzing the chromatin association of proteins involved in diverse cellular processes.     

Effects of hyperthermia, irradiation, and cytotoxic drugs on fluorescein isothiocyanate staining intensity for flow cytofluorometry

Measurement of fluorescein isothiocyanate (FITC) staining intensity of cultured lymphoblastoid cells following hyperthermia showed large increases without concomitant increases in nuclear protein. Similar measurements of cells following incubation with cytotoxic drugs showed fluorescent intensity increases that exceeded the increases in nuclear protein that were due to the cell cycle blocking action of the drug. The reverse, however, was true for cells following irradiation. In contrast, FITC staining intensity and nuclear protein measurements of cells proceeding through the cell cycle after removal of the cycle blocking agent showed nearly parallel changes, although there were reproducible minor differences, especially following blocking with hydroxyurea. These results suggest that FITC staining intensity is a function not only of nuclear protein content but also of stain access to the reaction sites of the protein constituents of the chromatin. Thus, it is possible that FITC staining may be used as a probe of changes in chromatin structure following experimental manipulation of cells in vitro or treatment of tumors in vivo.     

Double labeling of chromatin proteins,in vivo and in vitro,and their two-dimensional electrophoretic resolution

A modification of the two-dimensional electrophoretic method that involves nonequilibrium pH gradients has been adapted for high resolution of chromatin proteins from sea urchin embryos. A simple method of labeling the protein, in vitro, by reductive methylation with boro[³H]hydride to a specific activity of 100,000 cpm/μg of protein is detailed. Chromatin protein may be labeled, in vivo with ¹⁴C-amino acids, and newly synthesized (³H and ¹⁴C-labeled) and preexistent proteins (only ³H labeled) may be distinguished. The method reveals that sea urchin embryo chromatin contains over 200 proteins.     

Alternative splicing products of the gene for a human nuclear actin-related protein,hArpNbeta/Baf53, that encode a protein isoform,hArpNbetaS, in the cytoplasm

A human nuclear actin-related protein, hArpNbeta/ Baf53, is a component of chromatin remodeling and histone acetyltransferase complexes. We identified two alternative splicing products of the gene for hArpNbeta/ Baf53. They encoded a protein isoform, hArpNbetaS; and its fusion product with green fluorescent protein was to be found in the cytoplasm, not the nucleus. The isoforms may contribute to functional regulation of these complexes.     

Xenopus Drf1, a regulator of Cdc7, displays checkpoint-dependent accumulation on chromatin during an S-phase arrest

We have cloned a Xenopus Dbf4-related factor named Drf1 and characterized this protein by using Xenopus egg extracts. Drf1 forms an active complex with the kinase Cdc7. However, most of the Cdc7 in egg extracts is not associated with Drf1, which raises the possibility that some or all of the remaining Cdc7 is bound to another Dbf4-related protein. Immunodepletion of Drf1 does not prevent DNA replication in egg extracts. Consistent with this observation, Cdc45 can still associate with chromatin in Drf1-depleted extracts, albeit at significantly reduced levels. Nonetheless, Drf1 displays highly regulated binding to replicating chromatin. Treatment of egg extracts with aphidicolin results in a substantial accumulation of Drf1 on chromatin. This accumulation is blocked by addition of caffeine and by immunodepletion of either ATR or Claspin. These observations suggest that the increased binding of Drf1 to aphidicolin-treated chromatin is an active process that is mediated by a caffeine-sensitive checkpoint pathway containing ATR and Claspin. Abrogation of this pathway also leads to a large increase in the binding of Cdc45 to chromatin. This increase is substantially reduced in the absence of Drf1, which suggests that regulation of Drf1 might be involved in the suppression of Cdc45 loading during replication arrest. We also provide evidence that elimination of this checkpoint causes resumed initiation of DNA replication in both Xenopus tissue culture cells and egg extracts. Taken together, these observations argue that Drf1 is regulated by an intra-S-phase checkpoint mechanism that down-regulates the loading of Cdc45 onto chromatin containing DNA replication blocks.     

Alternative Splicing Products of the Gene for a Human Nuclear Actin-related Protein,hArpNβ/Baf53, that Encode a Protein Isoform,hArpNβS,in the Cytoplasm

A human nuclear actin-related protein, hArpNβ/Baf53, is a component of chromatin remodeling and histone acetyltransferase complexes. We identified two alternative splicing products of the gene for hArpNβ/Baf53. They encoded a protein isoform, hArpNβS; and its fusion product with green fluorescent protein was to be found in the cytoplasm, not the nucleus. The isoforms may contribute to functional regulation of these complexes.