Studies on the association of the high mobility group non-histone chromatin proteins with isolated nucleosomes

The Redox Protein High-Mobility Group Box 1 in Cell Death and Cancer

Significance: As a redox-sensitive protein, high-mobility group box 1 (HMGB1) is implicated in regulating stress responses to oxidative damage and cell death, which are closely related to the pathology of inflammatory diseases, including cancer. Recent Advances: HMGB1 is a nonhistone nuclear protein that acts as a deoxyribonucleic acid chaperone to control chromosomal structure and function. HMGB1 can also be released into the extracellular space and function as a damage-associated molecular pattern protein during cell death, including during apoptosis, necrosis, necroptosis, pyroptosis, ferroptosis, alkaliptosis, and cuproptosis. Once released, HMGB1 binds to membrane receptors to shape immune and metabolic responses. In addition to subcellular localization, the function and activity of HMGB1 also depend on its redox state and protein posttranslational modifications. Abnormal HMGB1 plays a dual role in tumorigenesis and anticancer therapy (e.g., chemotherapy, radiation therapy, and immunotherapy) depending on the tumor types and stages. Critical Issues: A comprehensive understanding of the role of HMGB1 in cellular redox homeostasis is important for deciphering normal cellular functions and pathological manifestations. In this review, we discuss compartmental-defined roles of HMGB1 in regulating cell death and cancer. Understanding these advances may help us develop potential HMGB1-targeting drugs or approaches to treat oxidative stress-related diseases or pathological conditions. Future Directions: Further studies are required to dissect the mechanism by which HMGB1 maintains redox homeostasis under different stress conditions. A multidisciplinary effort is also required to evaluate the potential applications of precisely targeting the HMGB1 pathway in human health and disease. Antioxid. Redox Signal. 39, 569-590.

HMGB1 in health and disease

Complex genetic and physiological variations as well as environmental factors that drive emergence of chromosomal instability, development of unscheduled cell death, skewed differentiation, and altered metabolism are central to the pathogenesis of human diseases and disorders. Understanding the molecular bases for these processes is important for the development of new diagnostic biomarkers, and for identifying new therapeutic targets. In 1973, a group of non-histone nuclear proteins with high electrophoretic mobility was discovered and termed high-mobility group (HMG) proteins. The HMG proteins include three superfamilies termed HMGB, HMGN, and HMGA. High-mobility group box 1 (HMGB1), the most abundant and well-studied HMG protein, senses and coordinates the cellular stress response and plays a critical role not only inside of the cell as a DNA chaperone, chromosome guardian, autophagy sustainer, and protector from apoptotic cell death, but also outside the cell as the prototypic damage associated molecular pattern molecule (DAMP). This DAMP, in conjunction with other factors, thus has cytokine, chemokine, and growth factor activity, orchestrating the inflammatory and immune response. All of these characteristics make HMGB1 a critical molecular target in multiple human diseases including infectious diseases, ischemia, immune disorders, neurodegenerative diseases, metabolic disorders, and cancer. Indeed, a number of emergent strategies have been used to inhibit HMGB1 expression, release, and activity in vitro and in vivo. These include antibodies, peptide inhibitors, RNAi, anti-coagulants, endogenous hormones, various chemical compounds, HMGB1-receptor and signaling pathway inhibition, artificial DNAs, physical strategies including vagus nerve stimulation and other surgical approaches. Future work further investigating the details of HMGB1 localization, structure, post-translational modification, and identification of additional partners will undoubtedly uncover additional secrets regarding HMGB1's multiple functions.

Retinol induces the ERK1/2-dependent phosphorylation of CREB through a pathway involving the generation of reactive oxygen species in cultured Sertoli cells

The ability to regulate cell cycle progression and apoptosis through the activation of nuclear receptors and gene transcription has been generally accepted as a potential chemopreventive and therapeutic property of retinoids. However, recent studies suggest that retinol and related compounds can exert rapid and non-genomic effects, which may increase the production of reactive oxygen species (ROS) and lead to cell cycle disruption and malignant transformation. In this work, we report that, in Sertoli cells, retinol (7 microM) induces the Src-dependent activation of ERK1/2 MAPK and the ERK1/2-mediated phosphorylation of the transcription factor CREB. We found that these retinol-induced effects were completely blocked by the antioxidant Trolox 100 microM (a hydrophilic analogue of alpha-tocopherol), the hydroxyl radical scavenger mannitol (1 mM) and the addition of native superoxide dismutase (200 U/ml), and also that retinol increased the production of ROS and several other parameters indicative of oxidative stress during the same incubation periods in which ERK1/2 and CREB were phosphorylated. The activation of the ERK1/2-CREB pathway appears to be involved in the onset of some of the malignant effects caused by retinol in Sertoli cells since inhibition of ERK1/2 activation blocked the retinol-induced cell transformation and proliferation.

Interaction of maize chromatin-associated HMG proteins with mononucleosomes: role of core and linker histones

Two groups of plant chromatin-associated high mobility group (HMG) proteins, namely the HMGA family, typically containing four A/T-hook DNA-binding motifs, and the HMGB family, containing a single HMG-box DNA-binding domain, have been identified. We have examined the interaction of recombinant maize HMGA and five different HMGB proteins with mononucleosomes (containing approx. 165 bp of DNA) purified from micrococcal nuclease-digested maize chromatin. The HMGB proteins interacted with the nucleosomes independent of the presence of the linker histone H1, while the binding of HMGA in the presence of H1 differed from that observed in the absence of H1. HMGA and the HMGB proteins bound H1-containing nucleosome particles with similar affinity. The plant HMG proteins could also bind nucleosomes that were briefly treated with trypsin (removing the N-terminal domains of the core histones), suggesting that the histone N-termini are dispensable for HMG protein binding. In the presence of untreated nucleosomes and trypsinised nucleosomes, HMGB1 could be chemically crosslinked with a core histone, which indicates that the trypsin-resistant part of the histones within the nucleosome is the main interaction partner of HMGB1 rather than the histone N-termini. In conclusion, these results indicate that specific nucleosome binding of the plant HMGB proteins requires simultaneous DNA and histone contacts.

Retinol-induced changes in the phosphorylation levels of histones and high mobility group proteins from Sertoli cells

Chromatin proteins play a role in the organization and functions of DNA. Covalent modifications of nuclear proteins modulate their interactions with DNA sequences and are probably one of the multiple factors involved in the process of switch on/off transcriptionally active regions of DNA. Histones and high mobility group proteins (HMG) are subject to many covalent modifications that may modulate their capacity to bind to DNA. We investigated the changes induced in the phosphorylation pattern of cultured Wistar rat Sertoli cell histones and high mobility group protein subfamilies exposed to 7 microM retinol for up to 48 h. In each experiment, 6 h before the end of the retinol treatment each culture flask received 370 KBq/ml [32P]-phosphate. The histone and HMGs were isolated as previously described [Moreira et al. Medical Science Research (1994) 22: 783-784]. The total protein obtained by either method was quantified and electrophoresed as described by Spiker [Analytical Biochemistry (1980) 108: 263-265]. The gels were stained with Coomassie brilliant blue R-250 and the stained bands were cut and dissolved in 0.5 ml 30% H2O2 at 60oC for 12 h. The vials were chilled and 5.0 ml scintillation liquid was added. The radioactivity in each vial was determined with a liquid scintillation counter. Retinol treatment significantly changed the pattern of each subfamily of histone and high mobility group proteins.

Distinctive patterns of histone H4 acetylation are associated with defined sequence elements within both heterochromatic and euchromatic regions of the human genome

The pattern of histone H4 acetylation in different genomic regions has been investigated by immunoprecipitating oligonucleosomes from a human lymphoblastoid cell line with antibodies to H4 acetylated at lysines 5, 8, 12 or 16. DNA from antibody-bound or unbound chromatin was assayed by slot blotting. Pol I and pol II transcribed genes located in euchromatin were shown to have levels of H4 acetylation at lysines 5, 8 and 12 equivalent to those in input chromatin, but to be slightly enriched in H4 acetylated at lysine 16. In no case did the acetylation level correlate with actual or potential transcriptional activity. All acetylated histone H4 isoforms were depleted in non-coding, simple repeat DNA in heterochromatin, though the extent of depletion varied with the type of heterochromatin and with the isoform. Two single copy genes that map within or adjacent to blocks of paracentric heterochromatin are depleted in H4 acetylated at lysines 5, 8 and 12, but not 16. Consensus sequences of repetitive elements of the Alu family (SINES, enriched in R bands) were associated with H4 that was more highly acetylated at all four lysines than input chromatin, while H4 associated with Kpn I elements (LINES, enriched in G bands) was significantly underacetylated.

Differential expression of nuclear HMG1, HMG2 proteins and H1(zero) histone in various blood cells

Changes in the levels of chromosomal high-mobility group proteins HMG1, HMG2 and histone H1 zero were investigated in blood cells of various types, proliferation activity and stage of differentiation. The relative amounts of proteins HMG1, HMG2 and histone H1 zero were evaluated densitometrically by SDS-PAGE of 5 per cent w/v perchloric acid extracts of blood cells. Concerning the HMG1 and HMG2, the main conclusions were: the expression of these HMG proteins was higher in malignant cells, namely leukemia cell lines, then in lymphocytes or granulocytes and the distribution of HMG1 and HMG2 was highly cell-specific. In comparison with lymphoid cells, the levels of HMG1/2 were higher in myeloid cells. The results revealed that in myeloid cells HMG2 prevails over HMG1. There was no direct correlation between HMG1/2 expression and proliferation activity. The levels of HMG1/2 did not depend on the transcription of chromatin either. However, there was some connection between irreversibly differentiated nonproliferating cells and a loss of HMG1/2 proteins. Reversibly differentiated leukemic cells retain their HMG1/2 levels. Similarly to HMG1/2,H1 zero showed a strong cell specificity. The level of H1 zero was different in the various blood cell types. As compared with lymphoid cells, the level of H1 zero was several-fold higher in myeloid cells, regardless of whether they were normal or malignant. Moreover, there was an accumulation of H1 zero in differentiating HL-60 cells accompanied by only a slight decline in cell proliferation; this agrees with the idea that H1 zero expression is not directly associated with the inhibition of cell growth. Rather higher expression of H1 zero is related to changes during cell differentiation.

SAR-dependent mobilization of histone H1 by HMG-I/Y in vitro: HMG-I/Y is enriched in H1-depleted chromatin

An experimental assay was developed to search for proteins capable of antagonizing histone H1-mediated general repression of transcription. T7 RNA polymerase templates containing an upstream scaffold-associated region (SAR) were highly selectively repressed by H1 relative to non-SAR control templates. This is due to the nucleation of H1 assembly into flanking DNA brought about by the numerous A-tracts (AT-rich sequences containing short homopolymeric runs of dA.dT base pairs) of the SAR. Partial, selective titration of these A-tracts by the high mobility group (HMG) protein HMG-I/Y led to the complete derepression of transcription from the SAR template by inducing the redistribution of H1 on to non-SAR templates. SARs are associated with many highly transcribed regulated genes where they may serve to facilitate the HMG-I/Y-mediated displacement of histone H1 in chromatin. Indeed, HMG-I/Y was found to be strongly enriched in the H1-depleted subfraction which can be isolated from chromatin.

A high-mobility-group protein and its cDNAs from Drosophila melanogaster

We have identified, purified, and characterized a high-mobility-group (HMG) protein and its cDNAs from Drosophila melanogaster. This protein, HMG D, shares most of the characteristics of vertebrate HMG proteins; it is extractable from nuclei with 0.35 M NaCl, is soluble in 5% perchloric acid, is relatively small (molecular weight of 12,000), has both a high basic (24%) and high acidic (24%) amino acid content, and is a DNA-binding protein. HMG D exhibits characteristics of both the vertebrate HMG 1 and 2 class and the HMG 14 and 17 class of proteins. Its amino acid sequence is similar (36% amino acid identity) to that of HMG1, while its size and selective extraction with ethidium bromide are similar to properties of the HMG 14 and 17 class of proteins. HMG D is encoded by a single-copy gene that maps to 57F8-11 on the right arm of chromosome 2. Two transcripts are observed during embryogenesis; the protein is relatively stable throughout development. By the biochemical criteria of size, solubility, and amino acid content, HMG D appears to be the major HMG protein of D. melanogaster.

A high-mobility-group protein and its cDNAs from Drosophila melanogaster

We have identified, purified, and characterized a high-mobility-group (HMG) protein and its cDNAs from Drosophila melanogaster. This protein, HMG D, shares most of the characteristics of vertebrate HMG proteins; it is extractable from nuclei with 0.35 M NaCl, is soluble in 5% perchloric acid, is relatively small (molecular weight of 12,000), has both a high basic (24%) and high acidic (24%) amino acid content, and is a DNA-binding protein. HMG D exhibits characteristics of both the vertebrate HMG 1 and 2 class and the HMG 14 and 17 class of proteins. Its amino acid sequence is similar (36% amino acid identity) to that of HMG1, while its size and selective extraction with ethidium bromide are similar to properties of the HMG 14 and 17 class of proteins. HMG D is encoded by a single-copy gene that maps to 57F8-11 on the right arm of chromosome 2. Two transcripts are observed during embryogenesis; the protein is relatively stable throughout development. By the biochemical criteria of size, solubility, and amino acid content, HMG D appears to be the major HMG protein of D. melanogaster.

Histone acetylation and globin gene switching

An affinity-purified antibody that recognises the epitope epsilon-acetyl lysine has been used to fractionate chicken erythrocyte mononucleosomes obtained from 5 and 15 day embryos. The antibody bound chromatin was enriched in multiply acetylated forms of the core histones H3, H4 and H2B, but not in ubiquitinated H2A. The DNA of these modified nucleosomes was probed with genomic sequences from the embryonic beta rho gene (active at 5 days) and from the adult beta A gene (active at 15 days). Both genes were found to be highly enriched in the acetylated nucleosomes fractionated from both 5 day and from 15 day erythrocytes. We conclude that globin switching is not linked to a change in acetylation status of the genes and that a 'poised' gene carries histones acetylated to a similar level as a transcriptionally active gene. Core histone acetylation is not therefore a direct consequence of the transcriptional process and might operate at the level of the globin locus as a general enabling step for transcription.

Tissue specificity of nucleo-cytoplasmic distribution of HMG1 and HMG2 proteins and their probable functions

The levels and distribution between nucleus and cytoplasm of HMG1 and HMG2 proteins have been investigated in different tissues of mammals. In lymphoid tissues and testis high amounts of these proteins are present in both nuclei and cytoplasm, while in the hepatic tissues and brain they accumulate in cytoplasm, mainly in the cytosol. In particular, very low amounts, if any, of HMG1 and 2 are present in the nuclei active for DNA replication (rat regenerating liver and primary hepatoma) or transcription (adult liver and brain). Therefore, it appears that HMG1 and 2 are not necessary for these processes. On the other hand, nuclear (chromosomal) HMG1 and 2 are characteristic for the tissues containing undifferentiated cells: lymphoid tissues, testis, neonatal liver. These proteins are bound to the chromatin regions solubilized early by sonication or DNase action. Comparison of the data obtained for different tissues shows an inverse correlation between the amounts of chromosomal HMG1 and 2, on the one hand, and of histone H1(0), on the other hand. These results suggest that chromosomal HMG1 and 2 take part in the processes that occur during cell differentiation, while histone H1(0) is induced to preserve differentiated cells from dedifferentiation.

Non-random reconstitution of HMG1 and HMG2 in chromatin. Determination of the histone contacts

We have studied how non-histone proteins HMG1 and HMG2 interact with rat liver chromatin using reconstitution and chemical cross-linking procedures. Both proteins were found to associate to chromatin only to some extent and always with a marked preference for short oligonucleosomes, mainly mono- and dinucleosomes. However, a slight reconstitution with the long polynucleosomal fraction can be observed in H1-depleted chromatin. Reconstitution is non-random and a clear preference for regions highly sensitive to staphylococcal nuclease (EC 3.1.31.1) is observed. Chemical cross-linking has allowed us to identify H1, H2A and H2B as the histones contacted by HMG1 and HMG2 upon reconstitution. Also, we present evidence that HMG1 and HMG2 interact with the nucleosomal particle without replacing H1 or any other histone.

Nonhistone proteins HMG1 and HMG2 suppress the nucleosome assembly at physiological ionic strength

The effect of nonhistone protein HMG1 and HMG2 from pig thymus on the in vitro nucleosome assembly has been examined with plasmid pSV2-gpt DNA and pig thymus core histones in the presence of DNA topoisomerase I. In the absence of core histones, the direct binding of HMG proteins could induce negative superhelical turns in DNA at low ionic strength, but not at physiological ionic strength. The nucleosome formation in the higher histone-to-DNA ratios at physiological ionic strength was not facilitated by HMG proteins, in contrast to poly(L-glutamic acid). HMG proteins suppressed the nucleosome assembly in the moderate histone-to-DNA ratios, resulting in the reduction of fully supercoiled DNA topoisomers. The suppression by HMG proteins was not cancelled by poly(L-glutamic acid). These suggest that the highly acidic carboxy terminal of HMG proteins does not act as an assembly factor, and that the HMG proteins, on the contrary, suppress the nucleosome formation, probably by binding to DNA in a way to inhibit the assembly into core particles.

A direct link between core histone acetylation and transcriptionally active chromatin

An antiserum raised against chemically acetylated histone H4 was found to recognize the epitope epsilon-N-acetyl lysine. Affinity-purified antibodies were used to fractionate oligo- and mononucleosomal chromatin fragments from the nuclei of 15-day chicken embryo erythrocytes. Antibody-bound chromatin was found to contain elevated levels of acetylated core histones. On probing with sequences of alpha D globin, an actively transcribed gene, the antibody-bound chromatin was 15- to 30-fold enriched relative to the input chromatin. Using ovalbumin sequences as a probe, no enrichment was observed. The results demonstrate directly that transcriptionally active genes carry acetylated core histones.

Non-histone chromatin proteins that recognize specific sequences of DNA

Numerous chromatographic procedures have recently been developed to purify to near homogeneity various eukaryotic non-histone chromatin proteins that recognize and bind to specific sequences of DNA. In this brief review we have discussed a number of these different methods that we feel are important and probably represent the starting points for much of the future research work in this area. We view this coverage as being only an introduction, however, and strongly recommend that the reader consult the original papers for details of methods and protocols. We, nevertheless, hope that the information presented here will be of some assistance to those researchers and students who wish to become acquainted with the latest developments in this rapidly advancing field of chromatography. Although it is evident from what has been presented that the purification of each DNA sequence-specific non-histone chromatin protein initially starts with common or classical isolation and fractionation procedures, the final (and often crucial) steps of enrichment and purification often involve distinctive or unique procedures for each individual protein of interest. In many cases these final steps involve new techniques such as DNA sequence-specific bioaffinity and photoaffinity chromatography which not only ensure the isolation of specific protein species from complex mixtures but also result in a tremendous enrichment for nuclear proteins that are often present in the nucleus in extremely low concentrations. Furthermore, the entire process of protein purification has been remarkedly facilitated with the advent of high-performance liquid chromatographic and fast protein liquid chromatographic techniques which now allow for the very rapid separation and purification of proteins in a matter of minutes from mixtures that in the recent past would have required hours or days to purify. Thus, separation and purification techniques are now available that set the stage for the rapid isolation of rare, DNA sequence-specific, NHC nuclear proteins from almost any cellular source. It is therefore reasonable to anticipate that in the near future there will be major advances made in our understanding of the specific nuclear proteins that regulate gene expression in eukaryotic cells.

Comparison of chicken erythroid cell nuclear isolation methods using morphological, immunochemical and biochemical criteria

Chicken erythroid nuclei were prepared using four published methods. Our findings indicate that nuclei prepared by nitrogen cavitation are less likely to be contaminated with plasma membrane fragments than those made by procedures involving cell disruption by hypotonic lysis. However, globin gene sequences were much less sensitive to DNase I digestion in nuclei prepared by nitrogen cavitation. This suggests that the conformation of chromatin was altered by the cavitation procedure. Analysis of the proteins solubilized during limited DNase I digestion of nuclei prepared by both hypotonic lysis and cavitation revealed no appreciable differences in HMG proteins but a notable difference in the RNP-associated proteins and core histones.

Interaction of non-histone proteins HMG1 and HMG2 with core histones in nucleosomes and core particles revealed by chemical cross-linking

Chemical cross-linking was used to study the interaction of the non-histone chromosomal proteins HMG1 and HMG2 with core histones in H1,H5-depleted nucleosomes or core particles. Cross-linking with a 'zero-length' cross-linker 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide and with a longer (cleavable) cross-linker dimethyl-3,3'-dithiobispropionimidate revealed an interaction of HMG1 and HMG2 with (or proximity to) core histones in both types of particles. These results indicated that the presence of the 40-50-base-pairs-long segment of the 'linker' DNA in nucleosomes was not necessary for the establishment of mutual contacts of HMG1 and HMG2 proteins with core histones. Possible implications of the interaction of HMG1 and HMG2 proteins with histones for the structure and functioning of chromatin are discussed.

Binding of the glucocorticoid receptor complex to the nucleosomal core in the P1798 mouse lymphosarcoma

Binding of the glucocorticoid receptor complex to nucleosomes has been studied using the mouse P1798 lymphosarcoma. Cells were incubated with [3H]triamcinolone acetonide (TA), and nuclei prepared and digested with 3 different concentrations of micrococcal nuclease. After fractionation with EDTA and NaCl, it was observed that [3H]TA bound with similar specific radioactivity to mononucleosomes containing both core and linker DNA, of 183 +/- 5, and 168 +/- 4 base pair lengths, respectively, as well as to core size DNA, of 148 +/- 3 base pair length, suggesting that the glucocorticoid receptor bound to the core portion of the nucleosome. Steroid binding was found to be associated with regions of the nucleosome that were depleted in histone H1 and enriched in high mobility group (HMG) proteins 1 and 2; only negligible binding was noted in nucleosomes enriched in histone H1 and depleted in HMG proteins. In addition to binding to core nucleosomes, the glucocorticoid receptor complex was also shown to bind to a fraction sedimenting at 5-6 S on sucrose gradients characterized by subnucleosome and mononucleosome size DNA, as well as by core histones. While binding of the steroid receptor complex to linker regions of the nucleosome cannot be ruled out, this data would appear to present the first concrete evidence that glucocorticoid binding, at least in the P1798 lymphosarcoma, is to core nucleosomes. Some caution in interpretation of the results is indicated, however, on 2 points: (1) receptor redistribution during nuclease digestion cannot be ruled out; (2) only the binding of a small proportion of the steroid receptor complex may be physiologically relevant.

Evidence that high mobility group protein 17 is not phosphorylated in human colon carcinoma cells

The high mobility group proteins 14 and 17 were reported previously to be phosphorylated in murine and human tumor cell lines. Recently, it was suggested that subgroups of HMG-14, HMG-14a and 14b, but not HMG-17, were phosphorylated in situ in HeLa cells. In order to definitively determine whether HMG-17 is indeed phosphorylated or whether the protein previously identified as [32P]HMG-17 was a subgroup of HMG-14, we have used the technique of electroblotting in conjunction with an immunochemical procedure utilizing anti-HMG-17 IgG. Our results indicate that HMG-17 was not phosphorylated in human colon carcinoma cell line HT-29 incubated for 18 h with 32Pi, but that HMG-14a and HMG-14b were phosphorylated. In contrast, HMG-14a, -14b and -17 were phosphorylated in vitro in isolated nuclei incubated with [gamma-32P]ATP.

Microheterogeneity of the mammalian high mobility group (HMG) proteins 1 and 2 investigated by reverse-phase high performance liquid chromatography

Microheterogeneity within the high mobility group (HMG)-1 and HMG-2 groups of nonhistone chromatin proteins has been investigated using reverse-phase high-performance liquid chromatography (RP-HPLC) under conditions (acetonitrile elution with 0.1% trifluoroacetic acid (TFA) as the counter ion) which separate proteins primarily on the basis of differences in their overall hydrophobicity. RP-HPLC proved to be a fast and efficient means for separating multiple subspecies of both the HMG-1 and HMG-2 proteins from both crude nuclear extracts and from ion-exchange column "purified" protein samples obtained from different types of mammalian cell nuclei. In crude nuclear extracts at least eight different HMG-2 protein species (two major and six minor), but only one major HMG-1 species, could be resolved by RP-HPLC. Three of the minor HMG-2 protein species could be isolated in "pure" form from crude extracts in one RP-HPLC step whereas under the same conditions the two major HMG-2 peaks (as well as the other minor species) were contaminated with either HMG-1 or HMG-3 (a degradation product of HMG-1). In crude extracts the major HMG-1 fraction always seems to be contaminated with one of the HMG-2 subfractions. RP-HPLC analysis of apparently "pure" protein preparations isolated by ion-exchange chromatography techniques revealed that "pure" HMG-1 can be resolved into at least three different protein species and "pure" HMG-2 into at least four different species. Amino acid analyses of different resolvable forms of the HMG proteins were not inconsistent with the suggestion that at least some of these may be primary sequence variants of the individual proteins, but other possibilities also exist.

High mobility group proteins of amphibian oocytes: a large storage pool of a soluble high mobility group-1-like protein and involvement in transcriptional events

Oocytes of several amphibian species (Xenopus laevis, Rana temporaria, and Pleurodeles waltlii) contained a relatively large pool of nonchromatin-bound, soluble high mobility group (HMG) protein with properties similar to those of calf thymus proteins HMG-1 and HMG-2 (protein HMG-A; A, amphibian). About half of this soluble HMG-A was located in the nuclear sap, the other half was recovered in enucleated ooplasms. This protein was identified by its mobility on one- and two-dimensional gel electrophoresis, by binding of antibodies to calf thymus HMG-1 to polypeptides electrophoretically separated and blotted on nitrocellulose paper, and by tryptic peptide mapping of radioiodinated polypeptides. Most, if not all, of the HMG-A in the soluble nuclear protein fraction, preparatively defined as supernatant obtained after centrifugation at 100,000 g for 1 h, was in free monomeric form, apparently not bound to other proteins. On gel filtration it eluted with a mean peak corresponding to an apparent molecular weight of approximately 25,000; on sucrose gradient centrifugation it appeared with a very low S value (2-3 S), and on isoelectric focusing it appeared in fractions ranging from pH approximately 7 to 9. This soluble HMG-A was retained on DEAE-Sephacel but could be eluted already at moderate salt concentrations (0.2 M KCl). In oocytes of various stages of oogenesis HMG-A was accumulated in the nucleus up to concentrations of approximately 14 ng per nucleus (in Xenopus), corresponding to approximately 0.2 mg/ml, similar to those of the nucleosomal core histones. This nuclear concentration is also demonstrated using immunofluorescence microscopy. When antibodies to bovine HMG-1 were microinjected into nuclei of living oocytes of Pleurodeles the lateral loops of the lampbrush chromosomes gradually retracted and the whole chromosomes condensed. As shown using electron microscopy of spread chromatin from such injected oocyte nuclei, this process of loop retraction was accompanied by the appearance of variously-sized and irregularly-spaced gaps within transcriptional units of chromosomal loops but not of nucleoli, indicating that the transcription of non-nucleolar genes was specifically inhibited by this treatment and hence involved an HMG-1-like protein. These data show that proteins of the HMG-1 and -2 category, which are usually chromatin-bound components, can exist, at least in amphibian oocytes, in a free soluble monomeric form, apparently not bound to other molecules. The possible role of this large oocyte pool of soluble HMG-A in early embryogenesis is discussed as well as the possible existence of soluble HMG proteins in other cells.

High mobility group nonhistone chromosomal proteins of the developing sea urchin embryo

The high mobility group or HMG proteins are nonhistone chromosomal proteins that have been found in relatively high amounts in nuclei of many tissues. A number of studies have shown that some of these proteins are preferentially associated with actively transcribed regions of the genome and may play a role in maintaining these regions in an active state. In this study, we undertook an investigation of the high mobility group proteins from the sea urchin, Stronglyocentrotus purpuratus. Initially the putative sea urchin HMGs were extracted from isolated nuclei of hatching blastula-stage embryos with 5% perchloric acid (PCA). The major proteins in this extract were characterized according to their electrophoretic mobility, amino acid composition, and association with isolated deoxyribonucleoprotein particles. The results indicate there is only one "major" sea urchin HMG protein, termed P2 in this paper. An estimate of the amount of P2 in relation to the inner histones, however, was low compared to what has been found for other HMG proteins. Of the other major 5% PCA-extractable proteins, one was identified as the cleavage stage H1. Another protein apparently resulted from H3 contamination in the 5% PCA extract, and the fourth major protein did not have all the characteristics of an HMG. In particular, it was not found associated with nucleosomal particles. The HMG proteins from other developmental stages were then examined. Five percent PCA extracts of nuclei from unfertilized eggs, 2-cell, 16-cell, hatching blastula, gastrula, and pluteus stages were analyzed on SDS- and acetic acid-urea gels. This analysis indicated that P2 exists in two different forms differing slightly in charge. The less basic form was found in the egg, 2-cell and 16-cell extracts. At the hatching blastula stage, both forms were present and by pluteus stage, the more basic form predominated. It appears that P2 is undergoing a developmental change from a less to more basic form. The presence of P2 in the 5% PCA extract of egg nuclei is proof that P2 does not initially appear sometime during embryogenesis but is already in the egg nucleus prior to fertilization.

Is high mobility group protein 17 phosphorylated in vivo? Re-examination of the HeLa cell cycle data

When in vivo [32P] phosphate labeled HMG proteins from unsynchronized HeLa cells are separated by electrophoresis in acid-urea polyacrylamide gels, as opposed to separation in SDS-polyacrylamide, HMG 17 does not show any 32P incorporation. Likewise, no 32P radioactivity was found in HMG 17 protein isolated at different stages of the cell cycle from synchronized cells. By contrast, HMG 14 reveals a previously reported (Bhorjee, J.S. (1981) Proc. Natl. Acad. Sci. U.S.A. 78, 6944-6948) cell cycle stage-specific dependent phosphorylation with maximum 32P radioactivity in the G2 phase relative to G1. Furthermore, HMG 14 is resolved into multiple electrophoretic forms as phosphoprotein in the acid-urea system. The results presented seriously question the data on the in vivo phosphorylation of HMG 17, and suggest that these be reevaluated.

Fractionation of mechanically sheared chromatin on ECTHAM-cellulose

Chromatography of chromatin on the weak ion-exchange resin ECTHAM-cellulose was re-examined using the combined salt-pH elution conditions of Stratling, W.H., Van, N.T. and O'Malley, B.W. (1976) Eur. J. Biochem. 66, 423-433. When mechanically sheared rat liver chromatin was chromatographed on ECTHAM-cellulose the histone composition of eluted fractions was very similar, whereas early eluting fractions were enriched in non-histone proteins, including certain high mobility group proteins, and in hnRNP particles, containing newly synthesised RNA. Later eluting fractions were depleted in all of these components. The majority of hnRNP particles in early eluting chromatin were shown to be physically associated with chromatin by centrifugation in metrizamide. Hen erythrocyte chromatin contained no early eluting material. Size of DNA fragments was not a significant factor in determining the elution position of chromatin fragments. Early eluting material was not generated by endogenous nuclease and protease action. The conditions of chromatin preparation, and of elution of early chromatin fractions caused no gross disruption of chromatin structure, or dissociation of chromatin proteins, although some nucleosome sliding may have occurred. The conditions required for elution of some of the later fractions are sufficient to cause dissociation of protein, and alteration of chromatin conformation.

Fractionation of chromatin, released by nuclease digestion, on ECTHAM-cellulose. Separation of active and inactive chromatin

Chromatin released by two nucleases under various ionic conditions has been fractionated by chromatography on ECTHAM-cellulose. Mg2+ -soluble chromatin, which according to Gottesfeld and Partington is enriched in transcribed DNA sequences (Gottesfeld, J.M. and Partington, G.A., (1977) Cell 12, 953-962) and produced by DNAase II digestion at intermediate ionic strength, comprises material eluting from ECTHAM-cellulose at 80-100 mM Cl-, pH 6.8-7.0, whereas bulk, Mg2+ -insoluble chromatin comprises more tightly binding material. Free hnRNP particles elute at 30 mM Cl-, pH 6.8. Oligonucleosomes, which according to Dimitriadis and Tata are enriched in transcribed sequences (Dimitriadis, G.J. and Tata, J.R. (1980) Biochem. J. 187, 467-477) and produced by micrococcal nuclease digestion at physiological ionic strength, also elute predominantly at 80-100 mM Cl-, pH 6.8-7.0. When liver nuclei are digested with micrococcal nuclease at low ionic strength, the most rapidly released chromatin is enriched in nascent RNA and hnRNP particles, and binds weakly to ECTHAM-cellulose. More slowly solubilised chromatin, containing fewer hnRNP particles, binds much more strongly to ECTHAM-cellulose. In confirmation of results with mechanically sheared chromatin, the affinity of particular chromatin fractions is not dependent on the size of chromatin particles, rather it reflects the differing composition, and in particular the non-histone protein and hnRNP content, which, we propose, determines the conformation adopted by different chromatin fractions in the cation conditions used for elution from ECTHAM-cellulose.

Active chromatin

Active genes are packaged into an altered nucleosome structure forming a chromosomal domain defined by increased sensitivity to nucleases. This structure, reflecting a potential for transcription, contains sites hypersensitive to nuclease digestion adjacent to the coding regions and may also be distinguished by specific non-histone proteins, variant or modified histones or modified DNA. Its formation, by unfolding of a tightly packed chromatin fibre by factors which might affect DNA supercoiling, may be the first step in gene activation.

Differential phosphorylation of nuclear nonhistone high mobility group proteins HMG 14 and HMG 17 during the cell cycle

The phosphorylation of the high-mobility group (HMG) proteins at different stages of the cell cycle was studied in synchronized HeLa cells. HMG proteins were extracted and analyzed by NaDodSO4/polyacrylamide gel electrophoresis. Although the molecular weight distribution of HMGs remains unchanged, their total amounts increase by as much as 20-25% in the G1 and S phases when compared with amounts in G2. However, the most significant finding is that there is a 7-fold increase of 32P incorporation into HMG 14 in the G2 phase compared with that in G1, and a 2-fold increase of 32P incorporation into HMG 17 in early S phase relative to the incorporation in the G1 and G2 stages. In contrast, HMG 1 and HMG 2 are not phosphorylated. The clear demonstration of differential phosphorylation of HMG 14 and 17 at specific stages of the cell cycle warrants a serious consideration of their role in tissue-specific maintenance of the altered chromatin structure characteristic of potentially active or actively transcribed chromatin domains.

Characterisation of a chromatin fraction bearing pulse-labelled RNA. 2. Quantification of histones and high-mobility-group proteins

The histone variants and high-mobility-group (HMG) proteins of a transcribing fraction of chromatin, described in the preceding paper of this journal, have been analysed qualitatively and quantitatively by a combination of one-dimensional and two-dimensional gel electrophoresis. The stoichiometry of the four core histones (all variants included) in this fraction is equimolar and is not detectably different from that in the nontranscribing fraction or in total chromatin. The molar ratio of histone H1 to the core histones is markedly lower, by approximately 72%, than that in the nontranscribing fraction. A minor histone variant identified as M1 (an H2A variant) is detected only in the transcribing fraction, while variant H3.1 is found only in the non-transcribing fraction. Proteins A24, HMG1 and HMG2 are essentially absent from the transcribing fraction; HMG14 is found uniquely in this fraction, while HMG17 occurs at a relatively lower level.

Structural studies of the non-histone chromosomal proteins HMG-T and H6 from trout testis

Trout testis contains two proteins of the high mobility group H6 and HMG-T that have been implicated in the structure of active chromatin. Protein H6 was studied by high resolution proton NMR and by circular dichroism and showed no evidence of secondary or tertiary structure formation in free solution. At low ionic strength protein H6 binds to DNA by a weak interaction in the N-terminal region between residues 10 and 35. Proteins H6 therefore behaves structurally like the homologous calf-thymus high-mobility-group proteins HMG-14 and HMG-17. Salt addition to solutions of protein HMG-T results in secondary and tertiary structure formation that is accompanied by aggregation. Circular dichroism shows that the helical content of protein HMG-T (approximately equal to 9%) is very much less than that of the homologous calf thymus proteins HMG-1 and HMG-2. At low ionic strength protein HMG-T precipitates DNA due to the formation of large scale aggregates that disperse only when the protein is released at approximately equal to 0.35 M NaCl. The NMR spectrum of the aggregated state does not show the presence of a large number of free acidic residues, in contrast to spectra of soluble complexes of HMG-1 and DNA at the same ionic strengths. It is concluded that HMG-T lacks the highly acidic domain found in HMG-1 (and HMG-2) that remains free from DNA under these conditions. It is concluded that the entire chain of HMG-T binds to DNA. There are therefore major structural differences between HMG-T and the homologous calf thymus proteins.

Analysis of putative high-mobility-group (HMG) proteins in neuronal and glial nuclei from rabbit brain

Putative high-mobility-group (HMG) proteins 1, 2, and 17 were detected in neuronal and glial nuclei isolated from the cerebral hemisphere of rabbit brain. Although divergent chromatin structures are present in these two populations of brain nuclei (i.e., neuronal nuclei exhibit a short DNA repeat length), no differences were apparent in the electrophoretic mobilities of putative HMG proteins 1, 2, and 17 on SDS gels.

Localization of chromosomal protein HMG-1 in polytene chromosomes of Chironomus thummi

The distribution of accessible antigenic sites in the chromosomal protein high mobility group one (HMG-1) in Chironomus thummi polytene chromosomes is visualized by immunofluorescence. The results indicate that (a) HMG-1 is distributed in a distinct banding pattern along the entire length of the chromosomes; (b) the banding pattern obtained with fluorescent antibody does not strictly correspond to that observed by phase-contrast microscopy; and (c) the amount of HMG-1 increases, and the fluorescent banding pattern changes, during the development of the organism. Our findings suggest that the protein may be involved in the modulation of the structure of selected loci in the chromosome.

Partial characterization of RNA polymerase II complex released by micrococcal nuclease digestion of rat liver nuclei

Two forms of RNA polymerase II were released from rat liver chromatin by micrococcal nuclease digestion of the nuclei. One from behaved like a free RNA polymerase II and the other like a complex with other nuclear components. Both forms of RNA polymerase II activity were recovered in the 0.16 M NaCl-soluble fraction of the nuclear digest, and the complexed from the RNA polymerase II could transcribe its endogenous template under conditions permitting only of elongation of the RNA synthesis. The RNA polymerase II complex was further purified by gel filtration chromatography and column electrophoresis. Analysis of protein and DNA of the partially purified complex suggested that the RNA polymerase II was bound to mono- or dinucleosomes carrying some characteristic nonhistone proteins. Furthermore, in experiments on tissues from starved rats, the two forms of RNA polymerase II were found to originate from different functional states of the chromatin-bound enzyme in vivo.

High mobility group proteins 1 and 2 are present in simian virus 40 provirions, but not in virions

Viral particles at the late stages of SV40 morphogenesis were examined for the presence of HMG proteins 1 and 2, by an immunochemical method involving the transfer of proteins from polyacrylamide gels to nitrocellulose membranes. It was found that these proteins are present in SV40 provirions, in which histone H1 is still associated with viral chromatin, but absent in mature SV40 virions.

Structural studies on two high-mobility-group proteins from calf thymus, HMG-14 and HMG-20 (ubiquitin), and their interaction with DNA

High mobility group (HMG) protein 14, which, like HMG-17, has been implicated in the structure of 'active chromatin' is shown by 270-MHz NMR and by circular dichroism to be in a disordered conformation in free solution. At low ionic strength protein HMG-14 binds to DNA by weak attachment of the N-terminal half of the molecule and is released by 0.3 M NaCl, the ionic strength at which the protein is extracted from chromatin. The protein HMG-20 (ubiquitin), a constituent of the conjugate protein A 24, is shown to be a highly stable compact globular protein that remains folded over a pH range of 1--13 and has a half-denaturation temperature of 85 degrees C when thermally denatured. Circular dichroism indicates 28% helix and 12% beta sheet. Despite having 15% basic residues it binds only very weakly to DNA. A detailed study of the folding of ubiquitin has been made by a combination of several NMR approaches, including decoupling, nuclear Overhauser enhancement and titration. Several line assignments have been made and it is shown that, although the tyrosine and histidine are buried residues, they are not adjacent to one another nor are they close to either of the phenylalanines, of which at least one is also a buried residue.

Different repeat lengths in rat satellite I DNA containing chromatin and bulk chromatin

The nucleosome repeat structure of a rat liver chromatin component containing the satellite I DNA (repeat length 370 bp) was investigated. Digestion experiments with micrococcal nuclease, DNAase II, and the Ca2+/Mg2+-dependent endogenous nuclease of rat liver nuclei revealed a repeat unit of 185 nucleotide pairs which is shorter by approximately 10 bp than the repeat unit of the bulk chromatin of this cell type. The difference seems not to be related to the histone composition which was found to be similar in the two types of chromatin.