Structural and transcriptional properties of different nucleosomal particles containing high mobility group proteins 14 and 17 (HMG 14/17)

The spectrum of anti-chromatin/nucleosome autoantibodies: independent and interdependent biomarkers of disease

Autoantibodies directed to chromatin components date back to the discovery of the LE cell and the LE cell phenomenon circa 1950, and subsequent evidence that major components of that reaction were chromatin components and histones in particular. Over time, immunoassays ranging from ELISA and line immunoassays to more modern bead-based assays incorporated histone and DNA mixtures, purified histones, and purified nucleosomes leading to a more thorough understanding of the genesis and pathogenetic relationships of antibodies to chromatin components in systemic lupus erythematosus and other autoimmune conditions. More recently, interest has focussed on other components of chromatin such as high mobility group (HMG) proteins both as targets of B cell responses and pro-inflammatory mediators. This review will focus on immunoassays that utilize chromatin components, their clinical relationships, and newer evidence implicating HMG proteins and DNA neutrophil extracellular traps (NETs) as important players in systemic autoimmune rheumatic diseases.

Genomic profiling of HMGN1 reveals an association with chromatin at regulatory regions

The interaction of architectural proteins such as the linker histone H1 and high-mobility-group (HMG) proteins with nucleosomes leads to changes in chromatin structure and histone modifications and alters the cellular transcription profile. The interaction of HMG proteins with chromatin is dynamic. However, it is not clear whether the proteins are constantly and randomly redistributed among all the nucleosomes or whether they preferentially associate with, and turn over at, specific regions in chromatin. To address this question, we examined the genome-wide distribution of the nucleosome binding protein HMGN1 and compared it to that of regulatory chromatin marks. We find that HMGN1 is not randomly distributed throughout the genome. Instead, the protein preferentially localizes to DNase I hypersensitive (HS) sites, promoters, functional enhancers, and transcription factor binding sites. Our results suggest that HMGN1 is part of the cellular machinery that modulates transcriptional fidelity by generating, maintaining, or preferentially interacting with specific sites in chromatin.

HMGN proteins act in opposition to ATP-dependent chromatin remodeling factors to restrict nucleosome mobility

The high-mobility group N (HMGN) proteins are abundant nonhistone chromosomal proteins that bind specifically to nucleosomes at two high-affinity sites. Here we report that purified recombinant human HMGN1 (HMG14) and HMGN2 (HMG17) potently repress ATP-dependent chromatin remodeling by four different molecular motor proteins. In contrast, mutant HMGN proteins with double Ser-to-Glu mutations in their nucleosome-binding domains are unable to inhibit chromatin remodeling. The HMGN-mediated repression of chromatin remodeling is reversible and dynamic. With the ACF chromatin remodeling factor, HMGN2 does not directly inhibit the ATPase activity but rather appears to reduce the affinity of the factor to chromatin. These findings suggest that HMGN proteins serve as a counterbalance to the action of the many ATP-dependent chromatin remodeling activities in the nucleus.

Effects of HMGN1 on chromatin structure and SWI/SNF-mediated chromatin remodeling

The dynamic modulation of chromatin structure is determined by many factors, including enzymes that modify the core histone proteins, enzymes that remodel the structure of chromatin, and factors that bind to genomic DNA to affect its structure. Previous work indicates that the nucleosome binding family of high mobility group proteins (HMGN) facilitates the formation of a chromatin structure that is more conducive for transcription. SWI/SNF complexes are ATP-dependent chromatin remodeling enzymes that alter nucleosome structure to facilitate the binding of various regulatory proteins to chromatin. Here we examine the structural consequences of reconstituting chromatin with HMGN1 and the resulting effects on hSWI/SNF function. We demonstrate that HMGN1 decreases the sedimentation velocity of nucleosomal arrays in low ionic strength buffers but has little effect on the structure of more highly folded arrays. We further demonstrate that HMGN1 does not affect SWI/SNF-dependent chromatin remodeling on either mononucleosomes or nucleosomal arrays, indicating that SWI/SNF functions independently of HMGN1.

High mobility group protein 14 and 17 can prevent the close packing of nucleosomes by increasing the strength of protein contacts in the linker DNA

High mobility group (HMG) proteins 14 and 17 are abundant chromatin-associated proteins found in all higher eukaryotic nuclei. This observation demonstrates that HMGs 14 and 17 must have an important and universal function with regard to the structure and function of chromatin. What this function is, including how they interact with a nucleosomal array in vivo, is not known. Recently, we have demonstrated that HMGs 14 and 17 can organize nucleosomes into a regular array and increase the repeat length from 145 to about 160-165 base pairs in vitro. In addition, they can increase the apparent repeat length of chromatin deficient in histones H2A/H2B from 125 to approximately 145 base pairs. Importantly, this template was transcriptionally active. In this study, we report five new observations that begin to address the mechanism by which HMGs 14 and 17 space nucleosomal particles. First, we demonstrate that both human placenta HMG 14 and HMG 17 can space nucleosomes to produce a chromatin template with a repeat length around 160 base pairs. This result further highlights the similarity between these proteins in terms of protein structure and perhaps function. Second, we show that digestion of HMG containing chromatin with micrococcal nuclease produces DNA fragments that were approximately 10 and 20 base pairs longer than nucleosome core-particle DNA. This suggests that HMG 14 or HMG 17 can protect, directly or indirectly, at least an additional 10 base pairs of linker DNA from micrococcal digestion. However, this HMG-containing particle does not produce a strong kinetic block, and further digestion results in the eventual accumulation of DNA fragments 145 base pairs in length. Third, by comparing the full-length protein with different domains, we demonstrate that the acidic carboxyl-terminal domain is absolutely required for nucleosome spacing, neither the nucleosome binding domain of HMG 14 or HMG 17 nor the amino-terminal domain plus the nucleosome binding domain of HMG 14 could space nucleosomes. Fourth, we demonstrate that extensive micrococcal nuclease digestion of chromatin deficient in histones H2A/H2B led to the accumulation of DNA fragments about 110 base pairs in length, which is presumably the length of DNA associated with a nucleosomal particle deficient in one H2A/H2B dimer. Incorporation of either HMG 14 or HMG 17 into this chromatin results in the disappearance of this band and increase in the accumulation of fragments around 140-150 base pairs in length. Finally, in contrast to spacing of complete nucleosomes, we find that the nucleosome binding domain of HMG 17 (but not the nucleosome binding of HMG 14) is the only domain required for spacing of H2A/H2B-deficient chromatin.

HMG17 is a chromatin-specific transcriptional coactivator that increases the efficiency of transcription initiation

We have examined the effect of HMG17 on transcription by RNA polymerase II by the assembly and analysis of HMG17-containing chromatin templates consisting of regularly spaced nucleosomal arrays. Structural analysis of the chromatin indicated that HMG17 is incorporated into chromatin in a physiological manner with the full complement of core histones. The transcriptional studies revealed that HMG17 stimulates transcription in conjunction with the sequence-specific activator GAL4-VP16. This effect was observed with chromatin, but not with non-nucleosomal templates, and required the presence of HMG17 during chromatin assembly. The incorporation of HMG17 into chromatin resulted in a 7- to 40-fold stimulation of GAL4-VP16-activated transcription to levels that were comparable to those observed with histone-free DNA templates. In contrast, transcription from HMG17-containing chromatin was not detectable in the absence of GAL4-VP16 or with a GAL4 derivative [GAL4(1-147)] lacking the VP16 activation domain. Finally, the incorporation of HMG17 into chromatin was found to increase the efficiency of transcription initiation, but not the extent of transcriptional elongation. Thus, HMG17 is a chromatin-specific transcriptional coactivator that increases the efficiency of initiation of transcription by RNA polymerase II.

Antibodies to HMG proteins in patients with drug-induced autoimmunity

OBJECTIVE

To determine the prevalence of autoantibodies to high-mobility group (HMG) proteins in sera from patients with drug-induced lupus (DIL).

METHODS

Forty-two patients who developed autoantibodies and/or lupus after treatment with procainamide or other drugs were tested for HMG autoantibodies by immunoblotting and enzyme-linked immunosorbent assay (ELISA).

RESULTS

Twenty-eight of the 42 sera (67%) bound HMG-14 and/or HMG-17. In comparison, 9 of 42 (21%) bound HMG-1 and/or HMG-2. There was a good correlation between ELISA results and binding on immunoblots.

CONCLUSION

The high prevalence of antibodies to the nucleosomal core HMGs (HMG-14 and HMG-17) in DIL patients adds evidence implicating nucleosomes as immunogens in drug-induced autoimmunity.

Transcription of mononucleosomal particles acetylated in the presence of n-butyrate

Although a correlation between chemical acetylation of the amino-terminal tails of core histones and stimulation of RNA synthesis has been reported for nucleosomal core particles (Piñeiro et al. (1991) Biochem. Biophys. Res. Commun. 177:370), no differences in transcription are detected between acetylated and nonacetylated mononucleosomal particles obtained from HeLa cells in the presence and absence of n-butyrate. Apparently, the lysine residues modified in the presence of n-butyrate are not the same responsible for the observed acetylation-induced transcription. The acetylation obtained with n-butyrate might be significantly different from that present in transcriptionally active chromatin.

The dynamic properties of neuronal chromatin are modulated by triiodothyronine

The effect of triiodothyronine (T3) on the rate of synthesis of nuclear proteins was studied during terminal differentiation of rat cortical neurons cultured in a serum-free medium. To this aim total and acid soluble nuclear proteins were analyzed by different electrophoretic techniques. Our results show that: 1) during maturation in vitro, neuronal nuclei undergo a dramatic change in the rate at which different classes of histones and high mobility group (HMG) proteins are synthesized; the synthetic activity, measured as incorporation of radioactive precursors into nuclear proteins, slows indeed down with age: especially evident is the decrease in core histones synthesis; at day 15, on the other hand, HMG 14 and 17 and ubiquitinated H2A (A24) are synthesized at a high rate, especially in T3-treated neurons; 2) neurons treated with T3 show, at any age tested, a higher level of lysine incorporation into nuclear proteins; 3) even if during the first days of culture neurons synthesize core histones more actively in the presence of T3, there is no accumulation of these proteins at later stages, as compared with untreated cells. Possible implications of these data and relationship with the chromatin rearrangement which accompanies neuronal terminal differentiation are discussed.

Effect of high mobility group proteins 14 and 17 on the structural and transcriptional properties of acetylated complete and H2A.H2B-deficient nucleosomal cores

Acetylation of H2A.H2B-deficient nucleosomal cores, like that of the complete particles, causes a substantial increase in the efficiency of the particles as in vitro transcription templates. Binding of the high mobility group proteins 14 and 17 (HMG 14/17) to chemically acetylated nucleosomal particles, both complete nucleosomal cores and those lacking one of the two H2A.H2B dimers, is accompanied by a small structural stabilization. The affinity of HMG 14/17 for the nucleosomal cores is not affected by acetylation of the particles. With acetylated complete and H2A.H2B-deficient cores, the binding of HMG 14/17 does not cause any significant change in the levels of RNA synthesis, which is compatible with the presence of these proteins in transcriptionally active nucleosomes.

HMG proteins 14 and 17 become cross-linked to the globular domain of histone H3 near the nucleosome core particle dyad

HMG proteins were derivatized with the photoactivatable cross-linker N-succinimidyl 3-((4-azidophenyl)dithio)propionate and then allowed to associate with nucleosome core particles. Following photolysis, peptide mapping of the principal dimeric adducts was carried out. Cross-linking occurred primarily from a central location in the HMGs to a central location in H3. The positions of these cross-links, considered along with other data from the literature, show that HMG proteins 14 and 17 make important contacts to H3 near the front face of the nucleosome. This raises the possibility that HMGs 14 and 17 participate in the reported conformational transition which exposes the H3 sulfhydryls of active nucleosomes.

Succinylation of histone amino groups facilitates transcription of nucleosomal cores

Treatment of nucleosomal cores with succinic anhydride, which modifies preferentially the amino-terminal domains of core histones, takes place without dissociation of the particles. Low levels of modification, which cause small structural effects, are accompanied by substantial increases in the efficiency of the nucleosomal cores as in vitro transcription templates for RNA polymerase II. The transcriptional properties of the succinylated nucleosomal cores are similar to those of the acetylated particles (Piñeiro et al., (1991) Biochem. Biophys. Res. Commun. 177, 370-376), indicating that no specific blocking by acetyl residues is required to facilitate in vitro transcription. Moreover, to obtain a certain level of stimulation, a smaller number of groups has to be modified by succinic than by acetic anhydride.

Interaction of RNA polymerase II with acetylated nucleosomal core particles

Chemical acetylation of nucleosomal cores is accompanied by an increase in their efficiency as in vitro transcription templates. Low amounts of acetic anhydride cause preferential modification of the amino-terminal tails of core histones. Modification of these domains, which causes moderate structural effects, is apparently correlated with the observed stimulation of RNA synthesis. In contrast, extensive modification of the globular regions of core histones, which is accompanied by a large structural relaxation of the particle, causes little additional effect on transcription. Acetylation of the amino-terminal domains of histones might stimulate transcription by changing the interaction of the histone tails with components of the transcriptional machinery.