Identification of poly (ADP-ribose) covalently bound to histone F1 in vivo

The Expanding Constellation of Histone Post-Translational Modifications in the Epigenetic Landscape

The emergence of a nucleosome-based chromatin structure accompanied the evolutionary transition from prokaryotes to eukaryotes. In this scenario, histones became the heart of the complex and precisely timed coordination between chromatin architecture and functions during adaptive responses to environmental influence by means of epigenetic mechanisms. Notably, such an epigenetic machinery involves an overwhelming number of post-translational modifications at multiple residues of core and linker histones. This review aims to comprehensively describe old and recent evidence in this exciting field of research. In particular, histone post-translational modification establishing/removal mechanisms, their genomic locations and implication in nucleosome dynamics and chromatin-based processes, as well as their harmonious combination and interdependence will be discussed.

Poly(ADP-ribose) polymerases covalently modify strand break termini in DNA fragments in vitro

Poly(ADP-ribose) polymerases (PARPs/ARTDs) use nicotinamide adenine dinucleotide (NAD⁺) to catalyse the synthesis of a long branched poly(ADP-ribose) polymer (PAR) attached to the acceptor amino acid residues of nuclear proteins. PARPs act on single- and double-stranded DNA breaks by recruiting DNA repair factors. Here, in in vitro biochemical experiments, we found that the mammalian PARP1 and PARP2 proteins can directly ADP-ribosylate the termini of DNA oligonucleotides. PARP1 preferentially catalysed covalent attachment of ADP-ribose units to the ends of recessed DNA duplexes containing 3′-cordycepin, 5′- and 3′-phosphate and also to 5′-phosphate of a single-stranded oligonucleotide. PARP2 preferentially ADP-ribosylated the nicked/gapped DNA duplexes containing 5′-phosphate at the double-stranded termini. PAR glycohydrolase (PARG) restored native DNA structure by hydrolysing PAR-DNA adducts generated by PARP1 and PARP2. Biochemical and mass spectrometry analyses of the adducts suggested that PARPs utilise DNA termini as an alternative to 2′-hydroxyl of ADP-ribose and protein acceptor residues to catalyse PAR chain initiation either via the 2′,1″-O-glycosidic ribose-ribose bond or via phosphodiester bond formation between C1′ of ADP-ribose and the phosphate of a terminal deoxyribonucleotide. This new type of post-replicative modification of DNA provides novel insights into the molecular mechanisms underlying biological phenomena of ADP-ribosylation mediated by PARPs.

Micro- and nanofluidic technologies for epigenetic profiling

This short review provides an overview of the impact micro- and nanotechnologies can make in studying epigenetic structures. The importance of mapping histone modifications on chromatin prompts us to highlight the complexities and challenges associated with histone mapping, as compared to DNA sequencing. First, the histone code comprised over 30 variations, compared to 4 nucleotides for DNA. Second, whereas DNA can be amplified using polymerase chain reaction, chromatin cannot be amplified, creating challenges in obtaining sufficient material for analysis. Third, while every person has only a single genome, there exist multiple epigenomes in cells of different types and origins. Finally, we summarize existing technologies for performing these types of analyses. Although there are still relatively few examples of micro- and nanofluidic technologies for chromatin analysis, the unique advantages of using such technologies to address inherent challenges in epigenetic studies, such as limited sample material, complex readouts, and the need for high-content screens, make this an area of significant growth and opportunity.

Modification of nuclear matrix proteins by ADP-ribosylation. Association of nuclear ADP-ribosyltransferase with the nuclear matrix

Nuclear matrices were isolated by treatment of isolated HeLa cell nuclei with high DNase I, pancreatic RNase and salt concentrations. ADP-ribosylated nuclear matrix proteins were identified by electrophoresis, blotting and autoradiography. In one experimental approach nuclear matrix proteins were labeled by exposure of permeabilized cells to the labeled precursor [32P]NAD. Alternatively, the cellular proteins were prelabeled with [35S]methionine and the ADP-ribosylated nuclear matrix proteins separated by aminophenyl boronate column chromatography. By both methods bands of modified proteins, though with differing intensities, were detected at 41, 43, 46, 51, 60, 64, 69, 73, 116, 140, 220 and 300 kDa. Approximately 2% of the total nuclear ADP-ribosyltransferase activity, but only 0.07% of the nuclear DNA, was tightly associated with the isolated nuclear matrix. The matrix-associated enzyme catalyzes the incorporation of [32P]ADP-ribose into acid-insoluble products of molecular mass 116 kDa and above, in a 3-aminobenzamide-inhibited, time-dependent reaction. The possible function of ADP-ribosylation of nuclear matrix proteins and of the attachment of ADP-ribosyltransferase to the nuclear matrix in the regulation of matrix-associated biochemical processes is discussed.

Evidence for polyphosphate in phosphorylated nonhistone nuclear proteins

Structural studies of eucaryotic nuclear proteins have revealed the presence of bound polymeric phosphates. 32P-labeled and nonlabeled nonhistone nuclear proteins (NHPs) were isolated from rat liver nuclei and subjected to various controlled hydrolytic conditions. The analysis of protease-trypsin limit peptides revealed the presence of six phosphorylated, homogeneous fragments with phosphate/amino acid molar ratios greater than unity, ranging from 1.3 to 79. Alkaline beta elimination of phosphoester bonds released polymeric phosphates with chain lengths from 2 to over 200, as determined by using two-dimensional chromatographic analysis. The identity of these labeled polymeric phosphates was established to be polyphosphate by a number of criteria, including chromatographic mobility, gravimetric precipitation to constant specific activity, generation of orthophosphate on hydrolysis, and the determination of the delta H of hydrolysis of phosphoanhydride bonds. The evidence suggests that, in addition to the phosphomonoesters of serine and threonine, multiple phosphoanhydride linkages can result in the formation of polyphosphorylated NHPs. Previous investigators have demonstrated that exogenous, free polyphosphate causes destabilization of chromatin and enhancement of transcription in vitro. Although the function of the polyphosphorylated NHPs is currently unknown, such findings have possible functional implications with regard to the postulated role of NHPs as positive modifiers of gene expression.

Immunofluorescent staining of poly(ADP-ribose) in situ in HeLa cell chromosomes in the M phase

Randomly and synchronously growing HeLa cells were tested for poly(ADP-ribose) by direct and indirect immunofluorescent antibody techniques. Fluorescence of poly(ADP-ribose) was seen only in the nuclei of intact cells when the direct immunofluorescent antibody technique was used but in both the nuclei and cytoplasm when the indirect immunofluorescent antibody technique was used; fluorescence in the cytoplasm was nonspecific. When randomly or synchronously growing HeLa cells were fixed in acetone and treated with DNase I before incubation with fluorescein-labeled antibody, intense fluorescence was observed only in the nuclei when the direct immunofluorescent staining technique was used. Addition of 3-aminobenzamide, a potent inhibitor of poly(ADP-ribose) polymerase, with the DNase I completely abolished the fluorescence in the nuclei of synchronously and randomly growing HeLa cells, except in M-phase nuclei. These results suggest that poly(ADP-ribose) can be synthesized even in the nuclei of acetone-fixed HeLa cells from "endogenous NAD+" during incubation with fluorescent antibody and also that the fluorescence of chromosomes of HeLa cells in the M phase is, in fact, due to the in situ presence of poly(ADP-ribose), not to poly(ADP-ribose) synthesized during incubation with antibody.

Polypeptide hormones and chromatin-associated proteins act as acceptors for cholera toxin-catalyzed ADP-ribosylation

Cholera toxin catalyzed the ADP-ribosylation of the pituitary protein hormones thyrotropin (TSH), lutropin (LH), follitropin (FSH), human chorionic gonadotropin (hCG), and corticotropin (ACTH)1-24, and ADP-ribosylation of the basic proteins histone subfraction H1 and protamine. Casein and phosvitin, acidic nuclear proteins, did not act as acceptors for toxin-catalyzed ADP-ribosylation. The isolated TSH A and B subunits were tested for their ADP-ribose acceptor activity. The TSH A subunit showed fourfold greater ADP-ribose acceptor activity than the TSH B subunit. The ADP-ribose acceptor protein protamine was analyzed by sodium dodecyl sulfate polyacrylamide gel electrophoresis following incubation with cholera toxin under ADP-ribosylating conditions. [3H]ADP-ribose incorporated into protein from [3H]NAD migrated with the acceptor protein protamine. In the absence of added acceptor protein, the [3H]ADP-ribose incorporated into protein migrated with the A1 fragment of cholera toxin. Cholera toxin A and B subunits were isolated and tested for their ability to catalyze the transfer of ADP-ribose to protamine. The cholera toxin A subunit showed 50-fold greater ADP-ribosyltransferase activity than the B subunit. Our data indicate that a variety of adenohypophyseal hormones and regulatory proteins act as acceptors for toxin-catalyzed ADP-ribosylation. These studies may help in understanding the role of endogenous ADP-ribosyltransferases and the physiological effects of this modification of protein.

Phosphodipeptide analysis of nonhistone nuclear proteins from Novikoff hepatoma ascites cells

To study the sites of phosphorylation in nuclear proteins a simple method was developed for the isolation and analysis of phosphodipeptides. Partial acid hydrolysates of unfractionated nonhistone nuclear proteins were subjected to Dowex-1 column chromatography followed by paper electrophoresis at pH 1.8. Phosphoserine- and phosphothreonine-containing dipeptides each had characteristic mobilities in the latter system. By subtractive Edman degradation these peptides were identified as having the general structure, X-PSer or X-PThr, where X is a nonphosphorylated amino acid. The two groups of phosphodipeptides were further purified into unique peptides by two-dimensional paper electrophoresis at pH 3.6 and 6.5. Amino acid analysis, and thus nearest neighbor analysis, of phosphodipeptides from nonhistone nuclear proteins revealed that a heterogeneous group of amino acids was on the amino terminal side of phosphoserine residues. In contrast, phosphothreonine residues were predominantly preceded by proline.

Adenosine diphosphate ribosylation of histone H1 by purified calf thymus polyadenosine diphosphate ribose polymerase

The mechanism of poly ADPR synthesis and the transfer of poly ADPR to histone H1 molecule by electrophoretically homogenous calf thymus poly ADPR polymerase containing DNA was examined. 1) An acid insoluble radioactive complex (I) was obtained after incubation of purified enzyme with [3H] NAD. The stability of (I) was examined by SDS-polyacrylamide gel electrophoresis. The complex (I) was stable against acid, SDS, urea, DNase and RNase, but labile against pronase, trypsin, alkali and snake venom phosphodiesterase treatment. The molecular weight of (I) was about 130 000 daltons estimated by SDS-gel electrophoresis. The radioactive products of successive alkali, venom phosphodiesterase and Pronase hydrolysis of (I) were PR-AMP and AMP. The mean chain length of poly ADPR of (I) was 20--30. These results suggest that the complex (I) is poly ADP-ribosylated poly ADPR polymerase. 2) Besides (I), a second radioactive peak (II) was observed when acid insoluble products obtained from an incubation mixture containing purified poly ADPR polymerase, [3H] NAD and purified histone H1 were analyzed on SDS-polyacrylamide gel electrophoresis. The molecular weight of (II) was estimated to be about 23 000 daltons. The complex (II) is eluted like histone H1 on CM-cellulose columns and hydrolyzed by alkali, trypsin and snake venom phosphodiesterase but not by DNase, or RNase. The comples (II) was extracted selectively by 5 per cent perchloric acid or 5 per cent trichloroacetic acid from mixture of (I) and (II). The mean chain length of poly ADPR of complex (II) and 5--20; these results suggest that the complex (II) is poly ADP-ribosylated histone H1. 3) Results 1) and 2) indicate that purified DNA containing, thus DNA independent, poly ADPR polymerase catalyzes two different reactions, the ADPR transfer onto the enzyme itself and onto histone H1 and the elongation of ADPR chains. Dimeric forms of ADP-ribosylated histone H1 was not observed. Free poly ADPR was observed only when very small quantities of enzyme were used for incubation.

Properties of purified calf thymus poly(adenosine diphosphate ribose) polymerase. Comparison of the DNA-independent and the DNA-dependent enzyme

The physicochemical properties of the purified calf thymus poly(ADP-ribose) polymerase were investigated. The enzyme purified to homogeneity was shown to contain about 10% DNA on a weight basis and its activity to be DNA independent. After removing this fragment of DNA, called the sDNA fraction, the enzyme becomes DNA dependent. The activity of this enzyme preparation was entirely dependent on, and completely restored by, added calf thymus DNA or sDNA. However, the calf thymus DNA concentration needed was a hundred times higher than that of sDNA. The properties of the two enzyme preparations, DNA independent and DNA dependent, were essentially the same. They both reacted against the specific antibody obtained with the DNA-independent poly(ADP-ribose) polymerase. The pH optimum was around 8; the activity was stimulated by Mg2+, Mn2+ and Ca2+, and inhibited by high ionic strength, p-chloromercuribenzoate, ADP-ribose, AMP and polylysine. Nicotinamide, thymidine and NADP were shown to be competitive inhibitors. The enzymatic activity was stimulated by histone H1 when the ratio of DNA to histone H1 was 2. Histones H2A, H2B, H3 and H4 had little effect on the DNA-independent enzyme activity, but were strongly inhibitory for the DNA-dependent enzyme. This inhibitory effect could be reversed by allowing the DNA-dependent enzyme to react with the sDNA fraction before adding histone subfractions. The apparent Km for NAD of the DNA-dependent poly(ADP-ribose) polymerase was shown to vary with the DNA concentration. It was minimum when the amount of sDNA was 10% of that of the enzyme. The ratio of the apparent Km for sDNA to the enzyme concentration was constant at any enzyme concentration. The minimum estimation of the number of base pairs of sDNA required for maximal activation of one enzyme molecule was 16. For calf thymus DNA, this estimation was of 640. These results suggest that the activation of the enzyme needs the formation of some complex between the protein and a specific part of the DNA. This complex was preserved in the DNA-independent enzyme preparation.

ADP-ribosylated histone H1 from HeLa cultures. Fundamental differences to (ADP-ribose)n-histone H1 conjugates formed into vitro

ADP-ribosylated histone H1 was isolated from intact HeLa cells grown for 24 h with[3H]-adenosine and compared with ADP-ribosylated histone H1 synthesized from [3H]NAD by isolated HeLa nuclei. Most (ADP-ribose)n-histone H1 conjugates formed in vivo carried single ADP-ribose units, less than one fourth of the total ADP-ribose residues being in the form of oligomeric or polymeric chains. (ADP-ribose)n linked to H1 in vivo was not released by neutral NH2OH to a significant extent. Alkali treatment (pH 10.5) liberated most but not all of the ADP-ribose residues which may indicate the existence of a new type of linkage so far found only in conjugates isolated from intact tissue. No ADP-ribosylated histone H1 complex of higher molecular weight ('H1 dimer') could be detected in intact cells. By contrast, isolated HeLa nuclei formed ADP-ribosylated histone H1 which contained predominantly polymeric ADP-ribose residues. The (ADP-ribose)n residues were linked by NH2OH-sensitive and by NH2OH-resistant, alkali (pH 10.5) labile bonds, the majority of the conjugates appearing in the form of the higher-molecular-weight complex. A comparison with the ADP-ribosylated non-histone proteins indicated that histone H1 formed in vivo carried less than 2.5% of the total protein-bound ADP-ribose residues and less than 1% of the protein-bound ADP-ribose synthesized in vitro.

Effect of DNA on poly (ADP-ribose) glycohydrolase and the degradation of histone H1-poly (ADP-ribose) complex from HeLa cell nuclei

A poly(ADP-ribose)-H1 histone complex has been isolated from HeLa cell nuclei incubated with NAD. The rate of poly(ADP-ribose) glycohydrolase catalyzed hydrolysis of the polymer in the complex is only 1/9 that of free poly(ADP-ribose), indicating that the polymer is in a protected environment within the complex. Comparison of the rate of hydrolysis of free poly(ADP-ribose) in the presence or absence of H1 to that in the complex synthesized de novo indicates a specific mode of packaging of the complex. This is further indicated by the fact that alkaline dissociation of the complex followed by neutralization markedly exposes the associated poly(ADP-ribose) to the glycohydrolase. The complex also partially unfolds when it binds to DNA as evidenced by a 2-fold increase in the rate of glycolytic cleavage of poly(ADP-ribose). This effect of DNA is not due to a stimulation of the glycohydrolase per se since hydrolysis of free polymer by the enzyme is strongly inhibited by DNA, especially single-stranded DNA. Inhibition of glycohydrolase by DNA results from the binding of the enzyme to DNA and conditions which decrease this binding (increased ionic strength or addition of histone H1 which competes for DNA binding) relieve the DNA inhibition.

Properties of the complex between histone H1 and poly(ADP-ribose synthesised in HeLa cell nuclei

Preparations of H1 histone from HeLa cell nuclei incubated with [3H]NAD to permit poly(ADP-ribose) synthesis were electrophoresed on polyacrylamide gels. The incorporated radioactivity migrated as a sharply defined peak in association with a protein band which moved more slowly than H1, the major protein component. The following observations indicate that this complex is composed of two molecules of H1 and a single chain of poly(ADP-ribose) with one detectable covalent linkage of polymer to protein. 1. The [14C]arginine/[3H]lysine ratio is identical in H1 histone and in the protein moiety of the complex. 2. Protein is displaced from H1 histone to the complex during poly(ADP-ribose) synthesis. At least 90% of the protein in the complex (stainable protein and labelled protein) is derived from H1. 3. Sedimentation rate studies indicate a molecular weight of the complex about twice that of H1 histone. 4. The average chain length of the polymer is 15 ADP-ribose units and there are 7--8 ADP-ribose units for each molecule of H1 histone in the 'complex'. 5. Poly(ADP-ribose) glycohydrolase, which hydrolyses the polymer exoglycosidically from the AMP terminus, degrades the complex producing ADP-ribose and mono-ADP-ribosylated H1 histone which co-electrophoreses with unmodified H1. Although only one covalent linkage between protein and polymer has been detected, the 'complex' does not dissociate when electrophoresed on dodecylsulfate gels. Nor can the noncovalently linked H1 histone of the complex readily exchange with free H1. Complex formation does not occur when purified poly(ADP-ribose) and H1 are mixed.

Alteration of poly (ADP-Rib) synthesis during progesterone- caused gene expression in oviducts of quails

The biological model of the selective induction of RNA synthesis in oviducts of estrogen stimulated immature quails by progesterone has been used to clarify whether poly (AD-Rib) is involved in DNA transcription. The chromatin-bound as well as the soluble poly (ADP-Rib) polymerase has been isolated from oviducts and the optimal reaction conditions have been determined. The activities, as measured by the incorporation rates of NAD+ into poly (ADP-Rib), of both, chromatin-bound "endogenous" polymerase (in the absense of "exogenous" DNA and histones) and soluble enzyme (native DNA-lysine-rich histone ratio: 4.3) from progesterone treated quail oviducts, have been determined to be only 30 per cent and 46 per cent respectively, as compared with the activities of the enzymes from the controls. This decrease in incorporation rates is apparently not due to an increased poly (ADP-Rib) degrading enzyme activity. Poly (ADP-Rib) synthesis in vivo was determined by incorporation studies with the precursor (14C) ribose. 12 h after intraperitoneal administration, 0.014 per cent of the total radioactivity was recovered in the oviduct histone fraction, 0.011 per cent in the oviduct nonhistone fraction and 0.009 per cent in the oviduct "HCIextract" containing the histone subfractions f1, f2 and f3. Among these histone subfractions f1 is ADP-ribosylated to the largest extent. ADP-ribosylation of f1 is less extensive in progesterone-stimulated oviducts (65 per cent) than in the controls (100 per cent). The present results suggest that in course of the selective, progesterone-induced DNA transcription the poly (ADP-Rib synthesis might drop.

Poly(adenosine diphosphate ribose) is covalently linked to nuclear proteins by two types of bonds

(ADP-ribose)n residues formed by short-term incubation of adult rat liver and Ehrlich carcinoma nuclei with labeled NAD were analyzed by Cs2SO4/guanidinium chloride/urea density gradient centrifugation. Comparison with samples in which the protein had been completely digested revealed that most, or probably all, acid-insoluble (ADP-ribose)n chains are covalently bound to nuclear proteins, as is true for the short, acid-soluble (ADP-ribose)n chains. Complete release of (ADP-ribose)n chains is effected by dilute alkali. In contrast, NH2OH liberated only part of the long and the short (ADP-ribose)n residues from the protein conjugates, indicating two types of bonds, both alkali-labile, but only one susceptible to neutral hydroxylamine. Both types of bonds were equally distributed among acid-soluble and acid-insoluble (ADP-ribose)n chains. -Stability of the (ADP-ribose)n protein conjugates during isolation is only guaranteed at pH values below 7.

Stimulation of nuclear poly (adenosine diphosphate-ribose) polymerase activity from HeLa cells by endonucleases

Isolated nuclei from HeLa cells can incorporate labeled ADP-ribose from NAD into an acid-precipitable product, poly(ADP-ribose). This reaction is stimulated by 4-6-fold by the addition of deoxyribonuclease I to the complete reaction mixture. If the nuclei are treated first with deoxyribonuclease I, no effect is seen; the stimulation is only apparent when the two enzymes deoxyribonuclease I and poly(ADP-ribose) polymerase, are operating at the same time. After making several minor modifications in the assay mixture, it was found that another endonuclease, micrococcal nuclease, can also stimulate the poly(ADP-ribose) polymerase activity of HeLa nuclei. A comparison of the two stimulatory effects indicated that the two endonucleases activated to the poly(ADP-ribose) polymerase activity of HeLa nuclei in the same way. Overall this evidence suggests that poly(ADP-ribose) polymerase may have a functional role in the process of DNA repair.

Chemical and metabolic properties of adenosine diphosphate ribose derivatives of nuclear proteins

1. ADP-ribose is found in rat liver nuclei covalently bound to histone F1, to a non-histone protein, and to a small peptide. 2. A single unit of ADP-ribose, covalently bound to phosphoserine, was isolated from an enzymic hydrolysate of histone F1. ADP-ribose-bearing peptides were isolated from a tryptic digest of the histone. 3. It is proposed that the 1'-hydroxyl group of ADP-ribose is linked to the phosphate group of phosphoserine in histone F1. 4. The incorporation of 32P into ADP-ribose on histone F1 a parallels the DNA content through the cell cycle. An increased incorporation of the nucleotide into the other derivatives is observed during S phase. 5. It is suggested that the ADP-ribose derivative of histone F1 has a role in maintaining the G0 state and that one or both of the other derivatives is concerned with control of DNA synthesis.