The metabolism of histone fractions. II. Conservation and turnover of histone fractions in mammalian cells

Nepsilon-formylation of lysine is a widespread post-translational modification of nuclear proteins occurring at residues involved in regulation of chromatin function

Post-translational modification of histones and other chromosomal proteins regulates chromatin conformation and gene activity. Methylation and acetylation of lysyl residues are among the most frequently described modifications in these proteins. Whereas these modifications have been studied in detail, very little is known about a recently discovered chemical modification, the N(epsilon)-lysine formylation, in histones and other nuclear proteins. Here we mapped, for the first time, the sites of lysine formylation in histones and several other nuclear proteins. We found that core and linker histones are formylated at multiple lysyl residues located both in the tails and globular domains of histones. In core histones, formylation was found at lysyl residues known to be involved in organization of nucleosomal particles that are frequently acetylated and methylated. In linker histones and high mobility group proteins, multiple formylation sites were mapped to residues with important role in DNA binding. N(epsilon)-lysine formylation in chromosomal proteins is relatively abundant, suggesting that it may interfere with epigenetic mechanisms governing chromatin function, which could lead to deregulation of the cell and disease.

Four distinct cyclin-dependent kinases phosphorylate histone H1 at all of its growth-related phosphorylation sites

In mammalian cells, up to six serines and threonines in histone H1 are phosphorylated in vivo in a cell cycle dependent manner that has long been linked with chromatin condensation. Growth-associated H1 kinases, now known as cyclin-dependent kinases (CDKs), are thought to be the enzymes responsible for this process. This paper describes the phosphorylation of histone H1 by four different purified CDKs. The four CDKs phosphorylate only the cell cycle specific phosphorylation sites of H1, indicating that they belong to the kinase class responsible for growth-related H1 phosphorylation in vivo. All four CDKs phosphorylate all of the interphase and mitotic-specific H1 sites. In addition to the (S/T)PXK consensus phosphorylation sites, these four CDKs also phosphorylate a mitotic-specific in vivo H1 phosphorylation site that lacks this sequence. There is no site selectivity among the growth-related phosphorylation sites by any of the four CDKs because all four CDKs phosphorylate all relevant sites. The results imply that the cell cycle dependent H1 phosphorylations observed in vivo must involve differential accessibility of H1 sites at different stages of the cell cycle.

High mobility group proteins cHMG1a, cHMG1b, and cHMGI are distinctly distributed in chromosomes and differentially expressed during ecdysone dependent cell differentiation

The mammalian high mobility group proteins HMGI/Y and HMG1/2 are thought to play an architectural role in assembly of nucleoprotein structures. Counterparts to these proteins have recently been found in the cells of the Dipteran insect Chironomus. In this report we investigate the distribution of three abundant HMG proteins in interphase giant chromosomes of the midge, Chironomus. By means of the indirect immunofluorescence technique the cHMG1b and cHMGI proteins were localized in chromosomal puffs, suggesting their involvement in the organization of transcriptionally active chromatin. In contrast, the highly abundant protein cHMG1a was rather uniformly distributed in the chromosomes. The cHMGI protein, but not cHMG1a or cHMG1b, was detected in nucleoli, which may indicate a role in the transcription of ribosomal genes. The regions of the interphase chromosomes containing AT-rich DNA did not contain higher levels of the cHMGI and cHMG1b proteins. A correlation between the specific location of these proteins in chromatin and their synthesis and turnover rates was observed.

Modulation in proportions of H1 histone subfractions by differential changes in synthesis and turnover during butyrate treatment of neuroblastoma cells

Mouse neuroblastoma cells treated with millimolar concentrations of butyrate adjusted their recipe of histone H1 subfractions over the course of several days, eventually attaining an enrichment of about 5-fold in H1(0). This adjustment in the proportions of the H1's, which was essentially complete by 4 days, was brought about by changes in synthesis and turnover that were different for each of the three H1 subfractions. As the cells stopped dividing, the synthesis of all histones slowed substantially, but core histones were affected more than the H1's. Transiently, therefore, there was an overproduction of H1's relative to core histones, but the excess H1 was eventually removed by turnover. The very slow turnover of H1(0) and the rapid turnover of H1c were not substantially affected by butyrate treatment, but the turnover of H1ab was greatly accelerated by butyrate. Acetylation of the core histones was not necessary for maintenance of elevated H1(0) levels in the nondividing cells, although we did not rule out its involvement in the initial accumulation of H1(0).

Changes in the H-1 histone complement during myogenesis. I. Establishment by differential coupling of H-1 species synthesis to DNA replication

Proportions of the four major chicken H-1 histones (referred to as H-1's a-d) change during in vitro skeletal myogenesis. As myoblasts fuse and differentiate into myotubes, the relative amount of H-1c increases dramatically. The change occurs primarily because synthesis of the H-1 species is coupled to DNA synthesis to different extents. H-1c synthesis is least tightly coupled to DNA replication in precursor myoblasts and in differentiated myotubes. Thus H-1c synthesis predominates after dividing myoblasts fuse into postmitotic myotubes. This results in the replacement of pre-existing H-1 and therefore increases the relative amount of H-1c. Differences in the stability of the H-1's are also involved in changing H-1 proportions. The results show that changes in H-1 proportions during myogenesis are a consequence of withdrawal from the cell cycle. The data provides a general mechanistic explanation of how tissue-specific H-1 proportions are established.

Exchange of histones H1, H2A, and H2B in vivo

We have asked whether histones synthesized in the absence of DNA synthesis can exchange into nucleosomal structures. DNA synthesis was inhibited by incubating hepatoma tissue culture cells in medium containing 5.0 mM hydroxyurea for 40 min. During the final 20 min, the cells were pulsed with [3H]lysine to radiolabel the histones (all five histones are substantially labeled under these conditions). By two electrophoretic techniques, we demonstrate that histones H1, H2A, and H2B synthesized in the presence of hydroxyurea do not merely associate with the surface of the chromatin but instead exchange with preexisting histones so that for the latter two histones there is incorporation into nucleosome structures. On the other hand, H3 and H4 synthesized during this same time period appear to be only weakly bound, if at all, to chromatin. These two histones have been isolated from postnuclear washes and purified. Some possible implications of in vivo exchange are discussed.

In vitro exchange of nucleosomal histones H2a and H2b

We have asked whether exogenous, radiolabeled histones can exchange with nucleosomal histones in an in vitro system. Using two different electrophoretic techniques, we were able to separate the histones contained in nucleosomes from those histones which were simply bound to the surface of the chromatin. Fluorography was used to determine which of the exogenous histones exchange with the nucleosomal histones. We observed substantial exchange of histones H1, H2a, and H2b when the chromatin and exogenous histones were incubated under approximately physiological conditions. We have also observed a small amount of exchange of H2a and H2b, as well as a substantial exchange of H1, from one chromatin fragment to another. Other conditions affecting the exchange of histones H2a and H2b are also reported.

A minireview of microheterogeneity in H1 histone and its possible significance

Subtypes of H1 histone vary in primary structure, and the higher organisms that have been studied each seem to have about a half-dozen subtypes. The proportions of these subtypes vary with the progress of differentiation as seen in embryonic development, hormonally induced changes, spermatogenesis, and terminal differentiation. The H1 subtypes differ among themselves in their ability to condense DNA and small chromatin fragments. They have the potential, therefore, of causing different parts of the chromatin to be condensed to different degrees.

Coupling of histone and DNA synthesis in the somatic cell cycle

The coupling of histone and DNA synthesis was examined in the temperature-sensitive hamster fibroblast cell line K12. By monitoring total cellular histone synthesis at various times after quiescent cells were stimulated to proliferate at permissive and nonpermissive temperatures, a direct correlation was found between the rates of DNA and histone synthesis. Furthermore, when DNA synthesis was blocked by the K12 mutation, histone synthesis was reduced to the basal rate.

Cell cycle kinetics of Chinese hamster (CHO) cells treated with the iron-chelating agent picolinic acid

Spontaneously transformed (tumorigenic) Chinese hamster cells (line CHO) do not exhibit picolinic acid-sensitive G1 and G2 cell cycle arrest points observed in normal and virus-transformed cells. Rather, picolinic acid arrests CHO cells in S phase only and produces culture growth behaviour similar to that produced by hydroxyurea. Prolonged treatment with picolinic acid permits a slow but significant traverse of cells through S phase. Thus, like hydroxyurea, picolinic acid is not a useful agent for synchronizing exponential CHO cells, but it can be used to resynchronize cultures in early S phase if a previous synchronization procedure (such as isoleucine deprivation) is used. The iron chelating properties of picolinic acid, and the similarities of its effects on cultured cells to those of hydroxyurea and the iron-chelating drug desferrioxamine, suggest that picolinic acid inhibits DNA synthesis by interfering with the iron-dependent production of a stable free organic radical which is essential for the ribonucleotide reductase formation of deoxyribonucleotides.

G1 and S phase mammalian cells synthesize histones at equivalent rates

To determine the effect of cell cycle position on protein synthesis, synchronized cell populations were metabolically labeled and the synthesis of the basic proteins, including histones, was examined by two-dimensional gel electrophoresis. Exponentially growing S49 mouse lymphoma or Chinese hamster ovary (CHO) cells were separated into G1 and S phase populations by centrifugal elutriation, selective mitotic detachment, fluorescence-activated cell sorting, or a combination of these, and pulse-labeled with radiolabeled amino acids. The histone proteins, both free and chromatin-bound, were completely resolved from some 300 other basic polypeptides in whole-cell lysates by a modification of the NEPHGE technique of O'Farrell, Goodman and O'Farrell (1977). Comparisons of matched autoradiograms from samples of G1 and S phase labeled cells revealed an equivalent rate of histone synthesis through the cell cycle of both S49 and CHO cells. Nuclei isolated from G1 phase S49 cells that were pulse-labeled containing between 13 and 15% of the newly synthesized nucleosomal histones present in S phase nuclei. Nuclei prepared from G1 phase cells that were pulse-labeled and then chased for 5 hr contained more than 90% of the labeled nucleosomal histones present in whole-cell lysates. It therefore seems likely tha differential alterations in the rate of histone synthesis do not occur to a significant degree as cells proceed through the cycle, but the association of newly synthesized histones with DNA takes place after the onset of DNA replication.

Synthesis of H1 histones by BHK cells in G1

The synthesis of histones and DNA was examined in BHK cells arrested in G1 by isoleucine starvation and in cells progressing into the S phase upon isoleucine refeeding. Approximately 2-3% of the cells were not arrested in G1 and synthesized DNA. The rate of synthesis of DNA and nucleosomal histones observed in cells starved for isoleucine could be accounted for by the presence of these asynchronous cells. Synthesis of H1 histones by cells in G1, however, was 3 times that of the nucleosomal histones and approximately 15% of the rate of H1 histone synthesis in mid-S. Upon entry into S, the histones were synthesized in the same molar ratio in which they are present in chromatin. The possible biological significance of H1 histone synthesis in G1 cells and its implications for the regulatory mechanisms controlling histome synthesis are discussed.

Action of heparin on mammalian nuclei. I. Differential extraction of histone H1 and cooperative removal of histones from chromatin

Heparin interacts strongly with the histone component of chromatin, forming heparin-histone complexes which resist dissociation by 0.2 M H2SO4. Heparin treatment of unfractionated histones isolated from nuclei of Chinese hamster cells indicates that the affinities of the histone classes for heparin appear in the order from greatest to least: (H3, H4) greater than (H2A, H2B) greater than H1. However, when isolated nuclei are treated with heparin, H1 is released from the chromatin more readily than the other four histone classes. The release of these four histones (H2A, H2B, H3, and H4) is coordinate and occurs in a highly cooperative manner, as indicated by (1) dependence of the initial kinetics of histone removal upon heparin concentration, (2) analysis of DNA and histones in the fractions obtained from differential sedimentation of heparin-treated nuclei, and (3) analysis of the products from heparin-treated nuclei by equilibrium centrifugation in metrizamide density gradients. The results suggest rapid procedures for using heparin as an agent for studying the accessibility of histones in chromatin of intact nuclei. The relationship of these results to current models of chromatin structure is discussed.

Stage-specific switches in histone synthesis during embryogenesis of the sea urchin

Histones H2A and H2B of the sea urchin embryo have been resolved by new methods into components that are synthesized at different stages of development. One form of H2A and one form of H2B are synthesized only during the period from fertilization to the blastula stage. Subsequently, two other types of H2A and H2B molecules are synthesized. In addition, a histonelike protein was detected which is synthesized only from fertilization until the 16-cell stage when the synthesis of still another H2A-like protein begins. None of the late-appearing forms are derived from histone polypeptide chains synthesized earlier in development. Since the early components do not disappear after their synthesis stops, these modulations of histone synthesis lead to an increase in histone multiplicity, concomitant with the beginning of cell diversification and a decrease in cell division rate.

Cell cycle-specific changes in histone phosphorylation associated with cell proliferation and chromosome condensation

Preparative polyacrylamide gel electrophoresis was used to examine histone phosphorylation in synchronized Chinese hamster cells (line CHO). Results showed that histone f1 phosphorylation, absent in G(1)-arrested and early G(1)-traversing cells, commences 2 h before entry of traversing cells into the S phase. It is concluded that f1 phosphorylation is one of the earliest biochemical events associated with conversion of nonproliferating cells to proliferating cells occurring on old f1 before synthesis of new f1 during the S phase. Results also showed that f3 and a subfraction of f1 were rapidly phosphorylated only during the time when cells were crossing the G(2)/M boundary and traversing prophase. Since these phosphorylation events do not occur in G(1), S, or G(2) and are reduced greatly in metaphase, it is concluded that these two specific phosphorylation events are involved with condensation of interphase chromatin into mitotic chromosomes. This conclusion is supported by loss of prelabeled (32)PO(4) from those specific histone fractions during transition of metaphase cells into interphase G(1) cells. A model of the relationship of histone phosphorylation to the cell cycle is presented which suggests involvement of f1 phosphorylation in chromatin structural changes associated with a continuous interphase "chromosome cycle" which culminates at mitosis with an f3 and f1 phosphorylation-mediated chromosome condensation.