Changes in the proportions of histone H1 subtypes in brain cortical neurons

Imaging analysis of six human histone H1 variants reveals universal enrichment of H1.2, H1.3, and H1.5 at the nuclear periphery and nucleolar H1X presence

Histone H1 participates in chromatin condensation and regulates nuclear processes. Human somatic cells may contain up to seven histone H1 variants, although their functional heterogeneity is not fully understood. Here, we have profiled the differential nuclear distribution of the somatic H1 repertoire in human cells through imaging techniques including super-resolution microscopy. H1 variants exhibit characteristic distribution patterns in both interphase and mitosis. H1.2, H1.3, and H1.5 are universally enriched at the nuclear periphery in all cell lines analyzed and co-localize with compacted DNA. H1.0 shows a less pronounced peripheral localization, with apparent variability among different cell lines. On the other hand, H1.4 and H1X are distributed throughout the nucleus, being H1X universally enriched in high-GC regions and abundant in the nucleoli. Interestingly, H1.4 and H1.0 show a more peripheral distribution in cell lines lacking H1.3 and H1.5. The differential distribution patterns of H1 suggest specific functionalities in organizing lamina-associated domains or nucleolar activity, which is further supported by a distinct response of H1X or phosphorylated H1.4 to the inhibition of ribosomal DNA transcription. Moreover, H1 variants depletion affects chromatin structure in a variant-specific manner. Concretely, H1.2 knock-down, either alone or combined, triggers a global chromatin decompaction. Overall, imaging has allowed us to distinguish H1 variants distribution beyond the segregation in two groups denoted by previous ChIP-Seq determinations. Our results support H1 variants heterogeneity and suggest that variant-specific functionality can be shared between different cell types.

The Histone H3 Family and Its Deposition Pathways

Within the cell nucleus, the organization of the eukaryotic DNA into chromatin uses histones as components of its building block, the nucleosome. This chromatin organization contributes to the regulation of all DNA template-based reactions impacting genome function, stability, and plasticity. Histones and their variants endow chromatin with unique properties and show a distinct distribution into the genome that is regulated by dedicated deposition machineries. The histone variants have important roles during early development, cell differentiation, and chromosome segregation. Recent progress has also shed light on how mutations and transcriptional deregulation of these variants participate in tumorigenesis. In this chapter we introduce the organization of the genome in chromatin with a focus on the basic unit, the nucleosome, which contains histones as the major protein component. Then we review our current knowledge on the histone H3 family and its variants-in particular H3.3 and CenH3^CENP-A-focusing on their deposition pathways and their dedicated histone chaperones that are key players in histone dynamics.

Mapping of six somatic linker histone H1 variants in human breast cancer cells uncovers specific features of H1.2

Seven linker histone H1 variants are present in human somatic cells with distinct prevalence across cell types. Despite being key structural components of chromatin, it is not known whether the different variants have specific roles in the regulation of nuclear processes or are differentially distributed throughout the genome. Using variant-specific antibodies to H1 and hemagglutinin (HA)-tagged recombinant H1 variants expressed in breast cancer cells, we have investigated the distribution of six H1 variants in promoters and genome-wide. H1 is depleted at promoters depending on its transcriptional status and differs between variants. Notably, H1.2 is less abundant than other variants at the transcription start sites of inactive genes, and promoters enriched in H1.2 are different from those enriched in other variants and tend to be repressed. Additionally, H1.2 is enriched at chromosomal domains characterized by low guanine–cytosine (GC) content and is associated with lamina-associated domains. Meanwhile, other variants are associated with higher GC content, CpG islands and gene-rich domains. For instance, H1.0 and H1X are enriched at gene-rich chromosomes, whereas H1.2 is depleted. In short, histone H1 is not uniformly distributed along the genome and there are differences between variants, H1.2 being the one showing the most specific pattern and strongest correlation with low gene expression.

Transgenerational epigenetics and brain disorders

Neurobehavioral and psychiatric disorders are complex diseases with a strong heritable component; however, to date, genome-wide association studies failed to identify the genetic loci involved in the etiology of these brain disorders. Recently, transgenerational epigenetic inheritance has emerged as an important factor playing a pivotal role in the inheritance of brain disorders. This field of research provides evidence that environmentally induced epigenetic changes in the germline during embryonic development can be transmitted for multiple generations and may contribute to the etiology of brain disease heritability. In this review, we discuss some of the most recent findings on transgenerational epigenetic inheritance. We particularly discuss the findings on the epigenetic mechanisms involved in the heritability of alcohol-induced neurobehavioral disorders such as fetal alcohol spectrum disorders.

The microheterogeneity of the mammalian H1(0) histone. Evidence for an age-dependent deamidation

Histone H1(0) is known to consist of two subfractions named H1(0)a and H1(0)b. The present work was performed with the aim of elucidating the nature of these two subfractions. By using reversed-phase high performance liquid chromatography in combination with hydrophilic interaction liquid chromatography, we fractionated human histone H1(0) into even four subfractions. Hydrophilic interaction liquid chromatographic analysis of the peptide fragments obtained after cleavage with cyanogen bromide and digestion with chymotrypsin suggested that the four H1(0) subfractions differ only in their small N-terminal end of the H1(0) molecule (30 residues). Edman degradation of the N-terminal H1(0) peptide fragments and mass spectra analysis have indicated that human histone H1(0) consists of intact histones H1(0) (named H1(0) Asn-3) and deamidated H1(0) forms (H1(0) Asp-3) having an aspartic acid residue at position 3 instead of asparagine. Moreover, both H1(0) Asn-3 and H1(0) Asp-3 are blocked (H1(0)a Asn-3, H1(0)a Asp-3) and unblocked (H1(0)b Asn-3, H1(0)b Asp-3) on their N terminus. Acid-urea gel electrophoretic analysis has shown that the histone subfraction, in the literature originally named H1(0)a, actually consists of a mixture of H1(0)a Asn-3 and H1(0)a Asp-3, whereas H1(0)b consists of H1(0)b Asn-3 and H1(0)b Asp-3. Furthermore, we found that hydrophilic interaction liquid chromatography separates rat and mouse histone H1(0) just like human H1(0) into four subfractions. Hydrophilic interaction liquid chromatographic analysis of brain and liver histone H1(0) from rats of different ages revealed an age-dependent increase of both the N-terminally acetylated and the deamidated forms of H1(0). In addition, we found that the relative proportions of the four forms of H1(0) histones differ from tissue to tissue.

Transgenic mice transcribing the human H1 zero histone gene exhibit a normal phenotype

The linker histone H1degree accumulates in terminally differentiating cells and replaces other members of the H1 histone family, even in the absence of cell division. To study the role of H1degree in vivo, we have created two lines of transgenic mice with either the human H1degree promoter (HH minigene) or the mouse metallothionein T promoter (MH minigene) upstream of the human H1degree gene. Mice bearing the minigenes HH or MH overexpress human H1degree mRNA at 10-20-fold higher levels than in normal mice in a constitutive or metal-inducible manner. In contrast to this increase in mRNA content, which was studied in liver, kidney and brain, no significant changes in the relative proportions of the H1 protein subtypes, including H1degree were observed. Transgenic mice exhibited normal anatomic phenotypes, growth rates and reproduction rates. Thus, our results suggest a posttranscriptional and/or translational mechanism that compensates the unbalanced linker-histone expression in different tissues.

In vivo phosphorylation of histone H1 variants during the cell cycle

In vivo phosphorylation of the five histone H1 variants H1a-H1e including H1(0) in NIH 3T3 mouse fibroblasts was examined during the cell cycle by using a combination of HPLC techniques and conventional AU gel electrophoresis. Phosphorylation starts during the late G1 phase and increases throughout the S phase. In the late S phase, the H1 variants exist as a combination of molecules containing 0 or 1 (H1a, H1c), 0-2 (H1d), or 0-3 (H1b, H1e) phosphate groups with a share of unphosphorylated protein ranging between 35% and 75%, according to the particular subtype. Pulse-chase experiments show that phosphorylation during the S phase is a dynamic phosphorylation process with a limited phosphorylation maximum. In most H1 subtypes, phosphorylation occurs very rapidly at the G2/M transition with only small amounts of intermediate phosphorylated molecules. Phosphorylation of mouse H1c, however, occurs stepwise during this transition. Phosphorylated mouse histone subtypes from cells in mitosis contain four phosphate groups in the case of H1a, H1c, and H1e and five in the case of H1b and H1d. Comparison of the mouse phosphorylation pattern to that in rat C-6 glioma cells showed differences for H1e and H1d. By comparing the different phosphorylation patterns of the individual H1 variants during the cell cycle, we were able to classify the H1 histones into subtypes with low (H1a, H1c, H1(0)) and high (H1b, H1d, H1e) phosphorylation levels.

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.

Differential regulation of the human H1 zero-histone-gene transcription in human tumor-cell lines

Cloning and sequence analysis of about 2 kb of the 5' flanking region of the human H1 zero histone gene reveals several potential regulatory elements upstream of the transcribed portion of this gene. Transfection studies using the chloramphenicol acetyl transferase (CAT) gene as a reporter gene with a series of promoter deletions revealed that the expression of the H1 zero gene may depend on a complex interplay of several transcription factors, including members of the retinoic acid and/or thyroid-hormone-receptor superfamily, at the 5' flanking region of the H1 zero gene. CAT assays demonstrate varied patterns of expression and regulation in different human tumor-cell lines. The leukemia cell line HL60 does not express H1 zero mRNA and shows no CAT activity. HeLa cells strongly express the CAT gene under the control of the H1 zero promoter. Under the same conditions, HepG2 cells also transcribe the CAT gene, although at a lower rate than HeLa cells. Using different promoter-deletion clones, the CAT activity differs in HepG2 and HeLa cells in the very distal promoter region. In both cell lines, the CAT activity decreases several fold when the region between nucleotides -450 and -600 upstream of the mRNA start site is deleted. It also decreases when just the proximal portion but not the distal promoter region is deleted. In summary, the regulatory patterns of these three cell lines differ, indicating a cell-type-specific regulation of the human H1 zero-histone-gene expression.

Increased histone H1(0) expression in differentiating mouse erythroleukemia cells is related to decreased cell proliferation

The amount of histone H1(0) increases relative to other H1 subtypes in terminally differentiated cells, and its expression has been associated with the onset of differentiation. We have studied the kinetics of H1(0) accumulation in mouse erythroleukemia (MEL) cells and found that the levels of H1(0) reflect the rate of cell proliferation rather than the state of differentiation. This suggests that changes in the relative amount of H1(0) during MEL cell differentiation are primarily a consequence of cell cycle arrest.

Qualitative differences in nuclear proteins correlate with neuronal terminal differentiation

1. Protein composition of neuronal nuclei was studied at two stages of brain maturation, i.e., before (embryonic day 16; E16) and after (postnatal day 10; P10) shortening of the nucleosomal repeat length. Glial nuclei were analyzed in parallel as a control. 2. Total nuclear or HCl- and 5% perchloric acid (PCA)-soluble proteins were analyzed by different electrophoretic techniques. 3. Our results show an increase in the concentration of histone H1 zero with differentiation, although the H1 class undergoes an overall decrease. 4. The chromatin of mature neurons is also enriched in the ubiquinated form of histone H2A (A24), while the high-mobility group (HMG) proteins 1 and 2 seem to decrease slightly relative to core histones. 5. Both quantitative and qualitative differences in the abundance of nonhistone proteins relative to histones accompany neuronal terminal differentiation.

Effects of antineoplastic phospholipids on parameters of cell differentiation in U937 cells

The proliferation of the human promonocytic leukemia cell line U937 is inhibited by several ether lipids, ether lipid analogues and by phorbol esters. An early effect of this retardation of cell growth is the induction of a basic chromosomal protein, histone H1(0). Northern blot analysis of H1(0) mRNA levels reveals an increase of the mRNA concentration within a few hours after addition of hexadecylphosphocholine and 1-O-octadecyl-2-O-methyl-rac-glycero-3-phosphocholine. This early effect on the synthesis of a subtype of H1 proteins precedes the expression of several parameters of the monocytic differentiation of U937 cells.

The expression of the histone H1 (0) gene in the human hepatoma cell line HepG2 is independent of the state of cell proliferation

The H1 histone subtype H1 (0) is a characteristic component of the chromatin of several mammalian tissues. Since H1 (0) is synthesized in nondividing cells upon terminal differentiation, it has been mostly considered either as a prerequisite for or as a consequence of an arrest of DNA replication during the process of differentiation. In several H1 (0)-expressing systems studied until now, inducers of differentiation or inhibitors of DNA synthesis cause an increase of the ratio between H1 (0) and the other H1 proteins. We have studied the steady-state levels of histone H1 (0) mRNA under varied growth conditions in the human hepatoma cell lines HepG2 and Hep3B, and we show in the HepG2 system that H1 (0) is not confined to resting cells, that the H1 (0) gene appears to be expressed throughout the cell cycle and that established inducers of de novo H1 (0) synthesis fail to cause a further increase of the high H1 (0) level. This constitutive expression of H1 (0) appears to reflect the chromatin structure of the liver cells, from which the HepG2 hepatoblastoma cells initially may have evolved. In contrast to the situation in nondividing adult liver cells, the H1 (0) gene is transcribed in HepG2 at a high level, and this expression is compatible with DNA replication.

Age-related changes of the H1 and H1(0) histone variants in murine tissues

The relative proportion of the histone H1(0) which is present in chromatin of nondividing and terminally differentiated cells is shown to increase with age. CNBr nonenzymatic cleavage and SDS-polyacrylamide gel electrophoresis of H1(0) extracted from liver chromatin of young and old mice and from age-related hepatocarcinomas showed that H1(0) consists of two variants, one contains methionine the other is methionine-free. The ratio between these two H1(0) variants also changes with age. The relative amounts of specific minor H1 and H1(0) histone fractions which are more loosely bound in chromatin and are extractable with 0.35 M NaCl, together with the HMG nonhistone proteins decrease in ageing mouse tissues. The age-related alteration of the ratio between H1(0) variants probably represents the chromatin repair process, whereas the age-related replacement of H1A and H1B subfractions by H1(0) histones may reflect the continuing process of differentiation.

Differential acetylation of core histones in rat cerebral cortex neurons during development and aging

Core histones can be modified by aceylation and this modification has been correlated with the modulation of chromatin condensation and histone deposition. We have now studied the levels of acetylation of the core histones in rat brain cortical neurons from the middle of the period of neuronal proliferation through postnatal development and aging. The results show that the level of acetylation of H4 decreases with age. The kinetics of H4 deacetylation show a perinatal fast phase followed by a much slower phase that spans the rest of the period examined. H4 deacetylation is accounted for by the decrease of the monoacetylated species, the proportions of the more highly acetylated species remaining essentially constant. By contrast to histone H4, the overall levels of acetylation and the proportions of the different acetylated species of H2A, H2B and H3 remain unchanged throughout the period examined. Furthermore, the variants belonging to a given histone class always show the same level of acetylation. The fact that in neurons the level of monoacetylated H4 decreases during development and aging, in sharp contrast with the constancy of the levels of all other acetylated histone species, raises the possibility that in interphase chromatin monoacetylated H4 may have a central role in the modulation of chromatin structure. The results also suggest that the slow decrease of the proportion of monoacetylated H4 may imply a gradual loss of chromatin structural plasticity and thus lead to aging.

Monoclonal autoantibodies recognizing histone variants

Balb/c mice were immunized with affinity purified Ro(SS-A) from human origin in order to allow the preparation of monoclonal anti-Ro(SS-A) antibodies. After fusion of mouse myeloma cells (line Sp2/0 A914) with spleen cells from one of these mice, anti-Ro(SS-A) monoclonals were not obtained, but, instead, two IgM producing hybridomas reactive with histone H1 and one with histone H2B. The specificity of the anti-H1 monoclonals was investigated by means of immunoblotting of very lysine-rich histone variants from mouse which were separated by two-dimensional gelelectrophoresis. One of them (CLB-ANA 105) has H1(0) specificity with respect to the histone variants of mouse and man, but recognizes H5 as well as H1 from Xenopus laevis. Another monoclonal (CLB-ANA 108) reacts with the variant H1c from mouse, exclusively. From the way these monoclonals were produced, we postulate that they were not the result of immunization, but comprise specificities of naturally occurring autoantibodies.

Histone acetylation: a step in gene activation

Cellular ageing appears to consist mainly in a loss of adaptability and a progressive decrease in the capacity of the cell to maintain homeostasis. Such age related phenomenon can be the result of stochastic or of programmed events, and may occur through changes in the base pairs or coding of the DNA, through increasing levels of error in transcription and finally through alterations at the translation step of proteins synthesis. The purpose of this chapter is to present histone acetylation as a key event in the control of chromatin structure and transcription.