Developmental regulation and butyrate-inducible transcription of the Xenopus histone H1(0) promoter

Changes in chromatin accessibility landscape and histone H3 core acetylation during valproic acid-induced differentiation of embryonic stem cells

Directed differentiation of mouse embryonic stem cells (mESCs) or induced pluripotent stem cells (iPSCs) provides powerful models to dissect the molecular mechanisms leading to the formation of specific cell lineages. Treatment with histone deacetylase inhibitors can significantly enhance the efficiency of directed differentiation. However, the mechanisms are not well understood. Here, we use CUT&RUN in combination with ATAC-seq to determine changes in both histone modifications and genome-wide chromatin accessibility following valproic acid (VPA) exposure. VPA induced a significant increase in global histone H3 acetylation (H3K56ac), a core histone modification affecting nucleosome stability, as well as enrichment at loci associated with cytoskeletal organization and cellular morphogenesis. In addition, VPA altered the levels of linker histone H1 subtypes and the total histone H1/nucleosome ratio indicative of initial differentiation events. Notably, ATAC-seq analysis revealed changes in chromatin accessibility of genes involved in regulation of CDK serine/threonine kinase activity and DNA duplex unwinding. Importantly, changes in chromatin accessibility were evident at several key genomic loci, such as the pluripotency factor Lefty, cardiac muscle troponin Tnnt2, and the homeodomain factor Hopx, which play critical roles in cardiomyocyte differentiation. Massive parallel transcription factor (TF) footprinting also indicates an increased occupancy of TFs involved in differentiation toward mesoderm and endoderm lineages and a loss of footprints of POU5F1/SOX2 pluripotency factors following VPA treatment. Our results provide the first genome-wide analysis of the chromatin landscape following VPA-induced differentiation in mESCs and provide new mechanistic insight into the intricate molecular processes that govern departure from pluripotency and early lineage commitment.

Histone variants: critical determinants in tumour heterogeneity

Malignant cell transformation could be considered as a series of cell reprogramming events driven by oncogenic transcription factors and upstream signalling pathways. Chromatin plasticity and dynamics are critical determinants in the control of cell reprograming. An increase in chromatin dynamics could therefore constitute an essential step in driving oncogenesis and in generating tumour cell heterogeneity, which is indispensable for the selection of aggressive properties, including the ability of cells to disseminate and acquire resistance to treatments. Histone supply and dosage, as well as histone variants, are the best-known regulators of chromatin dynamics. By facilitating cell reprogramming, histone under-dosage and histone variants should also be crucial in cell transformation and tumour metastasis. Here we summarize and discuss our knowledge of the role of histone supply and histone variants in chromatin dynamics and their ability to enhance oncogenic cell reprogramming and tumour heterogeneity.

H1.0 Linker Histone as an Epigenetic Regulator of Cell Proliferation and Differentiation

H1 linker histones are a class of DNA-binding proteins involved in the formation of supra-nucleosomal chromatin higher order structures. Eleven non-allelic subtypes of H1 are known in mammals, seven of which are expressed in somatic cells, while four are germ cell-specific. Besides having a general structural role, H1 histones also have additional epigenetic functions related to DNA replication and repair, genome stability, and gene-specific expression regulation. Synthesis of the H1 subtypes is differentially regulated both in development and adult cells, thus suggesting that each protein has a more or less specific function. The somatic variant H1.0 is a linker histone that was recognized since long ago to be involved in cell differentiation. Moreover, it has been recently found to affect generation of epigenetic and functional intra-tumor heterogeneity. Interestingly, H1.0 or post-translational forms of it have been also found in extracellular vesicles (EVs) released from cancer cells in culture, thus suggesting that these cells may escape differentiation at least in part by discarding H1.0 through the EV route. In this review we will discuss the role of H1.0 in development, differentiation, and stem cell maintenance, also in relation with tumorigenesis, and EV production.

The differentiation-associated linker histone, H1.0, during the in vitro aging and senescence of human diploid fibroblasts

There are numerous similarities between aging/senescence and differentiation. One key similarity is that in both biological processes chromatin remodeling events occur. It is now known that during both processes there is a reorganization of eu- and heterochromatic domains and an increase in heterochromatin, known as heterochromatinization. Previous work of more than two decades has shown that the replacement H1 linker histone subtype, H1.0, accumulates during terminal differentiation in numerous cell/tissue systems. However, work with this differentiation-associated H1 subtype in aging cell systems has only recently been accomplished. In this article, we outline the cumulative results from our investigations of H1.0 protein and mRNA levels in the in vitro aging cell system of human diploid fibroblasts (HDFs) and discuss the potential rationale of why this particular subtype was found to accumulate during both these processes.

Evaluation of γ-Hydroxybutyric Acid for Genotoxicity in the Mouse Micronucleus Assay

Gamma-hydroxybutyric acid (GHB) is an endogenous compound found in the brain and other tissues of mammals. Neurotransmitter/neuromodulator functions have been ascribed to GHB, which has lately become a drug of abuse. In this study, we tested GHB for genotoxicity by measuring its ability to induce micronuclei in polychromatic erythrocytes (reticulocytes) in the peripheral blood of mice. Intraperitoneal injection with a dose of 25 mg/kg/day for 3 days or 50 mg/kg/day x 3 days resulted in a significant (by Dunnett's test) increase of 1.9- to 2.1-fold in micronuclei. However, because increases were small and because no consistent dose-dependent increase in induced micronuclear frequency could be demonstrated, our results do not conclusively show that GHB is an in vivo genotoxicant in mammals.

Dynamics of histone acetylation in vivo. A function for acetylation turnover?

Histone acetylation, discovered more than 40 years ago, is a reversible modification of lysines within the amino-terminal domain of core histones. Amino-terminal histone domains contribute to the compaction of genes into repressed chromatin fibers. It is thought that their acetylation causes localized relaxation of chromatin as a necessary but not sufficient condition for processes that repackage DNA such as transcription, replication, repair, recombination, and sperm formation. While increased histone acetylation enhances gene transcription and loss of acetylation represses and silences genes, the function of the rapid continuous or repetitive acetylation and deacetylation reactions with half-lives of just a few minutes remains unknown. Thirty years of in vivo measurements of acetylation turnover and rates of change in histone modification levels have been reviewed to identify common chromatin characteristics measured by distinct protocols. It has now become possible to look across a wider spectrum of organisms than ever before and identify common features. The rapid turnover rates in transcriptionally active and competent chromatin are one such feature. While ubiquitously observed, we still do not know whether turnover itself is linked to chromatin transcription beyond its contribution to rapid changes towards hyper- or hypoacetylation of nucleosomes. However, recent experiments suggest that turnover may be linked directly to steps in gene transcription, interacting with nucleosome remodeling complexes.

Occurrence of histone H1 degrees protein in rat alveolar macrophages

Histone H1 of rat alveolar macrophages, neutrophilic granulocytes and monocytes extracted with 5% (v/v) perchloric acid was studied in order to see whether a protein similar to histone H1 degrees of rat liver exists in these specialized cells. The biochemical methods used involved SDS and acid-urea polyacrylamide gel electrophoresis, gel filtration on BioGel P100 and raising antisera against chromatographically purified rat liver H1 degrees and histone H1. The antiserum was applied for further characterization of the presumptive H1 degrees fraction using ELISA and Western blot analysis. The results from our studies showed that histone H1 degrees protein is present in rat alveolar macrophages, monocytes and neutrophilic granulocytes, but its quantity in neutrophilic granulocytes is very much less than macrophages and monocytes.

Histone H1 diversity: bridging regulatory signals to linker histone function

Genes encoding linker histone variants have evolved to link their expression to signals controlling the proliferative capacities of cells, i.e. cycling and growth-arrested cells express distinct and specific H1 subtypes. In metazoan, these variants show a tripartite structure, with considerably divergent sequences in their amino and carboxyl terminus domains. The aim of this review is to show how specific regulatory signals control the expression of an individual H1 and to discuss the functional significance of the two variables associated with a linker histone: its primary sequence and the timing of its expression.

The CpG island promoter of the human proopiomelanocortin gene is methylated in nonexpressing normal tissue and tumors and represses expression

Ectopic secretion of ACTH, from sites such as small cell lung cancer (SCLC), results in severe Cushing's syndrome. ACTH is cleaved from POMC. The syndrome may occur when the highly tissue-specific promoter of the human POMC gene (POMC) is activated. The mechanism of activation is not fully understood. This promoter is embedded within a defined CpG island, and CpG islands are usually considered to be unmethylated in all tissues. We demonstrate that much of this CpG island is methylated in normal nonexpressing tissues, in contrast to somatically expressed CpG island promoters reported to date, and is specifically unmethylated in expressing tissues, tumors, and the POMC-expressing DMS-79 SCLC cell line. A narrow 100-bp region is free of methylation in all tissues. E2F factors binding to the upstream domain IV region of the promoter have been shown to be involved in the expression of POMC in SCLC. We show that these sites are methylated in normal nonexpressing tissues, which will prevent binding of E2F, but are unmethylated in expressing tissue. Methylation in vitro is sufficient for silencing of expression, which is not reversed by treatment with Trichostatin A, suggesting that inhibition of expression may be mediated by means other than recruitment of histone deacetylase activity. The DMS-79 cells lack POMC demethylating activity, implying that the methylation and expression patterns are likely to be set early or before neoplastic transformation, and that targeted de novo methylation might be a potential therapeutic strategy.

Involvement of retinoblastoma protein and HBP1 in histone H1(0) gene expression

The histone H1(0)-encoding gene is expressed in vertebrates in differentiating cells during the arrest of proliferation. In the H1(0) promoter, a specific regulatory element, which we named the H4 box, exhibits features which implicate a role in mediating H1(0) gene expression in response to both differentiation and cell cycle control signals. For instance, within the linker histone gene family, the H4 box is found only in the promoters of differentiation-associated subtypes, suggesting that it is specifically involved in differentiation-dependent expression of these genes. In addition, an element nearly identical to the H4 box is conserved in the promoters of histone H4-encoding genes and is known to be involved in their cell cycle-dependent expression. The transcription factors interacting with the H1(0) H4 box were therefore expected to link differentiation-dependent expression of H1(0) to the cell cycle control machinery. The aim of this work was to identify such transcription factors and to obtain information concerning the regulatory pathway involved. Interestingly, our cloning strategy led to the isolation of a retinoblastoma protein (RB) partner known as HBP1. HBP1, a high-mobility group box transcription factor, interacted specifically with the H1(0) H4 box and moreover was expressed in a differentiation-dependent manner. We also showed that the HBP1-encoding gene is able to produce different forms of HBP1. Finally, we demonstrated that both HBP1 and RB were involved in the activation of H1(0) gene expression. We therefore propose that HBP1 mediates a link between the cell cycle control machinery and cell differentiation signals. Through modulating the expression of specific chromatin-associated proteins such as histone H1(0), HBP1 plays a vital role in chromatin remodeling events during the arrest of cell proliferation in differentiating cells.

Histone deacetylase activity is required for the induction of the MyoD muscle cell lineage in Xenopus

Acetylation of nucleosome core histones, which is positively correlated with transcriptional activity, is developmentally regulated in Xenopus. Here we have used the specific histone deacetylase (HDAC)-inhibitor trichostatin A (TSA) to induce precocious histone hyperacetylation in the early frog embryo in order to investigate the potential role of the endogenous changes in chromatin acetylation for the temporally programmed induction of skeletal myogenesis. We show that TSA-treatment (i) selectively blocked the transcriptional induction of the myoD gene, and (ii) severely reduced subsequent muscle differentiation. Both phenotypes required TSA application before gastrulation. This indicates that HDAC activity is required early for the formation of the frog embryonic musculature, apparently for the induction of the MyoD-dependent muscle cell lineage.

Linker histone transitions during mammalian oogenesis and embryogenesis

A unique characteristic of the oocyte is that, although it is a differentiated cell, it can to give rise to a population of undifferentiated embryonic cells. This transition from a differentiated to a totipotential condition is thought to be mediated in part by changes in chromatin composition or configuration. In many non-mammalian organisms, oocytes contain unique subtypes of the linker histone H1, which are replaced in early embryos by the so-called somatic histone H1 subtypes. We review evidence that such histone H1 subtype switches also occur in mammals. Immunologically detectable somatic H1 is present in mitotically proliferating oogonia but gradually becomes undetectable after the oocytes enter meiosis. Immunoreactive somatic H1 remains undetectable throughout oogenesis and the early cell cycles after fertilization. Following activation of the embryonic genome, it is assembled onto chromatin. In contrast to the absence of immunoreactive protein, mRNAs encoding each of the five mammalian somatic H1 subtypes are present in growing oocytes and newly fertilized embryos, indicating that post-transcriptional mechanisms regulate expression of these genes. This maternal mRNA is degraded at the late 2-cell stage, and embryonically encoded mRNAs accumulate after embryos reach the 4-cell stage. During the period when somatic H1 is not detectable, oocytes and embryos contain mRNA encoding a sixth subtype, histone H1(0) which accumulates in differentiated somatic cells, and the nuclei can be stained with an H1(0)-specific antibody. We propose that the linker histone composition of the oocyte lineage resembles that of other mammalian cells, namely, that the somatic H1 subtypes predominate in mitotically active oogonia, that histone H1(0) becomes prominent in differentiated oocytes, and that following fertilization and transcriptional activation of the embryonic somatic H1 genes, the somatic H1 subtypes are reassembled onto chromatin of the embryonic cells. Potential functions of these linker histone subtype switches are discussed, including stabilization by H1(0) of the differentiated state of the oocytes, protection of the oocyte chromatin from factors that remodel sperm chromatin after fertilization, and restoration by the incorporation of the somatic H1 subtypes of the totipotential state of embryonic nuclei.

Butyrate-inducible elements in the human gamma-globin promoter

OBJECTIVE

Several agents including hydroxyurea, erythropoietin and butyric acid have been shown to reactivate gamma gene expression during adult stage development by unknown molecular mechanisms. In addition to inhibiting the enzyme histone deacetylase, butyrate may modulate transcription factor binding to specific DNA sequences defined as butyrate response elements (BREs). The purpose of this study was to identify promoter sequences involved in gamma gene activation by butyrate using truncation mutants in stable cell lines.

MATERIALS AND METHODS

A detailed analysis of Agamma gene activation in the presence of alpha-aminobutyric acid and sodium butyrate was completed in stable mouse erythroleukemia (MEL) cell pools established with seven Agamma promoter truncation mutants. Functional studies were performed in a transient assay system followed by gel mobility shift assays to define protein binding patterns and to demonstrate transcription factor interactions in the gamma promoter BRE.

RESULTS

Agamma promoter analysis in stable MEL cell pools revealed BREs between nucleotide-141 and -201, and nucleotide-822 and -893 (gammaBRE). The gammaBRE required the minimal Agamma promoter (-201 to +36) to stimulate gene expression. We observed a 6.1-fold (p < 0.05) increase in CAT activity for the minimal Agamma promoter alone compared with an 11.5-fold (p < 0.05) increase when the gamma promoter was combined with the -822 to -893 fragment. Protein binding studies demonstrated altered protein-DNA interactions in the gammaBRE after butyrate induction. The pattern for binding observed suggest both negative- and positive-acting transcription factors may interact in this region.

CONCLUSION

The data supports the -822 to -893 region as a DNA regulatory element that contributes to Agamma gene inducibility by butyrate.

Transcriptional repression by XPc1, a new Polycomb homolog in Xenopus laevis embryos, is independent of histone deacetylase

The Polycomb group (Pc-G) genes encode proteins that assemble into complexes implicated in the epigenetic maintenance of heritable patterns of expression of developmental genes, a function largely conserved from Drosophila to mammals and plants. The Pc-G is thought to act at the chromatin level to silence expression of target genes; however, little is known about the molecular basis of this repression. In keeping with the evidence that Pc-G homologs in higher vertebrates exist in related pairs, we report here the isolation of XPc1, a second Polycomb homolog in Xenopus laevis. We show that XPc1 message is maternally deposited in a translationally masked form in Xenopus oocytes, with XPc1 protein first appearing in embryonic nuclei shortly after the blastula stage. XPc1 acts as a transcriptional repressor in vivo when tethered to a promoter in Xenopus embryos. We find that XPc1-mediated repression can be only partially alleviated by an increase in transcription factor dosage and that inhibition of deacetylase activity by trichostatin A treatment has no effect on XPc1 repression, suggesting that histone deacetylation does not form the basis for Pc-G-mediated repression in our assay.

Quantitative analysis of histone H1 degrees protein synthesis in HTC cells

H1 degrees, a member of histone H1 family associated with cell growth arrest and differentiation, is barely expressed in most mammalian cells in culture. Depending on the cell type, serum deprivation or drugs, such as sodium butyrate, significantly increase H1 degrees mRNA level and H1 degrees protein accumulates. However, probably because of a lack of a simple quantitative procedure, little is known about the relationship between H1 degrees mRNA content and its effective translation rate. Using a rat hepatoma cell line and sodium butyrate as a model system, we attempted to evaluate this in different cellular conditions by measuring H1 degrees synthesis with a rapid quantitative procedure we described previously. We found that although the amount of H1 degrees mRNA rapidly increased and then stabilized under sodium butyrate treatment, its transcription was delayed and H1 degrees protein was synthesized in a progressive wave. Butyrate removal from cell culture confirmed that mRNA level and protein synthesis were independently regulated, and provided evidence that sodium butyrate would not directly target the translation apparatus. In contrast, during the S phase of the cell cycle, H1 degrees gene transcription and protein synthesis were concomitantly activated. Taken together these data provide evidence that H1 degrees accumulation results from an increase of its synthesis and that, depending on conditions, a cell exhibits a H1 degrees translation efficiency which may or may not reflect the mRNA level.

Cooperation between phosphorylation and acetylation processes in transcriptional control

We previously reported that the activation of the M promoter of the human choline acetyltransferase (ChAT) gene by butyrate and trapoxin in transfected CHP126 cells is blocked by PD98059, a specific mitogen-activated protein kinase kinase (MEK) inhibitor (E. Espinos and M. J. Weber, Mol. Brain Res. 56:118-124, 1998). We now report that the transcriptional effects of histone deacetylase inhibitors are mediated by an H7-sensitive serine/threonine protein kinase. Activation of the ChAT promoter by butyrate and trapoxin was blocked by 50 microM H7 in both transient- and stable-transfection assays. Overexpression of p300, a coactivator protein endowed with histone acetyltransferase activity, stimulated the ChAT promoter and had a synergistic effect on butyrate treatment. These effects were blocked by H7 and by overexpressed adenovirus E1A 12S protein. Moreover, both H7 and PD98059 suppressed the activation of the Rous sarcoma virus (RSV) and simian virus 40 promoters by butyrate in transfection experiments. Similarly, the induction of the cellular histone H1(0) gene by butyrate in CHP126 cells was blocked by H7 and by PD98059. Previous data (L. Cuisset, L. Tichonicky, P. Jaffray, and M. Delpech, J. Biol. Chem. 272:24148-24153, 1997) showed that the induction of the H1(0) gene by butyrate is blocked by okadaic acid, an inhibitor of protein phosphatases. We now show that the activation of the ChAT and RSV promoters by butyrate in transfected CHP126 cells is also blocked by 200 nM okadaic acid. Western blotting and in vivo metabolic labeling experiments showed that butyrate has a biphasic effect on histone H3 phosphorylation, i.e., depression for up to 16 h followed by stimulation. The data thus strongly suggest that the transcriptional effects of histone deacetylase inhibitors are mediated through the activation of MEK1 and of an H7-sensitive protein kinase in addition to protein phosphatases.

Identification of a new family of higher eukaryotic histone deacetylases. Coordinate expression of differentiation-dependent chromatin modifiers

The histone deacetylase domain of almost all members of higher eukaryotic histone deacetylases already identified (HDAC family) is highly homologous to that of yeast RPD3. In this paper we report the cloning of two cDNAs encoding members of a new family of histone deacetylase in mouse that show a better homology to yeast HDA1 histone deacetylase. These cDNAs encode relatively large proteins, presenting an in vitro trichostatin A-sensitive histone deacetylase activity. Interestingly, one, mHDA2, encodes a protein with two putative deacetylase domains, and the other, mHDA1, contains only one deacetylase homology domain, located at the C-terminal half of the protein. Our data showed that these newly identified genes could belong to a network of genes coordinately regulated and involved in the remodeling of chromatin during cell differentiation. Indeed, the expression of mHDA1 and mHDA2 is tightly linked to the state of cell differentiation, behaving therefore like the histone H1 degrees-encoding gene. Moreover, like histone H1(0) gene, mHDA1 and mHDA2 gene expression is induced upon deacetylase inhibitor treatment. We postulate the existence of a regulatory mechanism, commanding a coordinate expression of a group of genes involved in the remodeling of chromatin not only during cell differentiation but also after abnormal histone acetylation.

S-phase-dependent action of cycloheximide in relieving chromatin-mediated general transcriptional repression

Chromatin plays a major role in the tight regulation of gene expression and in constraining inappropriate gene activity. Replication-coupled chromatin assembly ensures maintenance of these functions of chromatin during S phase of the cell cycle. Thus treatment of cells with an inhibitor of translation, such as cycloheximide (CX), would be expected to have a dramatic effect on chromatin structure and function, essentially in S phase of the cell cycle, due to uncoupled DNA replication and chromatin assembly. In this work, we confirm this hypothesis and show that CX can induce a dramatic S-phase-dependent alteration in chromatin structure that is associated with general RNA polymerase II-dependent transcriptional activation. Using two specific RNA polymerase II-transcribed genes, we confirm the above conclusion and show that CX-mediated transcriptional activation is enhanced during the DNA replication phase of the cell cycle. Moreover, we show co-operation between an inhibitor of histone deacetylase and CX in inducing gene expression, which is again S-phase-dependent. The modest effect of CX in inducing the activity of a transiently transfected promoter shows that the presence of the promoter in an endogenous chromatin context is necessary in order to observe transcriptional activation. We therefore suggest that the uncoupled DNA replication and histone synthesis that occur after CX treatment induces a general modification of chromatin structure, and propose that this general disorganization of chromatin structure is responsible for a widespread activation of RNA polymerase II-mediated gene transcription.

Xenopus NF-Y pre-sets chromatin to potentiate p300 and acetylation-responsive transcription from the Xenopus hsp70 promoter in vivo

We identify Xenopus NF-Y as a key regulator of acetylation responsiveness for the Xenopus hsp70 promoter within chromatin assembled in Xenopus oocyte nuclei. Y-box sequences are required for the assembly of DNase I-hypersensitive sites in the hsp70 promoter, and for transcriptional activation both by inhibitors of histone deacetylase and by the p300 acetyltransferase. The viral oncoprotein E1A interferes with both of these activation steps. We clone Xenopus NF-YA, NF-YB and NF-YC and establish that NF-Y is the predominant Y-box-binding protein in Xenopus oocyte nuclei. NF-Y interacts with p300 in vivo and is itself a target for acetylation by p300. Transcription from the hsp70 promoter in chromatin can be enhanced further by heat shock factor. We suggest two steps in chromatin modification at the Xenopus hsp70 promoter: first the binding of NF-Y to the Y-boxes to pre-set chromatin and second the recruitment of p300 to modulate transcriptional activity.

Multiple epigenetic events regulate mating-type switching of fission yeast

Two epigenetic events at mat1, one of which is DNA strand specific, are required to initiate recombination during mating-type switching. The third, a chromosomally borne imprinted event at the mat2/3 interval regulates silencing and directionality of switching, and prohibits interchromosomal recombination. We speculate that the unit of inheritance in the mat2/3 interval is both DNA plus its associated chromatin structure. Such a control is likely to be essential in maintaining particular states of gene expression during development.

Elements regulating differential activity of chicken histone H1 gene promoters

The chicken genome contains six closely related histone H1 genes, each of which encodes a different H1 protein. The four common regulatory elements previously identified in H1 histone promoters are very similar in sequence and location in all chicken H1 genes, which gives rise to the question of how the six H1 variants are expressed at significantly different levels. Transient transfections of reporter gene transcriptional fusions indicate that approximately 200 bp of each promoter is sufficient to generate the observed spectrum of H1 promoter activity. The differences in H1 promoter-driven expression are shown to be explained by the relative activity of the previously characterized G box region and that of a novel element found between CCAAT and TATA that we have termed differential upstream sequence (Dus). Gel shift analysis indicated that the primary nuclear binding protein to the G box is one or more avian homologues of the Sp1 transcription factor. The Dus region binds multiple nuclear proteins, one of which is the recently described IBR/IBF factor. The differential affinities of the G box and Dus sequences of the H1 promoters for their respective nuclear binding factors correlate well with their relative promoter activities.

The effects of sodium butyrate on transcription are mediated through activation of a protein phosphatase

In this study we have investigated the molecular mechanism by which sodium butyrate modulates gene expression when added to cultured cells. As a model system we used hepatoma tissue culture cells in which sodium butyrate treatment increases histone H1(0) mRNA level and decreases c-myc mRNA level. Because we observed that stimulation of histone H1(0) gene expression could take place in the absence of protein neosynthesis, we hypothesized that sodium butyrate induced a post-translational modification of a factor involved in the transcription process. Using different types of well known kinase and phosphatase inhibitors, we studied the implication of kinase or phosphatase activity in this pathway. Interestingly, cell treatment with potent serine-threonine-phosphatase inhibitors, calyculin A or okadaic acid, prevented the regulation of both histone H1(0) and c-myc gene expressions by sodium butyrate. On the other hand, the tyrosine phosphatase inhibitor, vanadate, or the protein kinase C inhibitor, staurosporine, did not significantly modify sodium butyrate effects. Using protein phosphatase 1 and 2A for in vitro assays, we found a 45% increase of phosphatase activity after cell treatment by sodium butyrate, possibly due to a protein phosphatase 1-type protein phosphatase. These data strongly suggest that signaling pathway(s) triggered by sodium butyrate to modulate gene expression involve(s) a serine-threonine-phosphatase activity.

Characterization of the two H1(zero)-encoding genes from Xenopus laevis

We have analyzed the promoter and the coding sequences of the two homologous histone H1(zero)-encoding genes from Xenopus laevis, here termed H1(zero)-1 and H1(zero)-2. Both genes encode proteins of 193 amino acids and differ at just 16 amino-acid residues. Putative regulatory sequences identified in the promoter region are the same and are highly conserved. However, significant differences exist in the 5' untranslated regions (UTR) of the transcribed sequences of these two genes, such as several deletions in the 5'-UTR of the H1(zero)-2 gene in comparison with the H1(zero)-1 gene 5'-UTR. The 3'-UTR is a short sequence of about 200 bp which is unexpected compared with the long 3'-UTR of mammalian H1(zero) mRNA, but it is in the same size range as in avian H5 mRNA. Thus, the main differences between these two genes are observed in sequences potentially involved in the regulation of the H1(zero) gene expression such as the 5'-UTR. The two genes are expressed during embryogenesis and in several adult tissues. We discuss these findings in terms of the evolution of histone H1(zero) genes in vertebrates and the appearance of histone H5 in avian species.

Chromatin modifications during oogenesis in the mouse: removal of somatic subtypes of histone H1 from oocyte chromatin occurs post-natally through a post-transcriptional mechanism

We examined the distribution of the somatic subtypes of histone H1 and the variant subtype, H1(0), and their encoding mRNAs during oogenesis and early embryogenesis in the mouse. As detected using immunocytochemistry, somatic H1 was present in the nuclei of oocytes of 18-day embryos. Following birth, however, somatic H1 became less abundant in both growing and non-growing oocytes, beginning as early as 4 days of age in the growing oocytes, and was scarcely detectable by 19 days. Together with previous results, this defines a period of time when somatic H1 is depleted in oocytes, namely, from shortly after birth when the oocytes are at prophase I until the 4-cell stage following fertilization. At the stages when somatic H1 was undetectable, oocyte nuclei could be stained using an antibody raised against histone H1(0), which suggests that this may be a major linker histone in these cells. In contrast to the post-natal loss of somatic H1 protein, mRNAs encoding four (H1a, H1b, H1d, H1e) of the five somatic subtypes were present, as detected using RT-PCR in growing oocytes of 9-day pups, and all five subtypes including H1c were present in fully grown oocytes of adults. All five subtypes were also present in embryos, both before and after activation of the embryonic genome. mRNA encoding H1(0) was also detected in oocytes and early embryos. Whole-mount in situ hybridization using cloned H1c and H1e cDNAs revealed that the mRNAs were present in the cytoplasm of oocytes and 1-cell embryos, in contrast to the sea urchin early embryo where they are sequestered in the cell nucleus. We suggest that, as in many somatic cell types, the chromatin of mouse oocytes becomes depleted of somatic H1 and relatively enriched in histone H1(0) postnatally, and that somatic H1 is reassembled onto chromatin in cleavage-stage embryos. The post-natal loss of somatic H1 appears to be regulated post-transcriptionally by a mechanism not involving nuclear localization.

Induction of an exceptionally high-level, nontranslated, Epstein-Barr virus-encoded polyadenylated transcript in the Burkitt's lymphoma line Daudi

An Epstein-Barr virus transcript (designated D-HIT [Daudi high-level-inducible transcript]), constitutively expressed at low levels in the Burkitt's lymphoma (BL)-derived cell line Daudi, can be induced with tetradecanoylphorbol acetate or n-butyrate or, in combination, to about 1% of the levels of high-molecular-weight RNAs in cells. The transcript can also be induced in some other EBV-positive BL-derived cells but to a much lesser extent, particularly in lines that can give rise to productive infection. D-HIT is viral in origin and is composed largely of repetitive sequence. It is polyadenylated but mainly nuclear in location and is highly structured, sensitive only to double-strand-specific RNase. It is endogenously expressed in interferon-sensitive Daudi strains but not in an insensitive strain, Daudi 100K. D-HIT contains a part of a viral open reading frame (designated LF3, and deleted in the prototype B95-8 strain), using an internal polyadenylation (AAUAAA) sequence as a signal to specify processing of its 3' end. In Daudi cells, the promoter contains a putative hinge structure, as found in some interferon-inducible genes and c-myc. Since D-HIT lies adjacent to, probably even encompassing, one of the two viral lytic origins (D(R)) of replication, it may have a role in the regulation of DNA replication. Alternatively, or in addition via its double-stranded structure, D-HIT may play a regulatory role in interferon pathways. Its promoter could be of value for studying expression in constructions containing heterologous genes.

A putative DNA binding surface in the globular domain of a linker histone is not essential for specific binding to the nucleosome

A fundamental step in the assembly of native chromatin is the specific recognition and binding of linker histones to the nucleoprotein subunit known as the nucleosome. A first step in defining this important interaction is the determination of residues within linker histones that are important for the structure-specific recognition of the nucleosome core. By combining in vitro assays for the native binding activity of linker histones and site-directed mutagenesis, we have examined a cluster of basic residues within the globular domain of H1(0), a somatic linker histone variant from Xenopus laevis. We show that these residues, which comprise a putative DNA binding surface within the globular domain, do not play an essential role in the structure-specific binding of a linker histone to the nucleosome.

Alternative splicing of the Drosophila melanogaster rotundRacGAP gene

The rotund (rn) gene in Drosophila melanogaster codes for a RacGTPase-activating protein, RnRacGAP. Cellular studies have shown that RacGAP proteins function as negative regulators of substrate Rac proteins which, in turn, control the localization and polymerization state of actin within the cell. Previous sequence analysis of rn genomic DNA and incomplete cDNA clones suggested that at least two differentially spliced forms of the transcript exist, rnRacGAP(1) and rnRacGAP(2). Using nested reverse transcription-polymerase chain reaction (RT-PCR) methods, we have cloned missing exon and intron sequences, and detected differences between rnRacGAP(1) and rnRacGAP(2) involving 24 nucleotides (nt) of coding sequences and 119 nt of 3'UTR. This translates to a difference of seven amino acids at the C-termini of the polypeptide products. Utilization, in RT-PCR analysis, of form-specific primers provided a simple assay for the tissue specificity of expression of the two forms. rnRacGAP(1) is the predominant species in the testes and is expressed at a low level in the ovary and somatic tissues. rnRacGAP(2) is only very weakly expressed and is detectable solely in the testes.

Regulation of H1(0) gene expression by nuclear receptors through an unusual response element: implications for regulation of cell proliferation

Cloning and sequence analysis of the 5'-flanking region of the human H1(0) histone gene, a differentiation-specific member of the H1 family, has revealed several potential regulatory elements. In this study, we have characterized the interactions of nuclear receptors with an unusual response element consisting of two half-sites arranged as a direct repeat with an 8-bp spacer (DR-8). Thyroid hormone receptors (TR) bind this DR-8 as homodimers and heterodimers with RXR. Retinoic acid receptors (RARs) also bind as heterodimers with RXR to the DR-8, and this binding is enhanced in the presence of retinoic acid (RA) and/or 9-cis RA. Reporter constructs containing the DR-8 allowed a several-fold induction by T3 in the presence of TRs. RAR alpha and RAR beta allowed RA-dependent transcriptional activation whereas RAR gamma mostly increased basal activity. 9-cis RA inhibited the T3 response, indicating a hormonal cross-talk among the subfamily of nuclear receptors. Two orphan receptors, COUP-TF and v-erbA, also bind the DR-8 sequence in the human H1(0) promoter. COUP-TF, which usually represses RAREs, enhances transcriptional activation through the DR-8 whereas v-erbA completely represses TR-RXR induction of the H1(0) gene. Thus, a number of signaling pathways that play important roles during development and differentiation are able to influence the transcription rate of this special H1 subtype directly through a DR-8 response element in its promoter. Because H1(0) expression levels inversely correlate with cell proliferation, our data suggest that several nuclear receptors and the v-erbA oncogene can influence cell proliferation via the regulation of H1(0) expression.

A H1 histone gene-specific AC-box-related element influences transcription from a major chicken H1 promoter

In comparing several histone H1 promoters, we have identified a highly conserved sequence element, 5'-TGTGTTA, located approx. 450-480 bp upstream from the cap site. This TG-box is a near perfect inverted repeat of the previously characterized AC-box (5'-AAACACA). The distance between these elements is also highly conserved. We performed transient transfection assays with cat gene reporter constructs which indicated that both the presence and correct position of the TG-box were essential for maximal expression of the chicken 02 H1 promoter. To the best of our knowledge, this study represents the first demonstration of an effect by the TG-box on transcription of a major histone-encoding H1 gene.

Mice develop normally without the H1(0) linker histone

H1 histones bind to the linker DNA between nucleosome core particles and facilitate the folding of chromatin into a 30-nm fiber. Mice contain at least seven nonallelic subtypes of H1, including the somatic variants H1a through H1e, the testis-specific variant H1t, and the replacement linker histone H1(0). H1(0) accumulates in terminally differentiating cells from many lineages, at about the time when the cells cease dividing. To investigate the role of H1(0) in development, we have disrupted the single-copy H1(0) gene by homologous recombination in mouse embryonic stem cells. Mice homozygous for the mutation and completely lacking H1(0) mRNA and protein grew and reproduced normally and exhibited no anatomic or histologic abnormalities. Examination of tissues in which H1(0) is normally present at high levels also failed to reveal any abnormality in cell division patterns. Chromatin from H1(0)-deficient animals showed no significant change in the relative proportions of the other H1 subtypes or in the stoichiometry between linker histones and nucleosomes, suggesting that the other H1 histones can compensate for the deficiency in H1(0) by occupying sites that normally contain H1(0). Our results indicate that despite the unique properties and expression pattern of H1(0), its function is dispensable for normal mouse development.

An upstream control region required for inducible transcription of the mouse H1(zero) histone gene during terminal differentiation

The replacement linker histone H1 (zero) is associated with terminal differentiation in many mammalian cell types, and its accumulation in chromatin may contribute to transcriptional repression occurring during terminal differentiation. H1 (zero) also accumulates in a variety of cell culture lines undergoing terminal differentiation. During in vitro mouse erythroleukemia cell differentiation, H1 (zero) gene expression is induced very rapidly, prior to the time when the cells actually commit to terminal differentiation. We have used a combination of transfection assays and in vitro DNA-protein interaction studies to identify nuclear protein binding sites in the H1 (zero) promoter that control expression and induction of the H1(zero) gene in mouse erythroleukemia cells. The results indicate that transcription of the H1 (zero) gene is controlled by three elements present in the upstream region of the promoter between positions -305 and -470. Site-directed mutagenesis of each of these elements showed that one of them controls inducibility of the gene in differentiating cells. The other two elements in the upstream control region affect primarily the level of transcription of the gene in undifferentiated and differentiating cells. These two elements share a DNA sequence motif consisting of a (dG)6 tract contained in an eight-base consensus, (A/C)GGGGGG(A/C). Additional copies of this motif are present elsewhere in the H1 (zero) promoter.

In vivo occupancy of histone gene proximal promoter elements reflects gene copy number-dependent titratable transactivation factors and cross-species compatibility of regulatory sequences

To assess systematically the structural and functional aspects of histone gene transcription within a chromosomal context, we stably integrated an extensive set of human histone H4 gene constructs into mouse C127 cells. Levels of expression were determined by S1 nuclease protection assays for multiple mouse monoclonal cell lines containing these human H4 genes. For each cell line, we quantitated the number of integrated human H4 genes by Southern blot analysis. The results indicate that the expression of the human H4 gene is in part copy number dependent at low gene dosages. However, the level of expression varies among different cell lines containing similar numbers of copies of the same H4 gene construct. This result suggests that position-dependent chromosomal integration effects contribute to H4 gene transcription, consistent with the roles of long-range gene organization and nuclear architecture in gene regulation. At high copy number, the level of human H4 gene expression per copy decreased, and endogenous mouse H4 mRNA levels were also reduced. Furthermore, in vivo occupancy at the human H4 gene immediate 5' regulatory elements, as defined by genomic fingerprinting, showed copy number-dependent protein/DNA interactions. Hence, human and mouse H4 genes compete for titratable transcription factors in a cellular environment. Taken together, these results indicate cross-species compatibility and suggest limited representation in vivo of the factors involved in regulating histone H4 gene transcription.

Developmentally regulated expression of linker-histone variants in vertebrates

The identification of histone H1 variants in vertebrates suggests that these proteins may have specialized functions. During embryonic development, a correspondence between the expression of each of the linker-histone variants and the proliferative and transcriptional activity of embryonic cells can be observed. Analysis of the developmentally regulated expression of these variants leads to the subdivision of these variants into distinct classes. This subdivision may also provide insight into the significance of the differential expression of variants and the roles individual linker histones have in chromatin structure and function.

Relationship between core histone acetylation and histone H1(0) gene activity

In this study we show a striking correlation between histone H1(0) gene expression and histone acetylation. Trichostatin A, a highly specific inhibitor of histone deacetylase, efficiently induces H1(0) gene expression. Moreover, using a cell line sensitive to trichostatin A (FM3A) and a derived cell line selected for its resistance to this inhibitor (TR303), it is shown that the level of H1(0) gene expression is related to the extent of chromatin acetylation. After showing the S-phase-dependent activation of H1(0) gene expression, we demonstrate that hyperacetylation has a dominant effect on H1(0) gene expression, since it enhances the expression of the gene independent of the position of cells in the cell cycle. This response to deacetylase inhibitors is specific to H1(0), since it is not shared by other cell-cycle-dependent histone genes (H1 and H4). Finally, by transfection of trichostatin-A-resistant and trichostatin-A-sensitive cells with a plasmid containing a H1(0) promoter, we show that the exogenous H1(0) promoter is also highly sensitive to trichostatin A treatment and that activation of transcription follows exactly the same pattern as activation of the endogenous gene. These data show that histone acetylation may be used to modulate H1(0) gene activity and offers insight into a possible mechanism in which the developmentally regulated chromatin acetylation acts to potentiate H1(0) gene expression.

Molecular basis of the activation of basal histone H1(0) gene expression

Histone H1(0) is encoded by a gene that is expressed only in cells committed to differentiation. We have previously cloned the Xenopus laevis H1(0) gene and studied elements involved in the regulation of its expression in transfected Xenopus laevis A6 cells, and in microinjected embryos. In this work, in order to understand the basis of the action of these elements, we used an A6 cell nuclear extract and showed that the H1(0) promoter is able to direct efficient in vitro transcription, which is highly dependent on a functional TATA box. However, in contrast to what we observed in vivo, in transfected A6 cells, the in vitro transcription was independent of major regulatory elements, defined in vivo. We then used this in vitro system to reconstitute H1(0) gene regulation. The creation of a repressive environment by the addition of purified histone H1 to the in vitro transcription system allowed us to obtain transcription dependent on the integrity of the regulatory elements. Investigating the basis of this regulation we found that protein-DNA interaction on the proximal promoter region was dependent on the integrity of proximal elements, and moreover the distal regulatory element, the UCE, was able to modulate this interaction. We conclude that the role of these regulatory elements is to maintain the basal TATA-dependent transcription of H1(0) under repressive condition: i.e., H1-mediated repression of transcription, or chromatin assembly in general.

Xenopus laevis B4, an intron-containing oocyte-specific linker histone-encoding gene

We have isolated genomic clones of the Xenopus laevis B4 gene, which encodes a linker histone, and characterized the B4 promoter. B4 mRNA is synthesized in X. laevis oocytes and disappears from the embryo by gastrulation. We find that B4 is present in only one or two copies per haploid genome and that it contains introns. Tissue-specific expression, a low copy number and presence of introns are all unusual features for vertebrate genes encoding linker histones.

Cell cycle controlled histone H1, H3, and H4 genes share unusual arrangements of recognition motifs for HiNF-D supporting a coordinate promoter binding mechanism

Cell cycle and growth control of the DNA binding and transactivation functions of regulatory factors provides a direct mechanism by which cells may coordinate transcription of a multitude of genes in proliferating cells. The promoters of human DNA replication dependent histone H4, H3, and H1 genes interact with at least seven distinct proteins. One of these proteins is a proliferation-specific nuclear factor, HiNF-D, that interacts with a key cis-regulatory element (H4-Site II; 41 bp) present in H4 genes. Here we describe binding sites for HiNF-D in the promoters of H3 and H1 genes using cross-competition, deletion analysis, and methylation interference assays, and we show that HiNF-D recognizes intricate arrangements of at least two sequence elements (CA- and AG-motifs). These recognition motifs are irregularly dispersed and distantly positioned in the proximal promoters (200 bp) of both the H3 and H1 genes. In all cases, these motifs either overlap or are in close proximity to other established transcriptional elements, including ATF and CCAAT sequences. Although HiNF-D can interact with low affinity to a core recognition domain, auxiliary elements in both the distal and proximal portions of each promoter cooperatively enhance HiNF-D binding. Thus, HiNF-D appears to bridge remote regulatory regions, which may juxtapose additional trans-activating proteins interacting within histone gene promoters. Consistent with observations in many cell culture systems, the interactions of HiNF-D with the H4, H3, and H1 promoters are modulated in parallel during the cessation of proliferation in both osteosarcoma cells and normal diploid osteoblasts, and these events occur in conjunction with concerted changes in histone gene expression. Thus, HiNF-D represents a candidate participant in coordinating transcriptional control of several histone gene classes.

Specific regulation of Xenopus chromosomal 5S rRNA gene transcription in vivo by histone H1

The incorporation of histone H1 into chromatin during embryogenesis directs the specific repression of the Xenopus oocyte 5S rRNA genes. An increase in histone H1 content specifically restricts TFIIIA-activated transcription, and a decrease in histone H1 within chromatin facilitates the activation of the oocyte 5S rRNA genes by TFIIIA. Variation in the amount of histone H1 in chromatin does not significantly influence somatic 5S rRNA gene transcription. Thus, the regulated expression of histone H1 during Xenopus development has a specific and dominant role in mediating the differential expression of the oocyte and somatic 5S rRNA genes. This example demonstrates that histones can exert dominant repressive effects on the transcription of a gene in vivo in spite of an abundance of transcription factors for that gene.

Two mRNA species encoding the differentiation-associated histone H1(0) are produced by alternative polyadenylation in mouse

Histone H1(0) is a differentiation-specific member of the histone H1 family. The accumulation of the protein is associated with the terminal stage of cell differentiation and is regulated at various levels. In mouse, the analysis of the expression of the single copy gene encoding H1(0) has shown that another H1(0)-related mRNA species (0.9 kb) is present in addition to the usual 2.1-kb mRNA. In this study, we have cloned and sequenced the smaller H1(0)-related mRNA. This mRNA seems to be produced by the use of an additional polyadenylation signal present in the 3' untranslated region (UTR) of the initial transcript. This smaller H1(0)-encoding mRNA is expressed only in mouse and is transferred into polysomes as efficiently as the larger version upon the induction of cell differentiation. The use of the described polyadenylation site removes over 1 kb of the 3' UTR of H1(0) mRNA and seems to be involved in the regulation of H1(0) mRNA stability.

Organization and expression of H1 histone and H1 replacement histone genes

The H1 family is the most divergent subgroup of the highly conserved class of histone proteins [Cole: Int J Pept Protein Res 30:433-449, 1987]. In several vertebrate species, the H1 complement comprises five or more subtypes, and tissue specific patterns of H1 histones have been described. The diversity of the H1 histone family raises questions about the functions of different H1 subtypes and about the differential control of expression of their genes. The expression of main type H1 genes is coordinated with DNA replication, whereas the regulation of synthesis of replacement H1 subtypes, such as H1 zero and H5, and the testis specific H1t appears to be more complex. The differential control of H1 gene expression is reflected in the chromosomal organization of the genes and in different promoter structures. This review concentrates on a comparison of the chromosomal organization of main type and replacement H1 histone genes and on the differential regulation of their expression. General structural and functional data, which apply to both H1 and core histone genes and which are covered by recent reviews, will not be discussed in detail.

Replication-coupled chromatin assembly is required for the repression of basal transcription in vivo

The chromatin assembly process coupled to DNA synthesis in the Xenopus oocyte nucleus is significantly more repressive toward basal transcription than chromatin assembly on duplex DNA. We show that chromatin assembly concurrent with DNA synthesis over the promoter region itself is causal for repression. However, the trans-activator Gal4-VP16 both relieves repression and activates transcription regardless of the chromatin assembly pathway. This activation is independent of whether Gal4-VP16 addition occurs before or after chromatin assembly. We propose that replication-coupled chromatin assembly represents a general mechanism to direct the efficient repression of basal transcription. However transcription induction by a specific activator, Gal4-VP16, occurs independent of this chromatin-mediated repression.

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.