Histone H4 Acetylation Patterns Research Articles

Determining histone H4 acetylation patterns in human peripheral blood mononuclear cells using mass spectrometry

Misregulated chromatin remodeling via erroneous histone acetylation has been linked with multiple diseases including many age-associated maladies. Previous studies on histone acetylation have utilized specific histone acetylation antibodies as a primary quantification tool. However, antibodies that target specific histone modifications frequently lack sufficient sensitivity and specificity, making signal quantification and data interpretation difficult. Here, we used mass spectrometry to quantify the acetylation patterns of histone H4 in peripheral blood mononuclear cells (PBMCs) from human patients of varying age. We observed that mono-acetylation of H4K16ac is lower in midlife human PBMCs, and that various changes occur in the H4 acetylation signature using PBMCs prepared from old patients. Our data corroborates previous work suggesting that ageing might be characterized by specific changes in the acetylation states of histone H4 and shows that targeted mass spectrometry together with appropriate quantification methods can be used to sensitively measure such changes.

The mouse RANKL gene locus is defined by a broad pattern of histone H4 acetylation and regulated through distinct distal enhancers

RANKL is a stromal cell-derived tumor necrosis factor (TNF)-like factor that plays a primary role in osteoclast formation and function. Recent studies suggest that 1,25(OH)(2) D(3) induces Rankl expression via vitamin D receptor (VDR) interaction at several enhancers located up to 76 kb upstream of the gene's transcriptional start site (TSS). In the current studies, we explored these interactions further using ChIP-chip and RNA analysis. We confirm VDR and RXR binding to the five enhancers described previously and identify two additional sites, one located within the Rankl coding region. We also show that RNA polymerase II is recruited to these enhancers, most likely through transcription factors TBP, TFIIB, and TAF(II) 250. Interestingly, the recruitment of these factors leads to the production of RNA transcripts, although their role at present is unknown. We also discovered that histone H4 acetylation (H4ac) marks many upstream Rankl enhancers under basal conditions and that H4ac is increased upon 1,25(OH)(2) D(3) treatment. Surprisingly, the hormone also induces C/EBPβ binding across the Rankl locus. C/EBPβ binding correlates directly with increased H4ac activity following 1,25(OH)(2) D(3) treatment. Finally, elevated H4ac is restricted to an extended region located between two potential insulator sites occupied by CTCF and Rad21. These data suggest a mechanism whereby 1,25(OH)(2) D(3) functions via the VDR and C/EBPβ to upregulate Rankl expression.

Differential acetylation of histone H4 lysine during development of in vitro fertilized, cloned and parthenogenetically activated bovine embryos

The oocyte is remarkable in its ability to remodel parental genomes following fertilization and to reprogram somatic nuclei after nuclear transfer (NT). To characterise the patterns of histone H4 acetylation and DNA methylation during development of bovine gametogenesis and embryogenesis, specific antibodies for histone H4 acetylated at lysine 5 (K5), K8, K12 and K16 residues and for methylated cytosine of CpG dinucleotides were used. Oocytes and sperm lacked the staining for histone acetylation, when DNA methylation staining was intense. In IVF zygotes, both pronuclei were transiently hyper-acetylated. However, the male pronucleus was faster in acquiring acetylated histones, and concurrently it was rapidly demethylated. Both pronuclei were equally acetylated during the S to G2-phase transition, while methylation staining was only still observed in the female pronucleus. In parthenogenetically activated oocytes, acetylation of the female pronucleus was enriched faster, while DNA remained methylated. A transient de-acetylation was observed in NT embryos reconstructed using a non-activated ooplast of a metaphase second arrested oocyte. Remarkably, the intensity of acetylation staining of most H4 lysine residues peaked at the 8-cell stage in IVF embryos, which coincided with zygotic genome activation and with lowest DNA methylation staining. At the blastocyst stage, trophectodermal cells of IVF and parthenogenetic embryos generally demonstrated more intense staining for most acetylated H4 lysine, whilst ICM cells stained very weakly. In contrast methylation of the DNA stained more intensely in ICM. NT blastocysts showed differential acetylation of blastomeres but not methylation. The inverse association of histone lysine acetylation and DNA methylation at different vital embryo stages suggests a mechanistically significant relationship. The complexities of these epigenetic interactions are discussed.

Drug-Induced Genetic and Epigenetic Marks in Sperm Affect Zygotic Development.

Exposure of male rats to a male mediated developmental toxicant and anticancer alkylating agent, cyclophosphamide (CPA), can result in increased pre- and post-implantation loss, and malformations in the offspring. CPA induces a stage specific stress response in male germ cells. The DNA damage induced by CPA is germ cell phase specific, with the greatest damage occurring during sperm chromatin remodeling. Drug induced insults to sperm chromatin may affect the function of the paternal genome in the zygote. Zygotes sired by drug-treated males display advanced developmental progression. In 1- and 2-cell embryos sired by CPA-treated males, the relative abundance of candidate gene transcripts is elevated. We hypothesized that paternal CPA exposure disrupts epigenetic programming and DNA damage recognition/repair in the early embryo. To test this hypothesis, we examined the temporal patterns of histone H4 acetylation at lysine 5, cytosine methylation at position 5, histone H2AX phosphorylation, and poly(ADP-ribose) polymerase-1 immunostaining in zygotes sired by CPA-exposed and control males. H4 was significantly hyperacetylated in both the male and female pronuclei in embryos sired by CPA-treated males, beginning in G1 and lasting into S-phase; in later stages of zygotic development, the extent of H4 acetylation did not differ. DNA methylation reprogramming was also dysregulated. In control zygotes, the male pronuclei underwent a gradual genome-wide demethylation, while the female pronuclei remained hypermethylated; in contrast, the male pronuclei in zygotes fertilized by CPA-exposed sperm were dramatically hypomethylated. Phosphorylated histone H2AX was increased in a biphasic manner in the paternal genome, while poly(ADP-ribose) polymerase-1 was markedly elevated in both the paternal and maternal genomes in zygotes fertilized by CPA-treated males. Collectively, these studies demonstrate that paternal drug exposure affects the epigenetic programming and DNA damage responses of not only the male, but also the female pronucleus, demonstrating the existence of pronuclear cross talk during zygotic development. Deregulation of epigenetic programming in the zygote may contribute to heritable instabilities later in development. Supported by CIHR

Drug-induced epigenetic changes produce drug tolerance.

Tolerance to drugs that affect neural activity is mediated, in part, by adaptive mechanisms that attempt to restore normal neural excitability. Changes in the expression of ion channel genes are thought to play an important role in these neural adaptations. The slo gene encodes the pore-forming subunit of BK-type Ca2+-activated K+ channels, which regulate many aspects of neural activity. Given that induction of slo gene expression plays an important role in the acquisition of tolerance to sedating drugs, we investigated the molecular mechanism of gene induction. Using chromatin immunoprecipitation followed by real-time PCR, we show that a single brief sedation with the anesthetic benzyl alcohol generates a spatiotemporal pattern of histone H4 acetylation across the slo promoter region. Inducing histone acetylation with a histone deacetylase inhibitor yields a similar pattern of changes in histone acetylation, up-regulates slo expression, and phenocopies tolerance in a slo-dependent manner. The cAMP response element binding protein (CREB) is an important transcription factor mediating experience-based neuroadaptations. The slo promoter region contains putative binding sites for the CREB transcription factor. Chromatin immunoprecipitation assays show that benzyl alcohol sedation enhances CREB binding within the slo promoter region. Furthermore, activation of a CREB dominant-negative transgene blocks benzyl alcohol–induced changes in histone acetylation within the slo promoter region, slo induction, and behavioral tolerance caused by benzyl alcohol sedation. These findings provide unique evidence that links molecular epigenetic histone modifications and transcriptional induction of an ion channel gene with a single behavioral event.

Transcriptional regulation of cyclooxygenase 2 by bradykinin and interleukin-1beta in human airway smooth muscle cells: involvement of different promoter elements, transcription factors, and histone h4 acetylation.

Bradykinin and interleukin-1beta (IL-1beta) induce cyclooxygenase 2 (COX-2) in human airway smooth muscle cells. Here we extended our study to explore the gene transcriptional regulation. By transfection with various COX-2 promoter reporter constructs, we found that the bp -327-to-+59 promoter region was essential for COX-2 gene transcription by bradykinin and IL-1beta and that the cyclic AMP response element (CRE) was critical in bradykinin-induced transcription, whereas nuclear factor IL-6 and CRE and, to a lesser extent, nuclear factor-kappaB (NF-kappaB) were involved in IL-1beta-induced transcription. An electrophoretic mobility shift assay revealed that both bradykinin and IL-1beta elicited CRE-binding protein-1 (CREB-1) binding, and IL-1beta also elicited CCAAT/enhancer-binding protein beta and NF-kappaB binding to their respective elements in the COX-2 promoter. These transcription factors were associated with the COX-2 promoter, which was dynamically linked to different patterns of histone H4 acetylation by bradykinin and IL-1beta, as demonstrated by chromatin immunoprecipitation. We also revealed that endogenous prostaglandin E(2) was critical in bradykinin-induced COX-2 transcription initiation and involved in IL-1beta-induced COX-2 transcription at a latter stage. Our result provide the first evidence that COX-2 transcriptional regulation by different stimuli involves different promoter elements and transcription factors and is associated with chromatin remodeling after selective histone H4 acetylation in a stimulus-specific manner.

Histone H4 Acetylation Patterns During Seed Germination and Early Plant Development

Here we studied whether early development of Silene latifolia is accompanied with changes in acetylation of nucleosomal histones H4. Using acid-urea-triton polyacrylamide gel and immunoblotting with specific antisera the histone acetylation in relationship with transcriptional activity, measured by [14C]-uridine incorporation, was analysed in dry and germinating seeds, seedlings, and adult leaves. We show that quiescent and germinating seeds, until the root tip is released from testa, are characterised by an absence of transcriptional activity and by a low H4 acetylation level: only mono-acetylated isoforms were present. During the postgermination period and early plantlet development, a high increase of transcriptional activity started and a sharp H4 hyperacetylation, up to the penta-acetylated isoform, was detected. We conclude that epigenetic modification by nucleosomal histone deacetylation plays a role in maintenance of global genome silencing in quiescent seeds.

Acetylation of histone H4 by Esa1 is required for DNA double-strand break repair.

Although the acetylation of histones has a well-documented regulatory role in transcription, its role in other chromosomal functions remains largely unexplored. Here we show that distinct patterns of histone H4 acetylation are essential in two separate pathways of double-strand break repair. A budding yeast strain with mutations in wild-type H4 acetylation sites shows defects in nonhomologous end joining repair and in a newly described pathway of replication-coupled repair. Both pathways require the ESA1 histone acetyl transferase (HAT), which is responsible for acetylating all H4 tail lysines, including ectopic lysines that restore repair capacity to a mutant H4 tail. Arp4, a protein that binds histone H4 tails and is part of the Esa1-containing NuA4 HAT complex, is recruited specifically to DNA double-strand breaks that are generated in vivo. The purified Esa1-Arp4 HAT complex acetylates linear nucleosomal arrays with far greater efficiency than circular arrays in vitro, indicating that it preferentially acetylates nucleosomes near a break site. Together, our data show that histone tail acetylation is required directly for DNA repair and suggest that a related human HAT complex may function similarly.

Glucocorticoid receptor recruitment of histone deacetylase 2 inhibits interleukin-1beta-induced histone H4 acetylation on lysines 8 and 12.

We have investigated the ability of dexamethasone to regulate interleukin-1beta (IL-1beta)-induced gene expression, histone acetyltransferase (HAT) and histone deacetylase (HDAC) activity. Low concentrations of dexamethasone (10(-10) M) repress IL-1beta-stimulated granulocyte-macrophage colony-stimulating factor (GM-CSF) expression and fail to stimulate secretory leukocyte proteinase inhibitor expression. Dexamethasone (10(-7) M) and IL-1beta (1 ng/ml) both stimulated HAT activity but showed a different pattern of histone H4 acetylation. Dexamethasone targeted lysines K5 and K16, whereas IL-1beta targeted K8 and K12. Low concentrations of dexamethasone (10(-10) M), which do not transactivate, repressed IL-1beta-stimulated K8 and K12 acetylation. Using chromatin immunoprecipitation assays, we show that dexamethasone inhibits IL-1beta-enhanced acetylated K8-associated GM-CSF promoter enrichment in a concentration-dependent manner. Neither IL-1beta nor dexamethasone elicited any GM-CSF promoter association at acetylated K5 residues. Furthermore, we show that GR acts both as a direct inhibitor of CREB binding protein (CBP)-associated HAT activity and also by recruiting HDAC2 to the p65-CBP HAT complex. This action does not involve de novo synthesis of HDAC protein or altered expression of CBP or p300/CBP-associated factor. This mechanism for glucocorticoid repression is novel and establishes that inhibition of histone acetylation is an additional level of control of inflammatory gene expression. This further suggests that pharmacological manipulation of of specific histone acetylation status is a potentially useful approach for the treatment of inflammatory diseases.

Histone H4 acetylation during interleukin-2 stimulation of mouse T cells

Proliferation and cell cycle progression of eukaryotic cells are closely linked to changes in chromatin structure and gene expression. By reversible histone acetylation the cell is able to modulate chromatin condensation and accessibility of specific regions within the chromatin. Here, we examined histone H4 acetylation patterns during growth induction of the murine interleukin-2 dependent T cell line B6.1. In order to detect acetylation on each of the four potential target residues we produced a set of antibodies recognizing specifically acetylated lysine 5, 8, 12 and 16 in the N-terminal tail of histone H4. Acetylation was generally low in resting T cells, but increased after stimulation with a specific kinetics for each lysine. Lysine 16 was acetylated during the G1 phase and deacetylated during S phase. H4 acetylation on lysine 5, 8 and 12, in contrast, was induced before cells started to replicate, and persisted until cells entered mitosis. Treatment of resting B6.1 cells with the specific deacetylase inhibitor trichostatin A (TSA) led to H4 hyperacetylation at all four lysine residues indicating that the histone modification can occur in the absence of replication. After release from TSA treatment normal H4 acetylation levels were reestablished by extremely rapid deacetylation of lysines 5, 8, 12 and 16. The deacetylation step was 60–100 times faster than TSA induced acetylation and equally efficient in resting and exponentially growing T cells. Our results indicate the presence of cell cycle regulated lysine specific acetylating and deacetylating activities in mouse T cells.

Patterns of histone H4 acetylation distinguish structural and functional domains within the human genome

Patterns of histone H4 acetylation distinguish structural and functional domains within the human genome

Distinctive patterns of histone H4 acetylation are associated with defined sequence elements within both heterochromatic and euchromatic regions of the human genome.

The pattern of histone H4 acetylation in different genomic regions has been investigated by immunoprecipitating oligonucleosomes from a human lymphoblastoid cell line with antibodies to H4 acetylated at lysines 5, 8, 12 or 16. DNA from antibody-bound or unbound chromatin was assayed by slot blotting. Pol I and pol II transcribed genes located in euchromatin were shown to have levels of H4 acetylation at lysines 5, 8 and 12 equivalent to those in input chromatin, but to be slightly enriched in H4 acetylated at lysine 16. In no case did the acetylation level correlate with actual or potential transcriptional activity. All acetylated histone H4 isoforms were depleted in non-coding, simple repeat DNA in heterochromatin, though the extent of depletion varied with the type of heterochromatin and with the isoform. Two single copy genes that map within or adjacent to blocks of paracentric heterochromatin are depleted in H4 acetylated at lysines 5, 8 and 12, but not 16. Consensus sequences of repetitive elements of the Alu family (SINES, enriched in R bands) were associated with H4 that was more highly acetylated at all four lysines than input chromatin, while H4 associated with Kpn I elements (LINES, enriched in G bands) was significantly underacetylated.

The pattern of histone H4 acetylation on the X chromosome during spermatogenesis of the desert locust Schistocerca gregaria.

We have used antibodies directed against histone H4 acetylated at lysine residue 5, 8, 12, or 16 and indirect immunofluorescence microscopy to probe chromosomes from spermatogonia and spermatocytes of the desert locust, Schistocerca gregaria. The autosomes showed bright overall fluorescence, indicative of high levels of H4 acetylation. In contrast, the X chromosome, which is facultatively heterochromatic during spermatogenesis of the locust, remained completely unstained in spermatogonia and secondary spermatocytes and showed only a small terminal fluorescent band in primary spermatocytes. This band probably corresponds to centromere associated constitutive heterochromatin. Thus, underacetylation is a cytogenetic marker for facultative heterochromatin, but not necessarily constitutive heterochromatin, during spermatogenesis of the locust. Scanning electron microscopy of chromosomes from prophase spermatogonia and prophase I spermatocytes revealed that underacetylation of histone H4 in the X chromosome was not accompanied by a chromatin organization visibly different from that of the autosomes. Transmission electron microscopy of mitotic spermatogonia showed that the X chromosome is separated from the autosomes in a small nuclear compartment of its own in prophase and telophase and associated with membranes in metaphase. In prophase I spermatocytes, autosomes and the sex univalent were in the same compartment. This compartmentalization may be responsible for the underacetylation and (or) transcriptional silencing of the X chromosome in spermatogonia mitosis.

Efficient transcriptional silencing in Saccharomyces cerevisiae requires a heterochromatin histone acetylation pattern.

Heterochromatin in metazoans induces transcriptional silencing, as exemplified by position effect variegation in Drosophila melanogaster and X-chromosome inactivation in mammals. Heterochromatic DNA is packaged in nucleosomes that are distinct in their acetylation pattern from those present in euchromatin, although the role these differences play in the structure of heterochromatin or in the effects of heterochromatin on transcriptional activity is unclear. Here we report that, as observed in the facultative heterochromatin of the inactive X chromosome in female mammalian cells, histones H3 and H4 in chromatin spanning the transcriptionally silenced mating-type cassettes of the yeast Saccharomyces cerevisiae are hypoacetylated relative to histones H3 and H4 of transcriptionally active regions of the genome. By immunoprecipitation of chromatin fragments with antibodies specific for H4 acetylated at particular lysine residues, we found that only three of the four lysine residues in the amino-terminal domain of histone H4 spanning the silent cassettes are hypoacetylated. Lysine 12 shows significant acetylation levels. This is identical to the pattern of histone H4 acetylation observed in centric heterochromatin of D. melanogaster. These two observations provide additional evidence that the silent cassettes are encompassed in the yeast equivalent of metazoan heterochromatin. Further, mutational analysis of the amino-terminal domain of histone H4 in S. cerevisiae demonstrated that this observed pattern of histone H4 acetylation is required for transcriptional silencing. This result, in conjunction with prior mutational analyses of yeast histones H3 and H4, indicates that the particular pattern of nucleosome acetylation found in heterochromatin is required for its effects on transcription and is not simply a side effect of heterochromatin formation.