Regulation of histone and beta A-globin gene expression during differentiation of chicken erythroid cells

The chicken model organism for epigenomic research

The chicken model organism has advanced the areas of developmental biology, virology, immunology, oncology, epigenetic regulation of gene expression, conservation biology, and genomics of domestication. Further, the chicken model organism has aided in our understanding of human disease. Through the recent advances in high-throughput sequencing and bioinformatic tools, researchers have successfully identified sequences in the chicken genome that have human orthologs, improving mammalian genome annotation. In this review, we highlight the importance of chicken as an animal model in basic and pre-clinical research. We will present the importance of chicken in poultry epigenetics and in genomic studies that trace back to their ancestor, the last link between human and chicken in the tree of life. There are still many genes of unknown function in the chicken genome yet to be characterized. By taking advantage of recent sequencing technologies, it is possible to gain further insight into the chicken epigenome.

Efficient genome replication of hepatitis B virus using adenovirus vector: a compact pregenomic RNA-expression unit

The complicated replication mechanisms of hepatitis B virus (HBV) have impeded HBV studies and anti-HBV therapy development as well. Herein we report efficient genome replication of HBV applying adenovirus vectors (AdVs) showing high transduction efficiency. Even in primary hepatocytes derived from humanized mice the transduction efficiencies using AdVs were 450-fold higher compared than those using plasmids. By using an expression unit consisting of the CMV promoter, 1.03-copy HBV genome and foreign poly(A) signal, we successfully generated an improved AdV (HBV103-AdV) that efficiently provided 58 times more pregenomic RNA than previously reported AdVs. The HBV103-AdV-mediated HBV replication was easily and precisely detected using quantitative real-time PCR in primary hepatocytes as well as in HepG2 cells. Notably, when the AdV containing replication-defective HBV genome of 1.14 copy was transduced, we observed that HBV DNA-containing circular molecules (pseudo-ccc DNA) were produced, which were probably generated through homologous recombination. However, the replication-defective HBV103-AdV hardly yielded the pseudo-ccc, probably because the repeated sequences are vey short. Additionally, the efficacies of entecavir and lamivudine were quantitatively evaluated using this system at only 4 days postinfection with HBV103-AdVs. Therefore, this system offers high production of HBV genome replication and thus could become used widely.

Modulation of chromatin function through linker histone H1 variants

In this review, the structural aspects of linker H1 histones are presented as a background for characterization of the factors influencing their function in animal and human chromatin. The action of H1 histone variants is largely determined by dynamic alterations of their intrinsically disordered tail domains, posttranslational modifications and allelic diversification. The interdependent effects of these factors can establish dynamic histone H1 states that may affect the organization and function of chromatin regions.

The chicken erythrocyte epigenome

BACKGROUND

Transcriptional regulation is impacted by multiple layers of genome organization. A general feature of transcriptionally active chromatin is sensitivity to DNase I and association with acetylated histones. However, very few of these active DNase I-sensitive domains, such as the chicken erythrocyte β-globin domain, have been identified and characterized. In chicken polychromatic erythrocytes, dynamically acetylated histones associated with DNase I-sensitive, transcriptionally active chromatin prevent histone H1/H5-induced insolubility at physiological ionic strength.

RESULTS

Here, we identified and mapped out all the transcriptionally active chromosomal domains in the chicken polychromatic erythrocyte genome by combining a powerful chromatin fractionation method with next-generation DNA and RNA sequencing. Two classes of transcribed chromatin organizations were identified on the basis of the extent of solubility at physiological ionic strength. Highly transcribed genes were present in multigenic salt-soluble chromatin domains ranging in length from 30 to over 150 kb. We identified over 100 highly expressed genes that were organized in broad dynamically highly acetylated, salt-soluble chromatin domains. Highly expressed genes were associated with H3K4me3 and H3K27ac and produced discernible antisense transcripts. The moderately- and low-expressing genes had highly acetylated, salt-soluble chromatin regions confined to the 5' end of the gene.

CONCLUSIONS

Our data provide a genome-wide profile of chromatin signatures in relation to expression levels in chicken polychromatic erythrocytes.

Assembly into chromatin and subtype-specific transcriptional effects of exogenous linker histones directly introduced into a living Physarum cell

The apparent diversity of linker histone subtypes may be related to their specific roles in defining functional states of chromatin in vivo. We have developed a novel method to study constitutive peptides throughout the cell cycle and have demonstrated that an exogenous linker histone could be introduced into a living cell of the slime mold Physarum polycephalum. Here, we have used this method to assess the functional differences between three somatic linker histone subtypes in vivo, and to demonstrate the general applicability of this method. Exogenous linker histone proteins H1 degrees, H5 and H1 were directly absorbed into living cell segments of the naturally synchronous Physarum macroplasmodia at precise cell cycle stages. Fluorescence microscopy, native nucleoprotein gels and immunoblotting of nuclei and chromatin with subtype-specific antibodies revealed that exogenous linker histones were efficiently transported into nuclei and were integrated into chromatin. The immunoreactivity of a preparation of anti-H1 degrees antibodies that are blocked from binding to specific H1 degrees epitopes in native chromatin indicates that the exogenous linker histones were similarly associated into Physarum chromatin. Interestingly, linker histones were found to be less stably associated with Physarum chromatin during S-phase than during G(2)-phase. Furthermore, we show that exogenous linker histones incorporated in early G(2)-phase inhibited transcription and that the level of inhibition correlates with the apparent role of the linker histone subtype in regulating transcription in cells where it normally occurs.

Effects of H1 histone variant overexpression on chromatin structure

The importance of histone H1 heterogeneity and total H1 stoichiometry in chromatin has been enigmatic. Here we report a detailed characterization of the chromatin structure of cells overexpressing either H1(0) or H1c. Nucleosome spacing was found to change during cell cycle progression, and overexpression of either variant in exponentially growing cells results in a 15-base pair increase in nucleosome repeat length. H1 histones can also assemble on chromatin and influence nucleosome spacing in the absence of DNA replication. Overexpression of H1(0) and, to a lesser extent, H1c results in a decreased rate of digestion of chromatin by micrococcal nuclease. Using green fluorescent protein-tagged H1 variants, we show that micrococcal nuclease-resistant chromatin is specifically enriched in the H1(0) variant. Overexpression of H1(0) results in the appearance of a unique mononucleosome species of higher mobility on nucleoprotein gels. Domain switch mutagenesis revealed that either the N-terminal tail or the central globular domain of the H1(0) protein could independently give rise to this unique mononucleosome species. These results in part explain the differential effects of H1(0) and H1c in regulating chromatin structure and function.

The N-terminally acetylated form of mammalian histone H1(o), but not that of avian histone H5, increases with age

We report here on the HPCE separation of two chicken H5 histones, which do not show the heterogeneity (Gln/Arg) at residue 15 first found by Greenaway and Murray [Greenaway and Murray (1971) Nat. New Biol. 229, 233-238]. The two subfractions obtained were identified using reversed-phase HPLC, hydrophilic interaction HPLC, Edman degradation, and MALDI-MS analysis. We found that the two H5 subcomponents differ only by an acetylated (designated H5a) and an unacetylated N-terminus (H5b). In contrast to the N-terminally acetylated form of rat kidney histone H1(o), which increased by about 40% with aging of the animal, the corresponding form of chicken H5 did not: the ratio N-terminally acetylated: unacetylated remained constant (30:70) when histone H5 was extracted from erythrocytes of newly hatched chickens and from adult chickens, respectively. The HPCE technique used in this investigation represents a quick and convenient method for analyzing N-terminally acetylated proteins in the presence of unacetylated forms.

Estrogen receptor diminishes DNA-binding activities of chicken GATA-1 and CACCC-binding proteins

The estrogen receptor (ER) repressed erythroid differentiation and erythroid-specific gene expression. In this study, we investigated the effect of ER alpha (referred to throughout as ER) on DNA-binding activities of transcription factors involved in regulating the expression of erythroid-specific genes, and, in particular, the histone H5 gene. Using electrophoretic mobility shift assays, we found that in the presence of rabbit reticulocyte lysate, human ER reduced the binding activities of chicken immature erythrocyte nuclear extracted proteins to GATA and CACCC sites in the H5 promoter and enhancer. In contrast, the binding activities of NF1 and Sp1 were not affected by ER. Binding of ER to an estrogen response element was enhanced by addition of rabbit reticulocyte lysate. This lysate was also necessary for ER to diminish the DNA-binding activity of GATA-1. These results suggest that additional factor(s) are necessary for full ER function. Both GATA-1 and CACCC-binding proteins are critical for the developmentally regulated expression of erythroid-specific genes. We hypothesize that interference in DNA-binding activities of GATA-1 and CACCC-binding proteins is the mechanism by which the ER inhibits regulation of these genes.

Characterization and expression of the mouse endonuclease G gene

Endonuclease G (Endo G) is a nuclease of prokaryotic lineage found in the mitochondria of vertebrates that has been suggested to play a role in mitochondrial DNA (mtDNA) replication. We have isolated and sequenced the entire mouse endo G gene, determined the limits of the mRNA, and mapped the promoter region. The coding sequence of the single copy gene is interrupted by two introns and analysis of the transcripts does not support a model by which more than one Endo G isoform could be produced by alternative splicing. We have also characterized a full-length human Endo G cDNA and comparison at the protein level of the human, bovine, and murine nucleases indicates a high degree of conservation except in the respective mitochondrial targeting signals. Endo G is ubiquitously expressed and the steady-state levels of its mRNA vary by a factor greater than seven between different tissues. The relationship between the mtDNA copy number and Endo G mRNA levels is not strictly proportional but tissues richer in mtDNA have higher amounts of the mRNA and vice versa.

In situ footprinting of chicken histone H5 gene in mature and immature erythrocytes reveals common factor-binding sites

In vitro DNAase I footprinting and gel mobility shift assays have shown that the activities of several nuclear factors (GATA-1, Sp1) that bind to the promoter and downstream enhancer regions of the chicken histone H5 gene are reduced in mature erythrocytes relative to those in immature erythrocytes. In this study we investigated site occupancy in the promoter and downstream enhancer regions of the H5 gene in mature and immature erythrocytes. The ligation-mediated polymerase chain reaction was used to detect DNAase I footprints generated in situ. Most of the sites that bound to Sp1 and/or Sp1-like proteins and GATA-1 in the promoter and enhancer were occupied in situ in mature and immature erythrocytes. However, the level of protection at Sp1/Sp-1-like binding sites in the H5 enhancer region of mature erythroid cells was generally less than that observed for immature cells, suggesting that for any given mature cell not all of the Sp1/Sp1-like binding sites are occupied. Nevertheless, the results of this study suggest that the enhancer and promoter of the H5 gene in mature erythrocytes should be functional, agreeing with nuclear run-on studies showing transcriptional activity of the H5 gene in mature permeabilized cells.

Differential effect of H1 variant overexpression on cell cycle progression and gene expression

To identify functional differences among non-allelic variants of the mammalian H1 linker histones a system for the overexpression of individual H1 variants in vivo was developed. Mouse 3T3 cells were transformed with an expression vector containing the coding regions for the H1c or H10 variant under the control of an inducible promoter. Stable, single colony transformants, in which the normal stoichiometry of H1 variants was perturbed, displayed normal viability, unaltered morphology and no long-term growth arrest. However, upon release from synchronization at different points in the cell cycle transformants significantly overproducing H10 exhibited transient inhibition of both G1 and S phase progression. Overexpression of H1c to comparable levels had no effect on cell cycle progression. Analysis of transcript levels for several cell cycle-regulated and housekeeping genes indicated that overexpression of H10 resulted in significantly reduced expression of all genes tested. Surprisingly, overexpression of H1c to comparable levels resulted in either a negligible effect or, in some cases, a dramatic increase in transcript levels. These results support the suggestion that functional differences exist among H1 variants.

Differential compaction of transcriptionally competent and repressed chromatin reconstituted with histone H1 subtypes

Chromatin fragments stripped of H1 histones regain the ability to form higher order structures and aggregates in 0.15 M NaCl following reconstitution with histone H1. However, transcriptionally competent chromatin fragments are resistant to chicken erythrocyte H1/H5 histone-induced 0.15 M NaCl aggregation/precipitation. In this study, we investigated the ability of stripped chromatin fragments reconstituted with one of four histone H1 subtypes (chicken erythrocyte H1, H5, trout liver H1a, H1b) at various stoichiometries to form salt precipitable higher order structures. Our results provide evidence that chicken erythrocyte histone H1 was more effective than histone H5 and trout liver histone H1b better than H1a in forming higher order structures. None of the histone H1 subtypes could render transcriptionally competent chromatin fragments insoluble in 0.15 M NaCl. These results are consistent with the ideas that the histone H1 subtypes differ in their capacities to compact chromatin fiber, and that the alterations in the structure of transcriptionally competent nucleosomes interfere with the capacity of all H1 subtypes to form higher order structures.

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.

Nuclear factor 1 is a component of the nuclear matrix

Chicken histone H5 is an H1-like linker histone that is expressed only in nucleated erythrocytes. The histone H5 promoter has binding sites for Sp1 (a high affinity site) and UPE-binding protein, while the 3' erythroid-specific enhancer has binding sites for Sp1 (one moderate and three weak affinity), GATA-1, and NF1. In this study we investigated whether trans-acting factors that bind to the chicken histone H5 promoter or enhancer are associated with adult chicken immature and mature erythrocyte nuclear matrices. We show that NF1, but not Sp1, GATA-1, or UPE-binding protein, is associated with the internal nuclear matrices of these erythroid cells. Further, we found that a subset of the NF1 family of proteins is bound to the mature erythrocyte nuclear matrix. These results suggest that in chicken erythrocytes NF1 may mediate an interaction between the histone H5 enhancer and the erythroid internal nuclear matrix. NF1 was also present in the internal nuclear matrices of chicken liver and trout liver. The observations of this study provide evidence that NF1 may have a role in a variety of cell types in targeting specific DNA sequences to the nuclear matrix.

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.

Immunochemical studies of histone H5 from Halobatrachus didactylus

1. Histone H5 from Halobatrachus didactylus was isolated by using perchloric acid (PCA) extraction of fish liver nuclei and trichloroacetic acid (TCA) precipitation. 2. A polyclonal antiserum was generated by immunizing rabbits with the antigen purified from SDS-PAGE. 3. By immunofluorescence the serum stains erythrocyte nuclei from H. didactylus but it does not react with mammalian cells. 4. By Western blotting, the anti-H5 antibody reacts with the isolated antigen at high titers. 5. Digestion of histone H5 with pepsin and cyanogen bromide suggests that the epitopes are located in the globular and C-terminal region of the H5 molecule excluding the N-terminal.

Nucleosome spacing is compressed in active chromatin domains of chick erythroid cells

We have cleaved the chromatin of embryonic and adult chicken erythroid cells using a novel nuclease that is capable of resolving clearly the nucleosomes of active chromatin. We found that in active chromatin, nucleosomes are spaced up to 40 base pairs closer together than in inactive chromatin. This was true for both "housekeeping" and "luxury" genes and was observed whether the digestion was carried out on isolated nuclei in vitro or by activating the endogenous nuclease in vivo. The close spacing extended several kilobases into flanking chromatin, indicating that this is a domain property of active chromatin, not just a characteristic of regions disrupted by transcription. A simple interpretation of our results is that the nucleosomes of active chromatin are mobile in vivo and, not being constrained by linker histones, freely move closer together.

Characterization of HMG2 complement changes in chicken tissues

Variations in the content of nonhistone proteins high mobility group 2a (HMG2a) and HMG2b have been determined in several cell types of chicken. HMG2a was found to accumulate during erythrocyte maturation. HMG2b is the major HMG2 subtype in testis and reaches the highest proportion, detected so far, in spermatid cells obtained by centrifugal elutriation. In hepatocytes HMG2b is barely detectable and HMG2a is the major subtype. In conclusion, the pattern of HMG2 composition is different in three quiescent and terminally differentiated cell types, no correlation between the state of cell proliferation and HMG2 composition can be established.

Bands, interbands and puffs in native Drosophila polytene chromosomes are recognized by a monoclonal antibody to an epitope in the carboxy-terminal tail of histone H1

A monoclonal antibody was raised against Drosophila melanogaster histone H1. Immunoscreening of proteolytic cleavage fragments of H1 and of a set of all possible overlapping synthetic octapeptides corresponding to the amino acid sequence of H1, revealed that the antibody recognizes an epitope within the sequence 207VTAAKPKA214 near the centre of the carboxy-terminal tail. This antibody gives positive immunofluorescence over the entire length of native D. melanogaster polytene chromosomes isolated from salivary glands by microdissection at physiological pH and ionic strength. Bands, interbands and puffs are all seen to contain H1. The immunofluorescence over puffs, albeit lower than that over bands and interbands, indicates that chromatin decondensation can occur without complete loss of H1 in these structures. The reaction of the antibody with bands suggests that the segment of the C-terminal tail containing the epitope may be exposed in the condensed 30 nm chromatin filament.

Transcription of the alpha A-globin gene of the duck. Development of a homologous in vitro system and identification of trans-acting factors

A homologous in vitro transcription system was developed in which the alpha A-globin gene of the duck was faithfully transcribed. Whole-cell extracts from duck erythrocytes were separated into fractions A, B, C and D by consecutive elution from phosphocellulose columns and were individually reconstituted in run-off transcription assays. Fractions A, C and D were required to achieve faithful initiation on the alpha A-globin gene. The latter fractions were mutually interchangeable with comparable fractions from HeLa cells. A fourth fraction, B, was not required but enhanced basal transcription when reconstituted with fractions A, C and D or a very low amount of HeLa whole-cell extract which by itself did not yield a detectable signal. Fraction B from duck erythrocytes was further purified by chromatography on DEAE-Sephadex and was shown to contain two trans-acting factors. One of these differentially acts on the alpha A-globin gene of the duck. The other component from duck erythrocytes surprisingly resembles the upstream stimulatory factor, previously isolated from HeLa cells. This latter protein binds to and trans-activates the adenovirus 2 major late promoter, but is not involved in the transcription of the alpha A-globin gene.