Chromatin transitions during early Xenopus embryogenesis: changes in histone H4 acetylation and in linker histone type

Histone mRNAs do not accumulate during S phase of either mitotic or endoreduplicative cycles in the chordate Oikopleura dioica

Metazoan histones are generally classified as replication-dependent or replacement variants. Replication-dependent histone genes contain cell cycle-responsive promoter elements, their transcripts terminate in an unpolyadenylated conserved stem-loop, and their mRNAs accumulate sharply during S phase. Replacement variant genes lack cell cycle-responsive promoter elements, their polyadenylated transcripts lack the stem-loop, and they are expressed at low levels throughout the cell cycle. During early development of some organisms with rapid cleavage cycles, replication-dependent mRNAs are not fully S phase restricted until complete cell cycle regulation is achieved. The accumulation of polyadenylated transcripts during this period has been considered incompatible with metazoan development. We show here that histone metabolism in the urochordate Oikopleura dioica does not accord with some key tenets of the replication-dependent/replacement variant paradigm. During the premetamorphic mitotic phase of development, expressed variants shared characteristics of replication-dependent histones, including the 3' stem-loop, but, in contrast, were extensively polyadenylated. After metamorphosis, when cells in many tissues enter endocycles, there was a global downregulation of histone transcript levels, with most variant transcripts processed at the stem-loop. Contrary to the 30-fold S-phase upregulation of histone transcripts described in common metazoan model organisms, we observed essentially constant histone transcript levels throughout both mitotic and endoreduplicative cell cycles.

Restricted specificity of Xenopus TFIIIA for transcription of somatic 5S rRNA genes

Xenopus transcription factor IIIA (TFIIIA) is phosphorylated on serine-16 by CK2. Replacements with alanine or glutamic acid were made at this position in order to address the question of whether phosphorylation possibly influences the function of this factor. Neither substitution has an effect on the DNA or RNA binding activity of TFIIIA. The wild-type factor and the alanine variant activate transcription of somatic- and oocyte-type 5S rRNA genes in nuclear extract immunodepleted of endogenous TFIIIA. The glutamic acid variant (S16E) supports the transcription of somatic-type genes at levels comparable to those of wild-type TFIIIA; however, there is no transcription of the oocyte-type genes. This differential behavior of the phosphomimetic mutant protein is also observed in vivo when using early-stage embryos, where this mutant failed to activate transcription of the endogenous oocyte-type genes. Template exclusion assays establish that the S16E mutant binds to the oocyte-type 5S rRNA genes and recruits at least one other polymerase III transcription factor into an inactive complex. Phosphorylation of TFIIIA by CK2 may allow the factor to continue to act as a positive activator of the somatic-type genes and simultaneously as a repressor of the oocyte-type 5S rRNA genes, indicating that there is a mechanism that actively promotes repression of the oocyte-type genes at the end of oogenesis.

Trichostatin A reduces hormone-induced transcription of theMMTVpromoter and has pleiotropic effects on its chromatin structure

The deacetylase inhibitor trichostatin A (TSA) has long been used to study the relationship between gene transcription and the acetylation status of chromatin. We have used Xenopus laevis oocytes to study the effects of TSA on glucocorticoid receptor (GR)-dependent transcription and we have related these effects to changes in the chromatin structure of a reporter mouse mammary tumor virus (MMTV) promoter. We show that TSA induces a low level of constitutive transcription. This correlates with a change of acetylation pattern and a more open chromatin structure over the MMTV chromatin, and with specific acetylation and remodeling events in the promoter region. Specifically, a repositioning of initially randomly positioned nucleosomes along the distal MMTV long terminal repeat is seen. This nucleosome rearrangement is similar to the translational nucleosome positioning that occurs upon hormone activation. We also note a reduced hormone response in the presence of TSA. TSA effects have for a long time been associated with transcriptional activation and chromatin opening through inhibition of the deacetylation of histones. However, our results and those of others show that TSA-induced changes in expression and chromatin structure can be quite different in different promoter contexts and, thus, the effects of TSA are more complex than previously believed.

Rapid H1 linker histone transitions following fertilization or somatic cell nuclear transfer: evidence for a uniform developmental program in mice

H1 linker histones (H1s) are key regulators of chromatin structure and function. The functions of different H1s during early embryogenesis, and mechanisms regulating their associations with chromatin are largely unknown. The developmental transitions of H1s during oocyte growth and maturation, fertilization and early embryogenesis, and in cloned embryos were examined. Oocyte-specific H1FOO, but not somatic H1s, associated with chromatin in oocytes (growing, GV-stage, and MII-arrested), pronuclei, and polar bodies. H1FOO associated with sperm or somatic cell chromatin within 5 min of intracytoplasmic sperm injection (ICSI) or somatic cell nuclear transfer (SCNT), and completely replaced somatic H1s by 60 min. The switching from somatic H1s to H1FOO following SCNT was developmentally regulated. H1FOO was replaced by somatic H1s during the late two- and four-cell stages. H1FOO association with chromatin can occur in the presence of a nuclear envelope and independently of pronucleus formation, is regulated by factors associated with the spindle, and is likely an active process. All SCNT constructs recapitulated the normal sequence of H1 transitions, indicating that this alone does not signify a high developmental potential. A paucity of all known H1s in two-cell embryos may contribute to precocious gene transcription in fertilized embryos, and the elaboration of somatic cell characteristics in cloned embryos.

Rapid replacement of somatic linker histones with the oocyte-specific linker histone H1foo in nuclear transfer

The most distinctive feature of oocyte-specific linker histones is the specific timing of their expression during embryonic development. In Xenopus nuclear transfer, somatic linker histones in the donor nucleus are replaced with oocyte-specific linker histone B4, leading to the involvement of oocyte-specific linker histones in nuclear reprogramming. We recently have discovered a mouse oocyte-specific linker histone, named H1foo, and demonstrated its expression pattern in normal preimplantation embryos. The present study was undertaken to determine whether the replacement of somatic linker histones with H1foo occurs during the process of mouse nuclear transfer. H1foo was detected in the donor nucleus soon after transplantation. Thereafter, H1foo was restricted to the chromatin in up to two-cell stage embryos. After fusion of an oocyte with a cell expressing GFP (green fluorescent protein)-tagged somatic linker histone H1c, immediate release of H1c in the donor nucleus was observed. In addition, we used fluorescence recovery after photobleaching (FRAP), and found that H1foo is more mobile than H1c in living cells. The greater mobility of H1foo may contribute to its rapid replacement and decreased stability of the embryonic chromatin structure. These results suggest that rapid replacement of H1c with H1foo may play an important role in nuclear remodeling.

HMG-D and histone H1 alter the local accessibility of nucleosomal DNA

There is evidence that HMGB proteins facilitate, while linker histones inhibit chromatin remodelling, respectively. We have examined the effects of HMG-D and histone H1/H5 on accessibility of nucleosomal DNA. Using the 601.2 nucleosome positioning sequence designed by Widom and colleagues we assembled nucleosomes in vitro and probed DNA accessibility with restriction enzymes in the presence or absence of HMG-D and histone H1/H5. For HMG-D our results show increased digestion at two spatially adjacent sites, the dyad and one terminus of nucleosomal DNA. Elsewhere varying degrees of protection from digestion were observed. The C-terminal acidic tail of HMG-D is essential for this pattern of accessibility. Neither the HMG domain by itself nor in combination with the adjacent basic region is sufficient. Histone H1/H5 binding produces two sites of increased digestion on opposite faces of the nucleosome and decreased digestion at all other sites. Our results provide the first evidence of local changes in the accessibility of nucleosomal DNA upon separate interaction with two linker binding proteins.

Evolution and expression of the amphioxus AmphiHMGB gene encoding an HMG-box protein

Amphioxus HMGB gene, AmphiHMGB, encoding a high mobility group (HMG) protein was identified from the gut cDNA library of Branchiostoma belcheri tsingtauense. Primary structural examination indicates that it is a member of HMGB family. Molecular phylogenetic analysis suggests that AmphiHMGB represents the archetype of chordate HMGB genes including HMGB1, HMGB2 and HMGB3 although it may have lost its C-terminal domain during evolution. Northern blotting revealed that AmphiHMGB expression was restricted mainly to guts in the adult, and AmphiHMGB transcripts were in greater abundance in gastrula and neurula though they were markedly low in 1-day larva.

Association of chromatin proteins high mobility group box (HMGB) 1 and HMGB2 with mitotic chromosomes

High mobility group box (HMGB) 1 and 2 are two abundant nonhistone nuclear proteins that have been found in association with chromatin. Previous studies based on immunofluorescence analysis indicated that HMGB1 dissociates from chromosomes during mitosis. In the present work, HMGB1 and 2 subcellular localization was reinvestigated in living cells by using enhanced green fluorescent protein- and Discosome sp. red fluorescent protein-tagged proteins. Contrary to previous reports, HMGB1 and 2 were shown to be present under two forms in mitotic cells, i.e., free and associated with the condensed chromatin, which rapidly exchange. A detailed analysis of HMGB2 interaction with mitotic chromosomes indicated that two sites encompassing HMG-box A and B are responsible for binding. Importantly, this interaction was rapidly inactivated when cells were permeabilized or exposed to chemical fixatives that are widely used in immunodetection techniques. A comparable behavior was also observed for two proteins of the HMG-nucleosome binding (HMGN) group, namely, HMGN1 and HMGN2.

Epigenomic replication: linking epigenetics to DNA replication

The information contained within the linear sequence of bases (the genome) must be faithfully replicated in each cell cycle, with a balance of constancy and variation taking place over the course of evolution. Recently, it has become clear that additional information important for genetic regulation is contained within the chromatin proteins associated with DNA (the epigenome). Epigenetic information also must be faithfully duplicated in each cell cycle, with a balance of constancy and variation taking place during the course of development to achieve differentiation while maintaining identity within cell lineages. Both the genome and the epigenome are synthesized at the replication fork, so the events occurring during S-phase provide a critical window of opportunity for eliciting change or maintaining existing genetic states. Cells discriminate between different states of chromatin through the activities of proteins that selectively modify the structure of chromatin. Several recent studies report the localization of certain chromatin modifying proteins to replication forks at specific times during S-phase. Since transcriptionally active and inactive chromosome domains generally replicate at different times during S-phase, this spatiotemporal regulation of chromatin assembly proteins may be an integral part of epigenetic inheritance.

Effect of histone deacetylase inhibitors on heat shock protein gene expression during Xenopus development

We examined the effect of histone deacetylase inhibitors (HDIs), trichostatin A (TSA), valproic acid (VPA), and sodium butyrate (NaB) on heat shock protein (hsp) gene expression during early Xenopus laevis development. HDIs enhance histone acetylation and result in the relief of repressed chromatin domains and ultimately increase the accessibility of transcription factors to target cis-acting regulatory sites. Treatment of embryos with HDIs enhanced the heat shock-induced accumulation of hsp70 mRNA in post-midblastula stage embryos. No effect was observed with actin mRNA or other hsp70 family members including heat shock cognate 70 and immunoglobulin binding protein. Normally, hsp30 genes are not heat-inducible until the late neurula or early tailbud stage of development. Treatment with HDIs resulted in heat-induced expression of hsp30 genes at the gastrula stage with enhanced heat-induced accumulation in neurula and tailbud stages. HDI treatment alone did not induce the accumulation of hsp70 or hsp30 mRNA. Whole-mount in situ hybridization verified the RNA blot analyses and additionally revealed that TSA treatment did not result in any major alterations in the spatial pattern of stress-induced hsp70 or hsp30 mRNA accumulation in early embryos. This study suggests that the states of Xenopus hsp70 and 30 chromatin are subject to repression beyond the midblastula transition.

An ACF1-ISWI chromatin-remodeling complex is required for DNA replication through heterochromatin

The mechanism by which the eukaryotic DNA-replication machinery penetrates condensed chromatin structures to replicate the underlying DNA is poorly understood. Here we provide evidence that an ACF1-ISWI chromatin-remodeling complex is required for replication through heterochromatin in mammalian cells. ACF1 (ATP-utilizing chromatin assembly and remodeling factor 1) and an ISWI isoform, SNF2H (sucrose nonfermenting-2 homolog), become specifically enriched in replicating pericentromeric heterochromatin. RNAi-mediated depletion of ACF1 specifically impairs the replication of pericentromeric heterochromatin. Accordingly, depletion of ACF1 causes a delay in cell-cycle progression through the late stages of S phase. In vivo depletion of SNF2H slows the progression of DNA replication throughout S phase, indicating a functional overlap with ACF1. Decondensing the heterochromatin with 5-aza-2-deoxycytidine reverses the effects of ACF1 and SNF2H depletion. Expression of an ACF1 mutant that cannot interact with SNF2H also interferes with replication of condensed chromatin. Our data suggest that an ACF1-SNF2H complex is part of a dedicated mechanism that enables DNA replication through highly condensed regions of chromatin.

When the embryonic genome flexes its muscles

During the development of multicellular organisms, both transient and stable gene expression patterns have to be established in a precisely orchestrated sequence. Evidence from diverse model organisms indicates that this epigenetic program involves not only transcription factors, but also the local structure, composition, and modification of chromatin, which define and maintain the accessibility and transcriptional competence of the nucleosomal DNA template. A paradigm for the interdependence of development and chromatin is constituted by the mechanisms controlling the specification and differentiation of the skeletal muscle cell lineage in vertebrates, which is the topic of this review.

Distribution of somatic H1 subtypes is non-random on active vs. inactive chromatin II: distribution in human adult fibroblasts

For nearly twenty years researchers have observed changes in the histone H1 subtype content of tissues as an organism develops into an adult. To better understand the consequences of such changes, immunofractionation of chromatin using previously characterized antibodies specific for human H1 subtypes was employed in the analysis of a fibroblast cell strain derived from a 37-year-old individual. DNAs isolated from immunoprecipitates were probed for the existence of a variety of DNA sequences. The results presented lend further support to a previously-proposed model (Parseghian et al. [2000] Chromosome Res 8:405-424) in which transcription of a sequence is accompanied by the selective depletion of subtypes. The data also suggest that there is more total H1 on actively transcribed sequences in these cells as compared to fetal fibroblasts and that there is less difference in the subtype compositions of active genes vs. inactive sequences in this strain. Specifically, the consequences of these changes appear to correlate with the attenuation of the heat shock response in aging fibroblasts. In a broader context, these results could explain why there are reductions in transcription in cells from mature tissue that approach senescence.

Replication timing and cell differentiation

Cell differentiation may depend in part upon a type of unbalanced growth in which several cell cycles occur with a reduced level of total protein synthesis. During this period the synthesis of the chromatin protein HMG-I/Y is reduced since its synthesis is correlated with that of total protein. The synthesis of histone H1 shows less reduction since its synthesis is entrained with that of DNA. This greater reduction of HMG-I/Y than of histone H1 is thought to delay or prevent replicon initiations within AT-enriched isochores. This shifts their time of replication from early to late S phase. This may restrict certain pathways of cell differentiation in multipotent progenitor cells and allow one particular type of differentiation.

The maternal effect gene, abnormal oocyte (abo), of Drosophila melanogaster encodes a specific negative regulator of histones

The abnormal oocyte (abo) gene of Drosophila melanogaster is a peculiar maternal effect gene whose mutations cause a maternal-effect lethality that can be rescued by specific regions of heterochromatin during early embryogenesis. Here we show that abo encodes an evolutionary conserved chromosomal protein that localizes exclusively to the histone gene cluster and binds to the regulatory regions of such genes. We also show a significant increase of histone transcripts in eggs of abo mutant mothers and a partial rescue of the abo maternal-effect defect by deficiencies of the histone gene cluster. On the basis of these results, we suggest that the Abo protein functions specifically as a negative regulator of histone transcription and propose a molecular model to account for the ability of heterochromatin to partially rescue the abo maternal-effect defect. Our model proposes that increased doses of specific heterochromatic regions titrate out abnormally high levels of histones present in embryos from mutant abo mothers and that a balanced pool of histones is critical for normal embryogenesis in Drosophila.

HMG-D and histone H1 interplay during chromatin assembly and early embryogenesis

HMG-D is an abundant chromosomal protein associated with condensed chromatin during the first nuclear cleavage cycles of the developing Drosophila embryo. We previously suggested that HMG-D might substitute for the linker histone H1 in the preblastoderm embryo and that this substitution might result in the characteristic less compacted chromatin. We have now studied the association of HMG-D with chromatin using a cell-free system for chromatin reconstitution derived from Drosophila embryos. Association of HMG-D with chromatin, like that of histone H1, increases the nucleosome spacing indicative of binding to the linker DNA between nucleosomes. HMG-D interacts with DNA during the early phases of nucleosome assembly but is gradually displaced as chromatin matures. By contrast, purified chromatin can be loaded with stoichiometric amounts of HMG-D, and this can be displaced upon addition of histone H1. A direct physical interaction between HMG-D and histone H1 was observed in a Far Western analysis. The competitive nature of this interaction is reminiscent of the apparent replacement of HMG-D by H1 during mid-blastula transition. These data are consistent with the hypothesis that HMG-D functions as a specialized linker protein prior to appearance of histone H1.

A compendium of the histone H1 family of somatic subtypes: An elusive cast of characters and their characteristics

The last 35 years has seen a substantial amount of information collected about the somatic H1 subtypes, yet much of this work has been overshadowed by research into highly divergent isoforms of H1, such as H5. Reports from several laboratories in the past few years have begun to call into question some of the traditional views regarding the general function of linker histones and their heterogeneity. Hence, the impression in some circles is that less is known about these ubiquitous nuclear proteins as compared with the core histones. The goal of the following review is to acquaint the reader with the ubiquitous somatic H1s by categorizing them and their characteristics into several classes. The reasons for our current state of misunderstanding is put into a historical context along with recent controversies centering on the role of H1 in the nucleus. Finally, we propose a model that may explain the functional role of H1 heterogeneity in chromatin compaction.Key words: histone H1, linker histones, chromatin organization, chromatin compaction, heat shock.

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.

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.

Somatic linker histone H1 is present throughout mouse embryogenesis and is not replaced by variant H1 degrees

A striking feature of early embryogenesis in a number of organisms is the use of embryonic linker histones or high mobility group proteins in place of somatic histone H1. The transition in chromatin composition towards somatic H1 appears to be correlated with a major increase in transcription at the activation of the zygotic genome. Previous studies have supported the idea that the mouse embryo essentially follows this pattern, with the significant difference that the substitute linker histone might be the differentiation variant H1 degrees, rather than an embryonic variant. We show that histone H1 degrees is not a major linker histone during early mouse development. Instead, somatic H1 was present throughout this period. Though present in mature oocytes, somatic H1 was not found on maternal metaphase II chromatin. Upon formation of pronuclear envelopes, somatic H1 was rapidly incorporated onto maternal and paternal chromatin, and the amount of somatic H1 steadily increased on embryonic chromatin through to the 8-cell stage. Microinjection of somatic H1 into oocytes, and nuclear transfer experiments, demonstrated that factors in the oocyte cytoplasm and the nuclear envelope, played central roles in regulating the loading of H1 onto chromatin. Exchange of H1 from transferred nuclei onto maternal chromatin required breakdown of the nuclear envelope and the extent of exchange was inversely correlated with the developmental advancement of the donor nucleus.

Histone acetylation is a checkpoint in FGF-stimulated mesoderm induction

We have previously demonstrated that the transcription factor, AP-1 (c-jun/c-fos heterodimer), mediates fibroblast growth factor (FGF) signaling during mesoderm induction in Xenopus embryo. In the present studies, we show that histone acetylation is involved in FGF-mediated signaling leading to mesoderm induction. Histone acetylation is a dynamic process regulated by the activities of two histone-modifying enzymes, the histone acetyltransferase(s) and histone deacetylase(s) (HDACs). We found that basal and FGF-regulated activator protein 1 (AP-1) activity in Xenopus embryo is markedly reduced by treatment of trichostatin A (TSA), a specific inhibitor of HDAC. However, activity of another transcription factor, NFkappaB, is enhanced by TSA treatment. AP-1-mediated mesoderm induction in the animal caps is dramatically suppressed by TSA at a dose-dependent manner. This suppression can be rescued by ectopic expression of HDAC3 at early stage. Finally, we found that histone acetylation in animal caps is inhibited by FGF whereas enhanced by TSA (as a control). Therefore, we propose that histone acetylation is a checkpoint for transduction of the FGF/AP-1 signals to induce mesoderm. Published 2000 Wiley-Liss, Inc.

CAF-1 and the inheritance of chromatin states: at the crossroads of DNA replication and repair

Chromatin is no longer considered to be a static structural framework for packaging DNA within the nucleus but is instead believed to be an interactive component of DNA metabolism. The ordered assembly of chromatin produces a nucleoprotein template capable of epigenetically regulating the expression and maintenance of the genome. Factors have been isolated from cell extracts that stimulate early steps in chromatin assembly in vitro. The function of one such factor, chromatin-assembly factor 1 (CAF-1), might extend beyond simply facilitating the progression through an individual assembly reaction to its active participation in a marking system. This marking system could be exploited at the crossroads of DNA replication and repair to monitor genome integrity and to define particular epigenetic states.

Histone acetylation and X inactivation

In mammals, the levels of X-linked gene products in males and females are equalised by the silencing, early in development, of most of the genes on one of the two female X chromosomes. Once established, the silent state is stable from one cell generation to the next. In eutherian mammals, the inactive X chromosome (Xi) differs from its active homologue (Xa) in a number of ways, including increased methylation of selected CpGs, replication late in S-phase, expression of the Xist gene with binding of Xist RNA and underacetylation of core histones. The latter is a common property of genetically inactive chromatin but, in the case of Xi, it is not clear whether it is an integral part of the silencing process or simply a consequence of some other property of Xi, such as late replication. The present review describes two approaches that address this problem. The first shows that Xi in marsupial mammals also contains underacetylated H4, even though its properties differ widely from those of the eutherian Xi. The continued presence of histone underacetylation on Xi in these evolutionarily distant mammals argues for its fundamental importance. The second approach uses mouse embryonic stem cells and places H4 deacetylation in a sequence of events leading to complete X inactivation. The results argue that histone underacetylation plays a role in the stabilisation of the inactive state, rather than in its initiation.

Control of gene expression in Xenopus early development

We examine the control of gene expression before and through the MBT in Xenopus laevis. The generalized repression of transcription that occurs before the midblastula transition (MBT) is regulated by a dynamic competition between chromatin and transcription complex assembly. Conditions favoring the access of basal factors (TBP) or transactivators can overcome this transcriptional repression. Changes in DNase I hypersensitivity patterns of the chromatin during early development show that it is more accessible to DNase I before the MBT (and by extension to other DNA interacting proteins) than after the MBT. We also show that at the level of genomic domains, organization of the chromatin matrix attachment sites is random before MBT. We propose that these three components, chromatin domain structure, DNA accessibility, and the transcription complex-chromatin dynamic competition, combine to regulate transcription in the embryo before and through the MBT.

Mouse embryos do not wait for the MBT: chromatin and RNA polymerase remodeling in genome activation at the onset of development

In Xenopus and Drosophila embryos, activation of the zygotic genome occurs after a series of rapid nuclear divisions in which DNA replication occupies most of the cell cycle. In these organisms, it has been proposed that zygotic transcription does not begin until a threshold nucleocytoplasmic ratio has been obtained in which repressive factors are titrated out and interphase becomes long enough to allow synthesis of transcripts. In mammalian embryos, however, a model of threshold nucleocytoplasmic ratios does not seem to apply, as beginning with the 1-cell stage, there are regulated cell cycles with the expression of zygotic transcripts during the cleavage period. By taking advantage of the slower kinetics at the onset of mouse development, we have characterized changes in chromatin structure and the basal transcription machinery throughout the transition from transcriptional incompetence, to minor activation of the zygotic genome during the 1-cell stage, and through major genome activation at the 2-cell stage. Further maturation of chromatin structure continues through subsequent cleavage cycles as a foundation for the first cellular differentiations in the blastocyst. The epigenetic chromatin modifications that occur during the cleavage period may have long range and inheritable effects and are undoubtedly important in the ability of the mammalian oocyte to remodel previously defined nuclear structures and cell fates.

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.

Regulation of gene expression at the beginning of mammalian development and the TEAD family of transcription factors

In mouse development, transcription is first detected in late 1-cell embryos, but translation of newly synthesized transcripts does not begin until the 2-cell stage. Thus, the onset of zygotic gene expression (ZGE) is regulated at the level of both transcription and translation. Chromatin-mediated repression is established after formation of a 2-cell embryo, concurrent with the developmental acquisition of enhancer function. The most effective enhancer in cleavage stage mouse embryos depends on DNA binding sites for TEF-1, the prototype for a family of transcription factors that share the same TEA DNA binding domain. Mice contain at least four, and perhaps five, genes with the same TEA DNA binding domain (mTEAD genes). Since mTEAD-2 is the only one expressed during the first 7 days of mouse development, it is most likely responsible for the TEAD transcription factor activity that first appears at the beginning of ZGE. All four mTEAD genes are expressed at later embryonic stages and in adult tissues; virtually every tissue expresses at least one family member, consistent with a critical role for TEAD proteins in either cell proliferation or differentiation. The 72-amino acid TEA DNA binding domains in mTEAD-2, 3, and 4 are approximately 99% homologous to the same domain in mTEAD-1, and all four proteins bind specifically to the same DNA sequences in vitro with a Kd value of 16-38 nM DNA. Since TEAD proteins appear to be involved in both activation and repression of different genes and do not appear to be functionally redundant, differential activity of TEAD proteins must result either from association with other proteins or from differential sensitivity to chromatin-packaged DNA binding sites.

Chromatin and chromosomal controls in development

Chromatin and chromosomes have major regulatory roles in development. Nucleosome positioning and modification, chromatin structural transitions and domain organization all contribute to the regulation of individual genes and gene families. Chromosomal position and nuclear compartmentalization represent important contributory factors in determining cell fate. These controls may explain many interesting and unexplored features of developmental systems.

Region-specific activation of the Xenopus brachyury promoter involves active repression in ectoderm and endoderm: a study using transgenic frog embryos

Tissue specification in the early embryo requires the integration of spatial information at the promoters of developmentally important genes. Although several response elements for signalling pathways have been identified in Xenopus promoters, it is not yet understood what defines the sharp borders that restrict expression to a specific tissue. Here we use transgenic frog embryos to study the spatial and temporal regulation of the Xbra promoter. Deletion analysis and point mutations in putative transcription factor-binding sites identified two repressor modules, which exert their main effects at different stages during gastrulation. One module is defined by a bipartite binding site for a Smad-interacting protein (SIP1) of the deltaEF1 repressor family and acts to confine expression to the marginal zone early in gastrulation. The other module is defined by two homeodomain-binding sites and is responsible for repression in dorsal mesoderm and ectoderm at mid-gastrula stages. In addition, an upstream region of the promoter is necessary to repress expression in neural tissues later in development. Together, our results show that repression plays an important role in the restriction of Xbra expression to the mesoderm, and we suggest that similar mechanisms may be involved in the spatial regulation of other genes in early embryonic development.

Alterations in titer and distribution of high mobility group proteins during embryonic development of Drosophila melanogaster

High mobility group proteins are thought to have an architectural function in chromatin. Here we describe changes in titers, extent of phosphorylation, and cellular distribution of the three abundant HMG proteins during embryonic development of Drosophila. The titers of the HMG proteins HMGD, HMGZ, and D1 are highest in ovaries and at the beginning of embryonic development. They decrease continuously until cellularization of the embryo. Relative to the histone H1 titer, the levels of HMGD and D1 remain almost constant during gastrulation and organogenesis, whereas the titer of HMGZ increases during late organogenesis. Up to gastrulation, the development is accompanied by dephosphorylation of D1. In contrast, HMGD and HMGZ appear to be constitutively phosphorylated. As the high extent of phosphorylation of D1 is also characteristic in ovaries, it is likely that the posttranslational modifications of this protein observed in early embryonic stages are of maternal origin. Using site specific antibodies against helices I and III of HMGD and HMGZ and against the AT-hook motif of D1, protein-specific staining patterns have been observed during embryonic development. Despite high levels of HMG proteins at the beginning of embryonic development, we were unable to detect any of these proteins in nuclei of stage 2 embryos. The accumulation of the HMG proteins correlates with the onset of transcription in stage 3. Our results argue against a proposal of a shared role of HMGD and histone H1 in Drosophila chromatin.

Initiation of a chromatin-based transcriptionally repressive state in the preimplantation mouse embryo: lack of a primary role for expression of somatic histone H1

A chromatin-based transcriptionally repressive state develops during the two-cell stage in preimplantation mouse embryos. Correlated with the initial formation of this state is the expression of somatic histone H1, which could confer repression by promoting the formation of a transcriptionally repressive chromatin structure. To ascertain if the expression of histone H1 could play such a primary role in initiating the formation of this transcriptionally repressive state, the endogenous pool of somatic histone H1 in the two-cell embryo was greatly expanded by injection of 25 or 100 pg of histone H1 at the one-cell stage. The expression of the transcription-requiring complex, which is an accepted marker for genome activation, was then assessed during the two-cell stage. No significant inhibition was noted following the injection of 25 pg of histone H1. A transient inhibition was observed following injection of 100 pg, but this was likely due to a delay in cleavage to the two-cell stage. We conclude that it is unlikely that the expression of somatic histone H1 is a major factor in the initial establishment of the chromatin-based transcriptionally repressive state that accompanies genome activation.

Reprogramming nuclei: insights from cloning, nuclear transfer and heterokaryons

Mammals and amphibians can be cloned following the transfer of embryonic nuclei into enucleated eggs or oocytes. As nuclear functions become more specialized in the differentiated cells of an adult, successful cloning using these nuclei as donors becomes more difficult. Differentiation involves the assembly of specialized forms of repressive chromatin including linker histones, Polycomb group proteins and methyl-CpG-binding proteins. These structures compartmentalize chromatin into functional domains and maintain the stability of the differentiated state through successive cell divisions. Efficient cloning requires the erasure of these structures. The erasure can be accomplished through use of molecular chaperones and enzymatic activities present in the oocyte, egg or zygote. We discuss the mechanisms involved in reprogramming nuclei after nuclear transfer and compare them with those that occur during remodeling of somatic nuclei after heterokaryon formation. Finally we discuss how one might alter the properties of adult nuclei to improve the efficiency of cloning.

Role of histone acetylation in the assembly and modulation of chromatin structures

The acetylation of the core histone N-terminal "tail" domains is now recognized as a highly conserved mechanism for regulating chromatin functional states. The following article examines possible roles of acetylation in two critically important cellular processes: replication-coupled nucleosome assembly, and reversible transitions in chromatin higher order structure. After a description of the acetylation of newly synthesized histones, and of the likely acetyltransferases involved, an overview of histone octamer assembly is presented. Our current understanding of the factors thought to assemble chromatin in vivo is then described. Genetic and biochemical investigations of the function the histone tails, and their acetylation, in nucleosome assembly are detailed, followed by an analysis of the importance of histone deacetylation in the maturation of newly replicated chromatin. In the final section the involvement of the histone tail domains in chromatin higher order structures is addressed, along with the role of histone acetylation in chromatin folding. Suggestions for future research are offered in the concluding remarks.

Translation of maternal TATA-binding protein mRNA potentiates basal but not activated transcription in Xenopus embryos at the midblastula transition

Early embryonic development in Xenopus laevis is characterized by transcriptional repression which is relieved at the midblastula stage (MBT). Here we show that the relative abundance of TATA-binding protein (TBP) increases robustly at the MBT and that the mechanism underlying this increase is translation of maternally stored TBP RNA. We show that TBP is rate-limiting in egg extract under conditions that titrate nucleosome assembly. Precocious translation of TBP mRNA in Xenopus embryos facilitates transcription before the MBT, without requiring TBP to be prebound to the promoter before injection. This effect is transient in the absence of chromatin titration and is sustained when chromatin is titrated. These data show that translational regulation of TBP RNA contributes to limitations on the transcriptional capacity before the MBT. Second, we examined the ability of trans-acting factors to contribute to promoter activity before the MBT. Deletion of cis-acting elements does not affect histone H2B transcription in egg extract, a finding indicative of limited trans-activation. Moreover, in the context of the intact promoter, neither the transcriptional activator Oct-1, nor TBP, nor TFIID enable transcriptional activation in vitro. HeLa cell extract, however, reconstitutes activated transcription in mixed extracts. These data suggest a deficiency in egg extract cofactors required for activated transcription. We show that the capacity for activated H2B transcription is gradually acquired at the early gastrula transition. This transition occurs well after the blastula stage when the basal transcription machinery can first be complemented with TBP.

Control of gene expression at the onset of bovine embryonic development

The objective of this study was to examine the timing and mechanisms involved in transcription initiation in bovine embryos. Transcriptional activity and its regulation were explored by labeling 1-cell zygotes and 2-cell embryos with [(3)H]uridine in the presence or absence of alpha-amanitin, aphidicolin, and tricostatin A (TSA) (inhibitors of mRNA synthesis, DNA replication, and histone deacetylases, respectively) followed by a total RNA isolation and determination of [(3)H]uridine incorporation. We also analyzed translation of zygotic/embryonic mRNAs by labeling zygotes and 2-cell embryos with [(35)S]methionine in the presence or absence of alpha-amanitin, aphidicolin, and TSA followed by two-dimensional PAGE and autoradiography. We show that bovine 1-cell zygotes and 2-cell embryos are transcriptionally and translationally active. The first and second rounds of DNA replication are important regulators of early gene expression as the inhibition of DNA replication resulted in a dramatic decrease in both transcriptional and translational activity. Moreover, acetylation of histones plays an important role in this early gene activation at the onset of embryonic development in the cow.

Mechanisms and control of embryonic genome activation in mammalian embryos

Activation of transcription within the embryonic genome (EGA) after fertilization is a complex process requiring a carefully coordinated series of nuclear and cytoplasmic events, which collectively ensure that the two parental genomes can be faithfully reprogrammed and restructured before transcription occurs. Available data indicate that inappropriate transcription of some genes during the period of nuclear reprogramming can have long-term detrimental effects on the embryo. Therefore, precise control over the time of EGA is essential for normal embryogenesis. In most mammals, genome activation occurs in a stepwise manner. In the mouse, for example, some transcription occurs during the second half of the one-cell stage, and then a much greater phase of genome activation occurs in two waves during the two-cell stage, with the second wave producing the largest onset of de novo gene expression. Changes in nuclear structure, chromatin structure, and cytoplasmic macromolecular content appear to regulate these periods of transcriptional activation. A model is presented in which a combination of cell cycle-dependent events and both translational and posttranslational regulatory mechanisms within the cytoplasm play key roles in mediating and regulating EGA.

Developmental regulation of replication fork pausing in Xenopus laevis ribosomal RNA genes

In early Xenopus embryos, replication forks move along the rRNA genes (rDNA) at a uniform rate and terminate at multiple, apparently random sites. In contrast, a polar replication fork barrier (RFB) is found at the 3' end of the rRNA genes in Xenopus cultured cells. We have now analysed the replication intermediates of Xenopus rDNA from a wide range of developmental stages by 2D gel electrophoresis. Surprisingly, up to 15 different replication fork pausing sites (RFPs) simultaneously appear in the rDNA at the midgastrula stage, when rRNA transcription abruptly increases. They disappear during the neurula stage, except for a polar RFP at the 3' end of Xthe transcription unit, which persists to the tadpole stage. The latter RFP is found at the same location as the RFB in cultured cells; however the arrest of replication forks at this RFP is not absolute, since termination occurs at multiple positions throughout the rDNA repeat. The efficiency of fork arrest at this RFP remains constant from midgastrula to early tadpole, and decreases around hatching. The transient appearance of multiple RFPs at midgastrula may reflect some chromatin remodeling associated with developmental activation of rRNA transcription.

Maternal histone deacetylase is accumulated in the nuclei of Xenopus oocytes as protein complexes with potential enzyme activity

Reversible acetylation of core histones plays an important regulatory role in transcription and replication of chromatin. The acetylation status of chromatin is determined by the equilibrium between activities of histone acetyltransferases (HATs) and histone deacetylases (HDACs). The Xenopus protein HDACm shows sequence homology to other putative histone deacetylases, but its mRNA is expressed only during early development. Both HDACm protein and acetylated non-chromosomal histones are accumulated in developing oocytes, indicating that the key components for histone deposition into new chromatin during blastula formation are in place by the end of oogenesis. Here we show that the 57 kDa HDACm protein undergoes steady accumulation in the nucleus, where it is organized in a multiprotein complex of approx. 300 kDa. A second, major component of the nuclear complex is the retinoblastoma-associated protein p48 (RbAp48/46), which may be used as an adaptor to contact acetylated histones in newly assembled chromatin. The nuclear complex has HDAC activity that is sensitive to trichostatin A, zinc ions and phosphatase treatment. The 57 kDa protein serves as a marker for total HDAC activity throughout oogenesis and early embryogenesis. The active HDACm complex and its acetylated histone substrates appear to be kept apart until after chromatin assembly has taken place. However, recombinant HDACm, injected into the cytoplasm of oocytes, not only is translocated to the nucleus, but also is free to interact with the endogenous chromatin.

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.

Hierarchical differentiation of multipotent progenitor cells

Selection of a pathway of differentiation in multipotent progenitor cells may depend on the amount of histone H1 or H1 zero relative to the core histones. With low levels of these linker histones, it is proposed that an evolutionarily more ancient cell differentiation occurs. Greater repetition of AT-rich regulatory motifs allows more frequent, hence earlier, transcription of genes, accounting for this type of cell differentiation. It is further proposed that a decrease of total cell protein accumulation leads to an increase of histone H1 or H1 zero relative to the core histones. It is suggested that these linker histones preferentially bind the more AT-rich regulatory sequences, thereby restricting the phylogenetically more ancient differentiation potency. This allows differentiation of an evolutionarily younger cell type.

Chromatin disruption and modification

Chromatin disruption and modification are associated with transcriptional regulation by diverse coactivators and corepressors. Here we discuss the possible structural basis and functional consequences of the observed alterations in chromatin associated with transcriptional activation and repression. Recent advances in defining the roles of individual histones and their domains in the assembly and maintenance of regulatory architectures provide a framework for understanding how chromatin remodelling machines, histone acetyltransferases and deacetylases function.

Histone deacetylase mRNA temporally and spatially regulated in its expression in sea urchin embryos

SpHDAC1, a cDNA homolog of the yeast Rpd3 and higher eukaryotic histone deacetylases (HDAC), was cloned from the sea urchin Strongylocentrotus purpuratus. Its predicted polypeptide and the Rpd3 homologs were highly identical in two-thirds of their lengths, but diverged in their carboxyl-terminal regions in both length and sequence. SpHDAC1 transcripts, which reached maximal concentration at the blastula stages, and diminished thereafter, were neither ubiquitously expressed nor restricted to particular cell lineages, but appeared successively in distinct embryonic regions. In the blastula, transcripts were concentrated in a ring within the vegetal plate, comprising primordial endoderm, and, at the outset of gastrulation, in primordial hindgut endoderm. However, in early to mid-gastrula transcripts, they also appeared in oral ectoderm. In the late-stage gastrula, expression developed in the foregut. These shifts in spatial expression, together with an observed developmental blockage prior to sea urchin gastrulation by the histone deacetylase inhibitor trichostatin A, suggest a stepwise involvement of SpHDAC1 gene expression or SpHDAC1 functionality in the events of normal gastrulation.

Persistent interactions of core histone tails with nucleosomal DNA following acetylation and transcription factor binding

In this study, we examined the effect of acetylation of the NH2 tails of core histones on their binding to nucleosomal DNA in the absence or presence of bound transcription factors. To do this, we used a novel UV laser-induced protein-DNA cross-linking technique, combined with immunochemical and molecular biology approaches. Nucleosomes containing one or five GAL4 binding sites were reconstituted with hypoacetylated or hyperacetylated core histones. Within these reconstituted particles, UV laser-induced histone-DNA cross-linking was found to occur only via the nonstructured histone tails and thus presented a unique tool for studying histone tail interactions with nucleosomal DNA. Importantly, these studies demonstrated that the NH2 tails were not released from nucleosomal DNA upon histone acetylation, although some weakening of their interactions was observed at elevated ionic strengths. Moreover, the binding of up to five GAL4-AH dimers to nucleosomes occupying the central 90 bp occurred without displacement of the histone NH2 tails from DNA. GAL4-AH binding perturbed the interaction of each histone tail with nucleosomal DNA to different degrees. However, in all cases, greater than 50% of the interactions between the histone tails and DNA was retained upon GAL4-AH binding, even if the tails were highly acetylated. These data illustrate an interaction of acetylated or nonacetylated histone tails with DNA that persists in the presence of simultaneously bound transcription factors.

Regulation of mammalian replication origin usage in Xenopus egg extract

Xenopus embryos initiate replication at random closely spaced sites until a certain concentration of nuclei is achieved within the embryo, after which fewer, more specific chromosomal sites are utilized as origins. We have examined the relationship between nucleo-cytosolic ratio and origin specification when Chinese hamster ovary (CHO) cell nuclei are introduced into Xenopus egg extracts. At concentrations of intact late-G1-phase nuclei that approximate early Xenopus embryos, the entire genome was duplicated nearly 4 times faster than in culture, accompanied by a de-localization of initiation sites at the dihydrofolate reductase (DHFR) locus. As the concentration of nuclei was increased, the number of initiation sites per nucleus decreased and initiation at the DHFR locus became localized to the physiologically utilized DHFR origin. Origin specification was optimal at nuclear concentrations that approximate the Xenopus mid-blastula transition (MBT). Higher concentrations resulted in an overall inhibition of DNA synthesis. By contrast, with intact early G1-phase nuclei, replication initiated at apparently random sites at all concentrations, despite an identical relationship between nucleo-cytosolic ratio and replicon size. Furthermore, permeabilization of late-G1-phase nuclei, using newly defined conditions that preserve the overall rate of replication, eliminated site-specificity, even at nuclear concentrations optimal for DHFR origin recognition. These data show that both nucleo-cytosolic ratio and nuclear structure play important but independent roles in the regulation of replication origin usage. Nucleo-cytosolic ratio clearly influences the number of replication origins selected. However, titration of cytosolic factors is not sufficient to focus initiation to specific sites. An independent mechanism, effecting changes within G1-phase nuclei, dictates which of many potential initiation sites will function as an origin.

The nucleosome: a powerful regulator of transcription

Nucleosomes provide the architectural framework for transcription. Histones, DNA elements, and transcription factors are organized into precise regulatory complexes. Positioned nucleosomes can facilitate or impede the transcription process. These structures are dynamic, reflecting the capacity of chromatin to adopt different functional states. Histones are mobile with respect to DNA sequence. Individual histone domains are targeted for posttranslational modifications. Histone acetylation promotes transcription factor access to nucleosomal DNA and relieves inhibitory effects on transcriptional initiation and elongation. The nucleosomal infrastructure emerges as powerful contributor to the regulation of gene activity.