Induction of early transcription in one-cell mouse embryos by microinjection of the nonhistone chromosomal protein HMG-I

Involvement of microRNA-1297, a new regulator of HMGA1, in the regulation of glioma cell growth in vivo and in vitro

MicroRNAs (miRNAs) are a class of versatile gene expression regulators, participating in the regulation of gene expression at the post-transcriptional level in both physiological and pathological conditions. Gliomas are the most common brain malignancy in adults, and deregulation of microRNAs takes part in the gliomagenesis process. Here, we found that the expression of miR-1297 is significantly reduced in both glioma cell lines and clinical glioma tissues. Using the MTT assay, soft agar colony formation assay and xenograft tumor formation assay, we show that miR-1297 is a tumor suppressor microRNA in gliomas. We demonstrate that the high mobility group protein A1 (HMGA1) is the functional target of miR-1297 in glioma cells. HMGA1 significantly promotes the growth of glioma cells both in vitro and in vivo. Together, we unveil a new molecular mechanism in gliomas that may shed new light on understanding this brain malignancy.

RNA-Mediated Regulation of HMGA1 Function

The high mobility group protein A1 (HMGA1) is a master regulator of chromatin structure mediating its major gene regulatory activity by direct interactions with A/T-rich DNA sequences located in the promoter and enhancer regions of a large variety of genes. HMGA1 DNA-binding through three AT-hook motifs results in an open chromatin structure and subsequently leads to changes in gene expression. Apart from its significant expression during development, HMGA1 is over-expressed in virtually every cancer, where HMGA1 expression levels correlate with tumor malignancy. The exogenous overexpression of HMGA1 can lead to malignant cell transformation, assigning the protein a key role during cancerogenesis. Recent studies have unveiled highly specific competitive interactions of HMGA1 with cellular and viral RNAs also through an AT-hook domain of the protein, significantly impacting the HMGA1-dependent gene expression. In this review, we discuss the structure and function of HMGA1-RNA complexes during transcription and epigenomic regulation and their implications in HMGA1-related diseases.

Anti-Transcription Factor RNA Aptamers as Potential Therapeutics

Transcription factors (TFs) are DNA-binding proteins that play critical roles in regulating gene expression. These proteins control all major cellular processes, including growth, development, and homeostasis. Because of their pivotal role, cells depend on proper TF function. It is, therefore, not surprising that TF deregulation is linked to disease. The therapeutic drug targeting of TFs has been proposed as a frontier in medicine. RNA aptamers make interesting candidates for TF modulation because of their unique characteristics. The products of in vitro selection, aptamers are short nucleic acids (DNA or RNA) that bind their targets with high affinity and specificity. Aptamers can be expressed on demand from transgenes and are intrinsically amenable to recognition by nucleic acid-binding proteins such as TFs. In this study, we review several natural prokaryotic and eukaryotic examples of RNAs that modulate the activity of TFs. These examples include 5S RNA, 6S RNA, 7SK, hepatitis delta virus-RNA (HDV-RNA), neuron restrictive silencer element (NRSE)-RNA, growth arrest-specific 5 (Gas5), steroid receptor RNA activator (SRA), trophoblast STAT utron (TSU), the 3' untranslated region of caudal mRNA, and heat shock RNA-1 (HSR1). We then review examples of unnatural RNA aptamers selected to inhibit TFs nuclear factor-kappaB (NF-κB), TATA-binding protein (TBP), heat shock factor 1 (HSF1), and runt-related transcription factor 1 (RUNX1). The field of RNA aptamers for DNA-binding proteins continues to show promise.

Inferring the choreography of parental genomes during fertilization from ultralarge-scale whole-transcriptome analysis

The mechanisms underlying parental genome coordination upon mammalian fertilization remain elusive due to difficulties in preparing large numbers of high-quality preimplantation cells. Here, Park et al. collect an unprecedented number of mouse oocytes and establish detailed transcriptional profiles for four early embryonic stages and parthenogenetic development. Bioinformatic analysis identifies a distinctive gene regulatory network activated in embryos after fertilization compared with parthenotes. This large-scale profile of early mouse embryos yields a valuable resource for developmental biology and stem cell research.

Fertilization precisely choreographs parental genomes by using gamete-derived cellular factors and activating genome regulatory programs. However, the mechanism remains elusive owing to the technical difficulties of preparing large numbers of high-quality preimplantation cells. Here, we collected >14 × 10⁴ high-quality mouse metaphase II oocytes and used these to establish detailed transcriptional profiles for four early embryo stages and parthenogenetic development. By combining these profiles with other public resources, we found evidence that gene silencing appeared to be mediated in part by noncoding RNAs and that this was a prerequisite for post-fertilization development. Notably, we identified 817 genes that were differentially expressed in embryos after fertilization compared with parthenotes. The regulation of these genes was distinctly different from those expressed in parthenotes, suggesting functional specialization of particular transcription factors prior to first cell cleavage. We identified five transcription factors that were potentially necessary for developmental progression: Foxd1, Nkx2-5, Sox18, Myod1, and Runx1. Our very large-scale whole-transcriptome profile of early mouse embryos yielded a novel and valuable resource for studies in developmental biology and stem cell research. The database is available at http://dbtmee.hgc.jp.

Analysis of active chromatin modifications in early mammalian embryos reveals uncoupling of H2A.Z acetylation and H3K36 trimethylation from embryonic genome activation

Early embryonic development is characterized by dramatic changes in cell potency and chromatin organization. The role of histone variants in the context of chromatin remodeling during embryogenesis remains under investigated. In particular, the nuclear distribution of the histone variant H2A.Z and its modifications have not been examined. Here we investigated the dynamics of acetylation of H2A.Z and two other active chromatin marks, H3K9ac and H3K36me3, throughout murine and bovine pre-implantation development. We show that H2A.Z distribution is dynamic during the earliest stages of mouse development, with protein levels significantly varying across stages and lowest at the 2-cell stage. When present, H2A.Z localizes preferentially to euchromatin at all stages analyzed. H2A.Z is acetylated in pre-implantation blastomeres and is preferentially localized to euchromatin, in line with the known role of H2A.Zac in transcriptional activation. Interestingly, however, H2A.Zac is undetectable in mouse embryos at the 2-cell stage, the time of major embryonic genome activation (EGA). Similarly, H3K36me3 is present exclusively in the maternal chromatin immediately after fertilization but becomes undetectable in interphase nuclei at the 2-cell stage, suggesting uncoupling of these active marks with global embryonic transcription activation. In bovine embryos, which undergo EGA at the 8-cell stage, H2A.Zac can be detected in zygotes, 4-, 8- and 16-cell stage embryos as well as in blastocysts, indicating that the dynamics of H2A.Zac is not conserved in mammals. In contrast, H3K36me3 displays mostly undetectable and heterogeneous localization pattern throughout bovine pre-implantation development. Thus, our results suggest that 'canonical' active chromatin marks exhibit a dynamic behavior in embryonic nuclei, which is both stage- and species-specific. We hypothesize that chromatin of early embryonic nuclei is subject to fine-tuning through differential acquisition of histone marks, allowing for proper chromatin remodeling and developmental progression in a species-specific fashion.

Roles of heat shock factors in gametogenesis and development

Heat shock factors form a family of transcription factors (four in mammals), which were named according to the first discovery of their activation by heat shock. As a result of the universality and robustness of their response to heat shock, the stress-dependent activation of heat shock factor became a ‘paradigm’: by binding to conserved DNA sequences (heat shock elements), heat shock factors trigger the expression of genes encoding heat shock proteins that function as molecular chaperones, contributing to establish a cytoprotective state to various proteotoxic stress and in several pathological conditions. Besides their roles in the stress response, heat shock factors perform crucial roles during gametogenesis and development in physiological conditions. First, during these process, in stress conditions, they are either proactive for survival or, conversely, for apoptotic process, allowing elimination or, inversely, protection of certain cell populations in a way that prevents the formation of damaged gametes and secure future reproductive success. Second, heat shock factors display subtle interplay in a tissue- and stage-specific manner, in regulating very specific sets of heat shock genes, but also many other genes encoding growth factors or involved in cytoskeletal dynamics. Third, they act not only by their classical transcription factor activities, but are necessary for the establishment of chromatin structure and, likely, genome stability. Finally, in contrast to the heat shock gene paradigm, heat shock elements bound by heat shock factors in developmental process turn out to be extremely dispersed in the genome, which is susceptible to lead to the future definition of ‘developmental heat shock element’.

[Embryonic genome organization after fertilization in mammals]

In mammals, the embryonic genome is first transcriptionally inactive after fertilization. Embryonic development is then strictly dependent on the maternally inherited RNA and proteins accumulated before ovulation and present in the oocyte cytoplasm. The onset of embryonic gene expression is initiated later during development, i.e. during the "embryonic genome activation (EGA)". EGA takes place at various preimplantation stages according to species and is dependent on the presence of the basal transcriptional machinery components but also on parental genomes reorganizations after fertilization. Indeed, during the first embryonic cycles, nuclei undergo intense remodeling that could be a key regulator of embryonic development.

Optimal transactivation by Epstein-Barr nuclear antigen 1 requires the UR1 and ATH1 domains

Epstein-Barr nuclear antigen 1 (EBNA1) is essential for Epstein-Barr virus to immortalize naïve B cells. EBNA1 transactivates viral promoters for genes that are necessary for immortalization when it is bound to a cluster of 20 cognate binding sites, termed the family of repeats. A region of EBNA1 from amino acids (aa) 40 to 89, termed linking region 1 (LR1), has been identified previously as being sufficient for transactivation. LR1 contains two domains that are conserved in the EBNA1 orthologs of other gamma herpesviruses. The first of these, termed unique region 1 (UR1), corresponds to aa 65 to 89 of EBNA1. UR1 is necessary for transactivation and contains a conserved recognition site for cyclic AMP-dependent protein kinase (PKA), corresponding to serine 78 of EBNA1. We have pharmacologically modulated PKA activity to determine if PKA controls EBNA1's ability to transactivate. Our results indicate that PKA activators and inhibitors do not affect transactivation by EBNA1. In addition, site-directed mutagenesis demonstrates that transactivation is not influenced by the phosphorylation status of serine 78 in the UR1 domain. The second conserved domain within LR1 is a glycine-arginine repeat, corresponding to aa 40 to 54 of EBNA1. This domain, termed ATH1, functions as an AT-hook, a DNA-binding motif found in architectural transcription factors such as HMGA1a. We demonstrate that deletion of the ATH1 domain decreases EBNA1 transactivation ability, which is consistent with a transcriptional role for ATH1. Furthermore, transactivation is restored when ATH1 is replaced by equivalent AT-hook motifs from HMGA1a. Our data strongly indicate a role for AT-hooks in EBNA1's ability to transactivate, a function necessary for EBV to immortalize naïve B-cells.

Cell-free extracts from mammalian oocytes partially induce nuclear reprogramming in somatic cells

Nuclear transfer has been regarded as the only reliable tool for studying nuclear reprogramming of mammalian somatic cells by oocytes. However, nuclear transfer is not well suited for biochemical analyses of the molecular mechanisms of reprogramming. A cell-free system from oocytes is an attractive alternative way to mimic reprogramming in vitro, since a large number of cells can be treated and analyzed. Nevertheless, a cell-free system using oocytes has not been developed in mammals. Here, cell extracts from porcine oocytes were prepared and their ability to induce nuclear reprogramming was evaluated. Extracts from metaphase II (MII) oocytes erased the machinery for regulating gene expression in reversibly permeabilized somatic cells. For example, the extracts caused histone deacetylation and the disappearance of TATA box-binding protein from the nuclei. However, MII-extract-treated cells did not show any obvious changes after cell culture. In contrast, extracts from germinal vesicle (GV) oocytes activated pluripotent marker genes, especially NANOG, and induced partial dedifferentiation after cell culture. The activation of pluripotent marker genes by GV extracts was associated with histone acetylation that was induced during extract treatment. These results indicate that GV- and MII-oocyte extracts have different roles on nuclear reprogramming. Furthermore, both oocyte extracts induced site-specific demethylation in the upstream region of NANOG. These results indicate that cell-free extracts derived from GV- and MII-oocytes could be useful for studying the mechanisms involved in nuclear reprogramming.

Effects of oviductal fluid on the development, quality, and gene expression of porcine blastocysts produced in vitro

In mammals, fertilization and early pre-implantation development occur in the oviduct. Previous results obtained in our laboratory have identified specific molecules in the oviduct that affect porcine sperm-egg interactions. The aim of the present study was to determine whether the contact between oocytes and oviductal fluid also affect embryo development, quality, and gene expression. In vitro matured porcine oocytes were exposed to bovine oviductal fluid (bOF) for 30 min prior to fertilization. Cleavage and blastocyst development rates were significantly higher from bOF-treated oocytes than from untreated oocytes. Blastocysts obtained from bOF-treated oocytes had significantly greater total cell numbers than those obtained from untreated oocytes. Using real-time PCR, grade 1 (very good morphological quality) and grade 2 (good morphological quality) blastocysts were analyzed for gene transcripts related to apoptosis (BAX, BCL2L1), mitochondrial DNA (mtDNA) transcription/replication (POLG, POLG2, and TFAM), blastomere connection and morula compaction (GJA1), and blastocyst formation and pluripotency (POU5F1). We found that the entire set of genes analyzed was differentially expressed between grade 1 and 2 blastocysts. Furthermore, bOF treatment reduced the ratio of BAX to BCL2L1 transcripts and enhanced the abundance of TFAM transcripts in grade 2 blastocysts. Not only do these findings demonstrate that factors within the bOF act on porcine oocytes both quickly and positively, but they also suggest that such factors could promote embryo development and quality by protecting them against adverse impacts on mtDNA transcription/replication and apoptosis induced by the culture environment.

Interaction of HSF1 and HSF2 with the Hspa1b promoter in mouse epididymal spermatozoa

The Hspa1b gene is one of the first genes expressed after fertilization, with expression observed in the male pronucleus as early as the one-cell stage of embryogenesis. This expression can occur in the absence of stress and is initiated during the minor zygotic genome activation. There is a significant reduction in the number of embryos developing to the blastocyte stage when HSPA1B levels are depleted, which supports the importance of this protein for embryonic viability. However, the mechanism responsible for allowing expression of Hspa1b during the minor zygotic genome activation (ZGA) is unknown. In this report, we investigated the role of HSF1 and HSF2 in bookmarking Hspa1b during late spermatogenesis. Western blot results show that both HSF1 and HSF2 are present in epididymal spermatozoa, and immunofluorescence analysis revealed that some of the HSF1 and HSF2 proteins in these cells overlap the 4',6'-diamidino-2-phenylindole-stained DNA region. Results from chromatin immunoprecipitation assays showed that HSF1, HSF2, and SP1 are bound to the Hspa1b promoter in epididymal spermatozoa. Furthermore, we observed an increase in HSF2 binding to the Hspa1b promoter in late spermatids versus early spermatids, suggesting a likely period during spermatogenesis when transcription factor binding could occur. These results support a model in which the binding of HSF1, HSF2, and SP1 to the promoter of Hspa1b would allow the rapid formation of a transcription-competent state during the minor ZGA, thereby allowing Hspa1b expression.

High-level expression of DNA architectural factor HMGA2 and its association with nucleosomes in human embryonic stem cells

The state of chromatin in human embryonic stem (hES) cells is a key factor determining stem cell identity. The non-histone chromatin-associated factor HMGA2 has been studied mostly in the mouse where its function seems critical for embryonic cell growth and adipocytic cell differentiation. Here we show that HMGA2 is highly expressed in two undifferentiated human embryonic stem cell lines at a level of at least 10(5) copies per individual stem cell. Interestingly, expression is further upregulated by a factor of three at day 7 of embryoid body formation, before it quickly drops to or below the level found in undifferentiated cells. We also show that HMGA2 is stably associated with inter- and metaphase hES cell chromatin, and that up to 12 HMGA2 protomers stably associate in vitro with a single nucleosome core particle of known atomic structure. Our data lend support to the possibility that HMGA2 interacts with nucleosomes in a way that imposes a global effect on the state of ES cell chromatin, which may contribute to the establishment of both ES cell identity and the initiation of specific differentiation programs.

Establishment of customized mouse stem cell lines by sequential nuclear transfer

Therapeutic cloning, whereby embryonic stem cells (ESCs) are derived from nuclear transfer (NT) embryos, may play a major role in the new era of regenerative medicine. In this study we established forty nuclear transfer-ESC (NT-ESC) lines that were derived from NT embryos of different donor cell types or passages. We found that NT-ESCs were capable of forming embryoid bodies. In addition, NT-ESCs expressed pluripotency stem cell markers in vitro and could differentiate into embryonic tissues in vivo. NT embryos from early passage R1 donor cells were able to form full term developed pups, whereas those from late passage R1 ES donor cells lost the potential for reprogramming that is essential for live birth. We subsequently established sequential NT-R1-ESC lines that were developed from NT blastocyst of late passage R1 ESC donors. However, these NT-R1-ESC lines, when used as nuclear transfer donors at their early passages, failed to result in live pups. This indicates that the therapeutic cloning process using sequential NT-ESCs may not rescue the developmental deficiencies that resided in previous donor generations.

Role of TIF1alpha as a modulator of embryonic transcription in the mouse zygote

The first events of the development of any embryo are under maternal control until the zygotic genome becomes activated. In the mouse embryo, the major wave of transcription activation occurs at the 2-cell stage, but transcription starts already at the zygote (1-cell) stage. Very little is known about the molecules involved in this process. We show that the transcription intermediary factor 1 α (TIF1α) is involved in modulating gene expression during the first wave of transcription activation. At the onset of genome activation, TIF1α translocates from the cytoplasm into the pronuclei to sites of active transcription. These sites are enriched with the chromatin remodelers BRG-1 and SNF2H. When we ablate TIF1α through either RNA interference (RNAi) or microinjection of specific antibodies into zygotes, most of the embryos arrest their development at the 2–4-cell stage transition. The ablation of TIF1α leads to mislocalization of RNA polymerase II and the chromatin remodelers SNF2H and BRG-1. Using a chromatin immunoprecipitation cloning approach, we identify genes that are regulated by TIF1α in the zygote and find that transcription of these genes is misregulated upon TIF1α ablation. We further show that the expression of some of these genes is dependent on SNF2H and that RNAi for SNF2H compromises development, suggesting that TIF1α mediates activation of gene expression in the zygote via SNF2H. These studies indicate that TIF1α is a factor that modulates the expression of a set of genes during the first wave of genome activation in the mouse embryo.

Architectural reorganization of the nuclei upon transfer into oocytes accompanies genome reprogramming

The ability of cloned embryos to sustain full-term development depends on the ability of the recipient ooplasm to reprogram the donor cell genome. As the nuclear architecture has recently emerged as a key-factor in the regulation of gene expression, we questioned whether early embryos obtained from transfer of ES metaphasic chromosomes into mouse ooplasm would adopt the somatic or embryonic type of nuclear organization. We have particularly focused on the arrangement of chromosomal territories with respect to the nucleolar compartment, and the pericentric heterochromatin domains called chromocenters. We found that nuclear transfer triggers profound chromatin rearrangements including the dispersion of the donor cell chromocenters components. These rearrangements lead to a typical 1-cell pronuclear organization, namely a radial arrangement of the chromosome territories with centromeres attached to the nucleoli, which adopt the compact fibrillar structure of nucleolar precursor bodies (NPBs). Subsequently, during the second cycle, the cloned embryos undergo further reorganization with the establishment of new chromocenters, clustered in one part of the nucleus, as during normal embryogenesis. We could also establish that the adequate distribution of chromosomal territories at the pronuclear stage seems important for the development until blastocyst.

Energetics of binding the mammalian high mobility group protein HMGA2 to poly(dA-dT)2 and poly(dA)-poly(dT)

The mammalian high mobility group protein A2 (HMGA2) is a chromosomal architectural transcription factor involved in oncogenesis and cell transformation. It has three "AT-hook" DNA binding domains, which specifically bind to the minor groove of AT DNAs. The interaction of HMGA2 with poly(dA-dT)2 and poly(dA)poly(dT) has been investigated using the ethidium displacement assay, isothermal titration calorimetry, and UV melting studies. Each AT hook DNA binding domain was found to bind to 5 bp and each HMGA2 molecule binds to 15 bp. Although an individual AT hook DNA binding domain binds to AT DNAs with moderate affinity, HMGA2 binds with very high affinity to both DNAs in solutions containing 20 mM Na+ at 25 degrees C. The K(a) and binding enthalpy for poly(dA-dT)2 were determined to be, respectively, 1.9x10(14)M(-1) and -29.1(+/-0.5)kcal/mol. The binding reaction is enthalpy-driven with a favorable free energy of -19.5 kcal/mol and unfavorable entropy of -32.5 cal/mol K (-TDeltaS= +9. 7kcal/mol) at a 1M reference state. Interestingly, although HMGA2 binds to poly(dA)poly(dT) with a binding constant of 9.6x10(12) M(-1), the binding reaction is entropy-driven with an unfavorable enthalpy of +0.6 kcal/mol, a free energy of -17.7 kcal/mol and an entropy of +61.4 cal/mol K (-TDeltaS=-18.3 kcal/mol) at the 1 M state. The enthalpy-entropy compensation is similar to that of several minor groove-binding drugs such as netropesin, distamycin A and Hoechst33258 and may be a reflection of dehydration difference of different ligand-DNA complexes. The salt-dependence of the binding constant of HMGA2 with both DNAs showed that electrostatic interaction is a dominant force for the binding reactions. The temperature dependence of binding enthalpy for poly(dA-dT)2 indicates a large heat capacity of binding of -705(+/-113) cal/molK, consistent with an important role of solvent displacement in the linked folding/binding processes in this system.

Transcriptional frequency and cell determination

The relative base composition of DNA regulatory sequences of certain genes of undetermined multipotent progenitor cells may account for the frequency of transcription of these genes in cell determination. The sequences of these regulatory regions of cell determination genes that are more AT-rich would create the potential for transcription at a higher frequency due to their lower melting temperature, as well as propensity to bend. An increase of one or more of the high mobility group (HMG) chromatin proteins would preferentially bind the more AT-rich regulatory sequences, thereby increasing the rate of transcription. The amount of unphosphorylated H1 histone reacting with these same regulatory sites may decrease transcription frequency. The level of cell growth, i.e. total protein synthesis of a cell, is correlated positively with the synthesis of HMG proteins. H1 histone synthesis is linked to DNA replication. Unbalanced growth would alter the amounts of HMG proteins and H1 histone, thus changing transcriptional frequency. The greater the enrichment of AT sequences in the regulatory regions of the cell determination genes, the greater may be the extent of evolutionary conservation. Higher frequency of transcription of the cell determination genes with the more AT-rich regulatory sequences could account for the earlier expression of the more conserved cell determination genes during embryonic development. Preferential binding of H1 histone to the more AT-rich regulatory sequences would subsequently restrict their transcription before that of less conserved cell determination genes.

Network of dynamic interactions between histone H1 and high-mobility-group proteins in chromatin

Histone H1 and the high-mobility group (HMG) proteins are chromatin binding proteins that regulate gene expression by modulating the compactness of the chromatin fiber and affecting the ability of regulatory factors to access their nucleosomal targets. Histone H1 stabilizes the higher-order chromatin structure and decreases nucleosomal access, while the HMG proteins decrease the compactness of the chromatin fiber and enhance the accessibility of chromatin targets to regulatory factors. Here we show that in living cells, each of the three families of HMG proteins weakens the binding of H1 to nucleosomes by dynamically competing for chromatin binding sites. The HMG families weaken H1 binding synergistically and do not compete among each other, suggesting that they affect distinct H1 binding sites. We suggest that a network of dynamic and competitive interactions involving HMG proteins and H1, and perhaps other structural proteins, constantly modulates nucleosome accessibility and the local structure of the chromatin fiber.

Early transcriptional activation of the hsp70.1 gene by osmotic stress in one-cell embryos of the mouse

In fertilized mouse eggs, de novo transcription of embryonic genes is first observed during the S phase of the one-cell stage. This transcription, however, is mostly limited to the male pronucleus and possibly uncoupled from translation, making the functional meaning obscure. We found that one-cell mouse embryos respond to the osmotic shock of in vitro isolation with migration of HSF1, the canonical stress activator of mammalian heat shock genes, to pronuclei and by transient transcription of the hsp70.1, but not hsp70.3 and hsp90, heat shock genes. Isolated growing dictyate oocytes also display a nuclear HSF1 localization, but, in contrast with embryos, they transcribe both hsp70.1 and hsp70.3 genes only after heat shock. Intranuclear injection of double-stranded oligodeoxyribonucleotides containing HSE, GAGA box or GC box consensus sequences, and antibodies raised to transcription factors HSF1, HSF2, Drosophila melanogaster GAGA factor, or Sp1 demonstrated that hsp70.1 transcription depends on HSF1 in both oocytes and embryos and that Sp1 is dispensable in oocytes and inhibitory in the embryos. Hsp70.1 thus represents the first endogenous gene so far identified to be physiologically activated and tightly regulated after fertilization in mammals.

Chromatin as a regulative architecture of the early developmental functions of mammalian embryos after fertilization or nuclear transfer

Nuclear transfer of a somatic nucleus into an enucleated oocyte has demonstrated in several mammalian species that the chromatin of a differentiated nucleus can be reprogrammed so as to be able to direct the full development of the reconstructed embryo. This review focus on the timing of the early events that allow the return of somatic chromatin to a totipotent state. Our understanding of the modifications associated with chromatin remodeling is limited by the low amount of biological material available in mammals at early developmental stages and the fact that very few genetic studies have been conducted with nuclear transfer embryos. However, the importance of several factors such as the covalent modifications of DNA through the methylation of CpG dinucleotides, the exchange of histones through a reorganized nuclear membrane, and the interaction between cytoplasmic oocyte components and nuclear complexes in the context of nuclear transfer is becoming clear. A better characterization of the changes in somatic chromatin after nuclear transfer and the identification of oocyte factors or structures that govern the formation of a functional nucleus will help us to understand the relationship between chromatin structure and cellular totipotency.

Epigenetic mechanisms for primary differentiation in mammalian embryos

This review examines main developments related to the interface between primary mammalian cell differentiation and various aspects of chromosomal structure changes, such as heterochromatin dynamics, DNA methylation, mitotic recombination, and inter- and intrachromosomal differentiation. In particular, X chromosome difference, imprinting, chromosomal banding, methylation pattern, single-strand DNA breaks, sister chromatid exchanges (SCEs), and sister chromatid asymmetry are considered. A hypothesis is put forward which implies the existence of an epigenetic asymmetry versus mirror symmetry of sister chromatids for any DNA sequences. Such epigenetic asymmetry appears as a result of asymmetry of sister chromatid organization and of SCE and is a necessary (not sufficient) condition for creating cell diversity. The sister chromatid asymmetry arises as a result of consecutive rounds of active and passive demethylation which leads after chromatin assembly events to chromatid difference. Single-strand DNA breaks that emerge during demethylation trigger reparation machinery, provend as sister chromatid exchanges, which are not epigenetically neutral in this case. Taken together, chromatid asymmetry and SCE lead to cell diversity regarding their future fate. Such cells are considered pluripotent stem cells which after interplay between a set of chromosomal domains and certain substances localized within the cytoplasmic compartments (and possibly cell interactions) can cause sister cells to express different gene chains. A model is suggested that may be useful for stem cell technology and studies of carcinogenesis.

Modification of position-effect variegation by competition for binding to Drosophila satellites

White-mottled (w(m4)) position-effect variegation (PEV) arises by translocation of the white gene near the pericentric AT-rich 1.688 g/cm3 satellite III (SATIII) repeats of the X chromosome of Drosophila. The natural and artificial A*T-hook proteins D1 and MATH20 modify w(m4) PEV in opposite ways. D1 binds SATIII repeats and enhances PEV, presumably via a recruitment of protein partners, whereas MATH20 suppresses it. We show that D1 and MATH20 compete for binding to identical sites of SATIII repeats in vitro and that conditional MATH20 expression results in a displacement of D1 from pericentric heterochromatin in vivo. In the presence of intermediate levels of MATH20, we show that this displacement becomes selective for SATIII repeats. These results strongly suggest that the suppression of w(m4) PEV by MATH20 is due to a displacement of D1 from its preferred binding sites and provide additional support for a direct role of D1 in the assembly of AT-rich heterochromatin.

The AT-hook protein D1 is essential for Drosophila melanogaster development and is implicated in position-effect variegation

We have analyzed the expression pattern of the D1 gene and the localization of its product, the AT hook-bearing nonhistone chromosomal protein D1, during Drosophila melanogaster development. D1 mRNAs and protein are maternally contributed, and the protein localizes to discrete foci on the chromosomes of early embryos. These foci correspond to 1.672- and 1.688-g/cm(3) AT-rich satellite repeats found in the centromeric heterochromatin of the X and Y chromosomes and on chromosomes 3 and 4. D1 mRNA levels subsequently decrease throughout later development, followed by the accumulation of the D1 protein in adult gonads, where two distributions of D1 can be correlated to different states of gene activity. We show that the EP473 mutation, a P-element insertion upstream of D1 coding sequences, affects the expression of the D1 gene and results in an embryonic homozygous lethal phenotype correlated with the depletion of D1 protein during embryogenesis. Remarkably, decreased levels of D1 mRNA and protein in heterozygous flies lead to the suppression of position-effect variegation (PEV) of the white gene in the white-mottled (w(m4h)) X-chromosome inversion. Our results identify D1 as a DNA-binding protein of known sequence specificity implicated in PEV. D1 is the primary factor that binds the centromeric 1.688-g/cm(3) satellite repeats which are likely involved in white-mottled variegation. We propose that the AT-hook D1 protein nucleates heterochromatin assembly by recruiting specialized transcriptional repressors and/or proteins involved in chromosome condensation.

The HMG I proteins: dynamic roles in gene activation, development, and tumorigenesis

The high mobility group I, Y, and I-C proteins are low-molecular-weight, nonhistone chromosomal proteins that play a general role modulating gene expression during development and the immune response. Consistent with their role in early development, all three proteins are expressed at high levels during embryogenesis, and their expression is markedly diminished in differentiated cells. Exceptions to the general repression of these genes in adult tissues involve (1) A burst of synthesis of the HMG I protein during the immune response (during lymphocyte activation and preceding cytokine/adhesion molecule gene expression), (2) A constitutive expression of the HMG I and Y proteins in photoreceptor cells, and (3) Derepression of HMG I, Y, and often I-C expression in neoplastic cells. Work from several laboratories has now uncovered how these proteins participate in gene activation: (1) By altering the chromatin structure around an inducible gene-and thus influencing accessibility of the locus to regulatory proteins-(2) By facilitating the loading of transcription factors onto the promoters, and (3) By bridging adjacent transcription factors on a promoter via protein/protein interactions. Despite the similar structures and biochemical properties of the three proteins, the work has also provided clues to a division of labor between these proteins. HMG I and Y have demonstrable roles in enhanceosome formation, whereas HMG I-C has a specific role in adipogenesis. C-terminal truncations of HMG I-C and wild-type HMG Y appear to function in a manner analogous to oncogenes, as assessed by cellular transforation assays and transgenic mice. Future work should clearly define the similarities and differences in the biological roles of the three proteins, and should evolve to include attempts at pharmaceutical intervention in disease, based upon structural information concerning HMG I interactions with DNA and with regulatory proteins.

Mouse oocytes and preimplantation embryos bear the two sub-units of interferon-gamma receptor

Cytokines and growth factors play important roles in implantation and maintenance of pregnancy, but also during early development. Among them interferon-gamma (IFNgamma) is highly expressed by mammalian trophoblast cells during implantation and seems to be involved in some cases of pregnancy loss. In the present study we investigated the possible presence of IFNgamma receptors (IFNGR) on mouse oocytes and preimplantation embryos. The two receptor chains IFNgammaRalpha (IFNGR-1) and IFNgammaRbeta (IFNGR-2) have been detected by indirect immunofluorescence at the surface of mouse oocytes (in germinal vesicle and metaphase II stages), as well as at all stages of in vitro embryo development from the one-cell to blastocyst stage. IFNGR appeared to colocalize partly with ganglioside GM1 at the cell surface of oocytes and embryos, indicating a possible preferential localization of this receptor in "rafts" microdomains. This was analyzed in more detail using software developed in the laboratory. IFNgamma was found to bind to its receptor at all stages analyzed. RT-PCR and Southern blot experiments confirmed the presence of the transcriptionally regulated IFNGR-2 chain mRNA, in mouse oocytes and preimplantation embryos. These results show, for the first time, that mouse oocytes and preimplantation embryos bear a complete and theoretically functional IFNGR, suggesting that this cytokine could play a role during early development.

Molecular biology of HMGA proteins: hubs of nuclear function

Members of the HMGA (a.k.a. HMGI/Y) family of 'high mobility group' (HMG) proteins participate in a wide variety of nuclear processes ranging from chromosome and chromatin mechanics to acting as architectural transcription factors that regulate the expression of numerous genes in vivo. As a consequence, they function in the cell as highly connected 'nodes' of protein-DNA and protein-protein interactions that influence a diverse array of normal biological processes including growth, proliferation, differentiation and death. The HMGA proteins, likewise, participate in pathological processes by, for example, acting as regulators of viral gene transcription and by serving as host-supplied proteins that facilitate retroviral integration. HMGA genes are bona fide proto-oncogenes that promote tumor progression and metastasis when overexpressed in cells. High constitutive HMGA protein levels are among the most consistent feature observed in all types of cancers with increasing concentrations being correlated with increasing malignancy. The intrinsic attributes that endow the HMGA proteins with these remarkable abilities are a combination of structural, biochemical and biological characteristics that are unique to these proteins. HMGA proteins have little, if any, secondary structure while free in solution but undergo disordered-to-ordered structural transitions when bound to substrates such as DNA or other proteins. Each protein contains three copies of a conserved DNA-binding peptide motif called the 'AT-hook' that preferentially binds to the minor groove of stretches of AT-rich sequence. In vivo HMGA proteins specifically interact with a large number of other proteins, most of which are transcription factors. They are also subject to many types of in vivo biochemical modifications that markedly influence their ability to interact with DNA substrates, other proteins and chromatin. And, most importantly, both the transcription of HMGA genes and the biochemical modifications of HMGA proteins are direct downstream targets of numerous signal transduction pathways making them exquisitely responsive to various environmental influences. This review covers recent advances that have contributed to our understanding of how this constellation of structural and biological features allows the HMGA proteins to serve as central 'hubs' of nuclear function.

The expression of HMGA genes is regulated by their 3'UTR

Many benign mesenchymal tumors are characterized by chromosomal abnormalities of the regions 12q15 or 6p21.3 leading to aberrant expression of either HMGA2 (formerly HMGIC) or HMGA1 (formerly HMGIY). The proteins of both genes belong to the HMGA (formerly HMGI(Y)) family of architectural transcription factors. As a rule, aberrant HMGA transcripts found in a variety of benign tumors have intact coding regions at least for the DNA binding domains with a truncation of their 3' untranslated regions. Adding this to the finding that an altered HMGA protein level is not always correlated with an increased amount of corresponding mRNA indicates a posttranscriptional expression control mediated by regulatory elements within the 3'UTR. To check if HMGA expression is under control of such elements we performed luciferase assays with several HMGA2 and HMGA1 3'UTRs of different length. Experiments showed that an up to 12-fold increase in luciferase activity is obtained by the truncation of the 3'UTRs suggesting that the expression of HMGA2 and HMGA1 is controlled by negatively acting regulatory elements within their 3'UTR. Chromosomal aberrations affecting the HMGA genes may therefore influence their expression by an altered stability of the truncated transcripts as a result of the cytogenetic aberrations.

Regulation of Zygotic Gene Activation in the Preimplantation Mouse Embryo: Global Activation and Repression of Gene Expression1

Superimposed on the activation of the embryonic genome in the preimplantation mouse embryo is the formation of a transcriptionally repressive state during the two-cell stage. This repression appears mediated at the level of chromatin structure, because it is reversed by inducing histone hyperacetylation or inhibiting the second round of DNA replication. We report that of more than 200 amplicons analyzed by mRNA differential display, about 45% of them are repressed between the two-cell and four-cell stages. This repression is scored as either a decrease in amplicon expression that occurs between the two-cell and four-cell stages or on the ability of either trichostatin A (an inhibitor of histone deacetylases) or aphidicolin (an inhibitor of replicative DNA polymerases) to increase the level of amplicon expression. Results of this study also indicate that about 16% of the amplicons analyzed likely are novel genes whose sequence doesn't correspond to sequences in the current databases, whereas about 20% of the sequences expressed during this transition likely are repetitive sequences. Lastly, inducing histone hyperacetylation in the two-cell embryos inhibits cleavage to the four-cell stage. These results suggest that genome activation is global and relatively promiscuous and that a function of the transcriptionally repressive state is to dictate the appropriate profile of gene expression that is compatible with further development.

HMGI/Y proteins: flexible regulators of transcription and chromatin structure

The mammalian HMGI/Y (HMGA) non-histone proteins participate in a wide variety of cellular processes including regulation of inducible gene transcription, integration of retroviruses into chromosomes and the induction of neoplastic transformation and promotion of metastatic progression of cancer cells. Recent advances have contributed greatly to our understanding of how the HMGI/Y proteins participate in the molecular mechanisms underlying these biological events. All members of the HMGI/Y family of 'high mobility group' proteins are characterized by the presence of multiple copies of a conserved DNA-binding peptide motif called the 'AT hook' that preferentially binds to the narrow minor groove of stretches of AT-rich sequence. The mammalian HMGI/Y proteins have little, if any, secondary structure in solution but assume distinct conformations when bound to substrates such as DNA or other proteins. Their intrinsic flexibility allows the HMGI/Y proteins to participate in specific protein-DNA and protein-protein interactions that induce both structural changes in chromatin substrates and the formation of stereospecific complexes called 'enhanceosomes' on the promoter/enhancer regions of genes whose transcription they regulate. The formation of such regulatory complexes is characterized by reciprocal inductions of conformational changes in both the HMGI/Y proteins themselves and in their interacting substrates. It may well be that the inherent flexibility of the HMGI/Y proteins, combined with their ability to undergo reversible disordered-to-ordered structural transitions, has been a significant factor in the evolutionary selection of these proteins for their functional role(s) in cells.

Developmental system drift and flexibility in evolutionary trajectories

The comparative analysis of homologous characters is a staple of evolutionary developmental biology and often involves extrapolating from experimental data in model organisms to infer developmental events in non-model organisms. In order to determine the general importance of data obtained in model organisms, it is critical to know how often and to what degree similar phenotypes expressed in different taxa are formed by divergent developmental processes. Both comparative studies of distantly related species and genetic analysis of closely related species indicate that many characters known to be homologous between taxa have diverged in their morphogenetic or gene regulatory underpinnings. This process, which we call "developmental system drift" (DSD), is apparently ubiquitous and has significant implications for the flexibility of developmental evolution of both conserved and evolving characters. Current data on the population genetics and molecular mechanisms of DSD illustrate how the details of developmental processes are constantly changing within evolutionary lineages, indicating that developmental systems may possess a great deal of plasticity in their responses to natural selection.

High-mobility group proteins 14 and 17 maintain the timing of early embryonic development in the mouse

The high-mobility group (HMG) proteins 14 and 17 are abundant chromosomal proteins that bind to nucleosomes and enhance transcription. We report that both mRNA species and both proteins are present throughout oogenesis and preimplantation development of the mouse. When antisense oligonucleotides targeting each mRNA species are injected into one-cell embryos, the proteins become depleted at the two- and four-cell stages and reaccumulate at the eight-cell stage. One-cell embryos injected with antisense oligonucleotides targeting both HMG-14 and HMG-17 cleave to the two-cell stage. Subsequent cleavages, however, are delayed compared with control-injected embryos. Nevertheless, these embryos ultimately reach the blastocyst stage. Similarly, injection into the nuclei of two-cell embryos of a peptide corresponding to the common nucleosome-binding domain of HMG-14 and HMG-17 delays progression to the four-cell stage. Furthermore, both RNA and protein synthesis is transiently reduced in antisense-injected embryos compared with injected controls. These results identify HMG-14 and HMG-17 as constitutive components of mouse oocyte and embryonic chromatin and establish a link between the structure of embryonic chromatin and the normal progression of embryonic development.

Structural changes induced by binding of the high-mobility group I protein to a mouse satellite DNA sequence

Using spectroscopic methods, we have studied the structural changes induced in both protein and DNA upon binding of the High-Mobility Group I (HMG-I) protein to a 21-bp sequence derived from mouse satellite DNA. We show that these structural changes depend on the stoichiometry of the protein/DNA complexes formed, as determined by Job plots derived from experiments using pyrene-labeled duplexes. Circular dichroism and melting temperature experiments extended in the far ultraviolet range show that while native HMG-I is mainly random coiled in solution, it adopts a beta-turn conformation upon forming a 1:1 complex in which the protein first binds to one of two dA.dT stretches present in the duplex. HMG-I structure in the 1:1 complex is dependent on the sequence of its DNA target. A 3:1 HMG-I/DNA complex can also form and is characterized by a small increase in the DNA natural bend and/or compaction coupled to a change in the protein conformation, as determined from fluorescence resonance energy transfer (FRET) experiments. In addition, a peptide corresponding to an extended DNA-binding domain of HMG-I induces an ordered condensation of DNA duplexes. Based on the constraints derived from pyrene excimer measurements, we present a model of these nucleated structures. Our results illustrate an extreme case of protein structure induced by DNA conformation that may bear on the evolutionary conservation of the DNA-binding motifs of HMG-I. We discuss the functional relevance of the structural flexibility of HMG-I associated with the nature of its DNA targets and the implications of the binding stoichiometry for several aspects of chromatin structure and gene regulation.