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PubMed2004

Beyond the double helix: writing and reading the histone code.

Chromatin is the physiological carrier of not only genetic information, encoded in the DNA, but also of epigenetic information including DNA methylation and histone modifications. As such histone modifications are involved in many aspects of nuclear processes including gene regulation and chromosome segregation. Recently, a 'histone code' hypothesis was put forward to explain how patterns of histone modification may function in downstream processes. In support of the 'histone code' hypothesis, we found in vivo and in vitro evidence that effector proteins, HP1 (heterochromatin protein 1) and Pc (Polycomb) can discriminate and 'read' histone methylation marks on K9 and K27, respectively. Moreover, we propose a 'binary switch' model and suggest that binding and release of effector proteins to their cognate sites can be regulated by modifications on adjacent or nearby residues. Thus, combinations of adjacent histone modifications would function differently from singular modification, and static modifications (e.g. Lys methylation) may well be regulated by dynamic modifications (e.g. phosphorylation). Finally, we describe a novel histone phosphorylation event linking the function of Mst1 kinase and H2B Ser14 phosphorylation with apoptotic chromatin condensation in vertebrates. As this modification is not found during mitotic chromosome condensation, these findings suggest the intriguing possibility that a unique 'death' mark exists for chromatin condensation during apoptosis.

Acetylation↗
PubMed1983

Role of the esc+ gene product in ensuring the selective expression of segment-specific homeotic genes in Drosophila.

The product of the extra sex combs+ (esc+) gene is required during embryogenesis for the correct determination of segments in Drosophila. If this product is absent, most segments develop like the normal eighth abdominal segment. Here, I extend previous results (Struhl, 1981a) showing that this phenotype results in large part from indiscriminate expression of the bithorax-complex genes which are normally active only in particular segments of the thorax and abdomen. In addition, I test whether the esc+ gene product is required for the correct expression of other homeotic genes. First, I have examined two genes of the Antennapedia-complex (Sex combs reduced+ and Antennapedia+): I find that both genes are normally required in only some of the body segments, but that in the absence of the esc+ gene product, both appear to function adventitiously in other segments. Second, comparing esc+ and esc- embryos lacking both these genes as well as the bithorax-complex, I find that additional homeotic genes (possibly those normally involved in specifying head segments) appear to be expressed indiscriminately when the esc+ gene product is absent. Finally, I present evidence that the products of the esc+ gene and the Polycomb+ gene (a second gene required for the correct regulation of the bithorax-complex) act independently. On the basis of these results, I propose a tentative outline of the roles and realms of action of all of these genes.

Animals↗
PubMed1982

Control of body segment differentiation in Drosophila by the bithorax gene complex.

The bithorax complex is a gene cluster whose function is to regulate still other genes in such a way that each segment of the body commencing with the second thoracic segment and proceeding posteriorly, develops a unique pattern of structures. Numerous cis-regulatory regions have been identified within the complex and are believed to bind to repressor-like substances elaborated by the wild-type alleles of at least two major trans-regulatory genes, Polycomb and extra sex combs. The more proximal is a gene in the complex (with the exception of postbithorax) the more likely it is to be derepressed; the more posterior is a segment in the organism, the greater is the number of BX-C genes that become derepressed in that segment. A gradient in repressor substance(s) and a gradient in affinity of the cis-regulatory regions for repressor can account in a formal sense for the regulation of the BX-C genes themselves.

Animals↗
PubMed1996

Genetic analysis of genomic methylation patterns in plants and mammals.

While it is now accepted that methylation of cytosine residues plays a role in various epigenetic phenomena in mammals and flowering plants, the involvement of methylation patterns in the regulation of normal development has remained a controversial and essentially untested issue in the 20 years since such a role was first proposed. Antisense suppression of a DNA methyltransferase in Arabidopsis and characterization of methylation-defective mutants of Arabidopsis have shown that perturbations of methylation patterns disrupt the development of plants, and targeted mutation of the murine gene that encodes the one known from of DNA methyltransferase has shown that methylation is required for cellular differentiation, genomic imprinting, and X chromosome inactivation in mammals. Ectopic expression of homeotic genes and homeotic transformations of floral organs in methylation-defective plants suggest that (in plants and perhaps mammals) heritable methylation patterns reinforce and may have supplanted heritable gene control mediated by chromosomal proteins of the Polycomb and trithorax groups. It is also possible that the developmental abnormalities are the result of ectopic gene expression caused by activation of transcription from nearby parasitic sequence elements that are normally repressed by methylation. Application of modern methods of genetic analysis promises to give definite answers to long-standing questions as to the roles and significance of genomic methylation patterns in normal development and genome defense.

Animals↗
PubMed1996

Chromatin and gene regulation at the onset of embryonic development.

Major transitions in chromosome and chromatin structure occur during development. Recent genetic and biochemical experiments demonstrate that these alterations in genome organization make significant contributions to establishing and maintaining states of differential transcriptional activity. Developmentally regulated changes in histone variants have a causal role in determining patterns of gene activity, directing the repression of specific eukaryotic genes. Chromosomal proteins such as Polycomb stabilize and maintain transcriptionally repressed states. Proteins regulating mitotic chromosome condensation have a role in determining the overall transcriptional activity of a chromosome. In this review, I place the developmental roles of these chromosomal constituents in a structural and functional context. Considerable insight now exists into the molecular mechanisms regulating chromosomal activity during development. Chromosomal architecture is emerging as a key controlling influence in the developmental regulation of gene expression. Recent genetic experiments using Caenorhabditis elegans, Drosophila melanogaster and the mouse have provided clear evidence for the functional differentiation of chromosomal structures during development. Chromosomes are visualized as highly specialized entities, within which the activity of particular domains is largely determined by defined structural proteins. At a more local level, the mechanisms regulating gene transcription during early embryogenesis in Xenopus and the mouse have been found to be dependent on the biochemical composition of individual nucleosomes. Thus, variation in the type and modification of chromosomal and chromatin structural proteins provides a dominant means of controlling the transcriptional activity of individual genes, individual chromosomal domains and of entire chromosomes. The focus of this review is to summarize these recent advances and to discuss their implications for developmental biology.

Animals↗
PubMed1998

Translocations, fusion genes, and acute leukemia.

Genes involved in chromosomal translocations, associated with the formation of fusion proteins in leukemia, are modular in nature and regulatory in function. It is likely that they are involved in the initiation and maintenance of normal hematopoiesis. A conceptual model is proposed by which disruption of these different genes leads to the development of acute leukemia. Central to this model is the functional interaction between the mammalian trithorax and polycomb group protein complexes. Many of the genes identified in leukemia-associated translocations are likely upstream regulators, co-participators or downstream targets of these complexes. In the natural state, these proteins interact with each other to form multimeric higher-order structures, which sequentially regulate the development of the normal hematopoietic state, either through HOX gene expression or other less defined pathways. The novel interaction domains acquired by the chimaeric fusion products subvert normal cellular control mechanisms, which result in both a failure of cell maturation and activation of anti-apoptotic pathways. The mechanisms by which these translocation products are able to affect these processes are thought to lie at the level of chromatin-mediated transcriptional activation and/or repression. The stimuli for proliferation and development of clinically overt disease may require subsequent mutations in more than one oncogene or tumor suppressor gene, or both. A more comprehensive catalogue of mutation events in malignant cells is therefore required to understand the key regulatory networks that serve to maintain multipotentiality and in particular the modifications which initiate and coordinate commitment in differentiating hematopoietic cells. We propose a model in which common pathways for leukemogenesis lie along the cell cycle control of chromatin structure in terms of transcriptional activation or repression. A clearer understanding of this cascade will provide opportunities for the design and construction of novel biological agents that are able to restore normal regulatory mechanisms.

Acute Disease↗
PubMed1998

Specific interaction between the XNP/ATR-X gene product and the SET domain of the human EZH2 protein.

Mutations in the XNP gene result in different inherited disorders, including the ATR-X syndrome which is characterized by mental retardation (MR) associated with alpha-thalaessemia. Amino acid sequence analysis revealed that the XNP protein is a new member of the SNF2-like family, which comprises numerous members involved in a broad range of biological functions: transcriptional regulation, DNA repair and chromosome segregation. Since experiments on fibroblasts from ATR-X patients have provided no evidence for either a DNA repair defect or abnormal chromosome breakage or segregation, it seems more likely that the XNP protein is somehow involved in regulation of gene expression. Recent genetic and biochemical studies have led to the emerging concept that SNF2-like proteins are components of a large protein complex which may exert its functions by modulating chromatin structure. To investigate whether XNP could mediate the activity of gene-specific activators through chromatin remodelling, we performed a yeast two-hybrid analysis using XNP and several human heterochromatin-associated proteins. We found a specific interaction between the XNP and the EZH2 proteins. In light of these observations, we discuss how the XNP protein may regulate gene transcription at the chromatin level.

Animals↗
PubMed1998

Structure and function in the nucleus.

Current evidence suggests that the nucleus has a distinct substructure, albeit one that is dynamic rather than a rigid framework. Viral infection, oncogene expression, and inherited human disorders can each cause profound and specific changes in nuclear organization. This review summarizes recent progress in understanding nuclear organization, highlighting in particular the dynamic aspects of nuclear structure.

Animals↗
PubMed2005

The many faces of SAM.

Protein-protein interactions are essential for the assembly, regulation, and localization of functional protein complexes in the cell. SAM domains are among the most abundant protein-protein interaction motifs in organisms from yeast to humans. Although SAM domains adopt similar folds, they are remarkably versatile in their binding properties. Some identical SAM domains can interact with each other to form homodimers or polymers. In other cases, SAM domains can bind to other related SAM domains, to non-SAM domain-containing proteins, and even to RNA. Such versatility earns them functional roles in myriad biological processes, from signal transduction to transcriptional and translational regulation. In this review, we describe the structural basis of SAM domain interactions and highlight their roles in the scaffolding of protein complexes in normal and pathological processes.

Animals↗
PubMed1997

The product of the murine homolog of the Drosophila extra sex combs gene displays transcriptional repressor activity.

The heterogeneous nuclear ribonucleoprotein K protein represents a novel class of proteins that may act as docking platforms that orchestrate cross-talk among molecules involved in signal transduction and gene expression. Using a fragment of K protein as bait in the yeast two-hybrid screen, we isolated a cDNA that encodes a protein whose primary structure has extensive similarity to the Drosophila melanogaster extra sex combs (esc) gene product, Esc, a putative silencer of homeotic genes. The cDNA that we isolated is identical to the cDNA of the recently positionally cloned mouse embryonic ectoderm development gene, eed. Like Esc, Eed contains six WD-40 repeats in the C-terminal half of the protein and is thought to repress homeotic gene expression during mouse embryogenesis. Eed binds to K protein through a domain in its N terminus, but interestingly, this domain is not found in the Drosophila Esc. Gal4-Eed fusion protein represses transcription of a reporter gene driven by a promoter that contains Gal4-binding DNA elements. Eed also represses transcription when recruited to a target promoter by Gal4-K protein. Point mutations within the eed gene that are responsible for severe embryonic development abnormalities abolished the transcriptional repressor activity of Eed. Results of this study suggest that Eed-restricted homeotic gene expression during embryogenesis reflects the action of Eed as a transcriptional repressor. The Eed-mediated transcriptional effects are likely to reflect the interaction of Eed with multiple molecular partners, including K protein.

Amino Acid Sequence↗
PubMed2004

Nucleotide variation of seven genes in Drosophila kikkawai.

We examined levels and patterns of nucleotide variation in 21 strains of Drosophila kikkawai from Miyako island, Japan for the partial regions of the following seven nuclear genes: Adh, Ddc, esc, ksr, Pgi, su(f), and Tpi. The nucleotide variation at total sites (pi(t)) ranged from 0.0013 in the ksr, to 0.0173 in the Adh. The nucleotide divergence at total sites (K(t)) between D. kikkawai and D. lini ranged from 0.0286 in the Tpi to 0.0687 in the su(f). The levels of nucleotide polymorphism and divergence were heterogeneous among the investigated gene regions. The HKA test, which tests imbalance between the intra and interspecific nucleotide variation, showed that the intraspecific nucleotide variation in the Pgi region was much lower than the interspecific variation, while intraspecific variation in the Tpi region was only slightly lower than interspecific variation. The MK test showed an excess of low frequency replacement polymorphic changes in the Adh region, suggesting that most replacement mutations are deleterious. Fay and Wu's test detected an excess of newly arisen variants in the Ddc region. In total, four of the seven gene regions showed significant deviation from the neutrality.

Alcohol Dehydrogenase↗
PubMed2000

Mammalian chromodomain proteins: their role in genome organisation and expression.

The chromodomain is a highly conserved sequence motif that has been identified in a variety of animal and plant species. In mammals, chromodomain proteins appear to be either structural components of large macromolecular chromatin complexes or proteins involved in remodelling chromatin structure. Recent work has suggested that apart from a role in regulating gene activity, chromodomain proteins may also play roles in genome organisation. This article reviews progress made in characterising mammalian chromodomain proteins and emphasises their emerging role in the regulation of gene expression and genome organisation. BioEssays 22:124-137, 2000.

Amino Acid Sequence↗
PubMed2000

Pc-G/trx-G and the SWI/SNF connection: developmental gene regulation through chromatin remodeling.

Pc-G and trx-G genes are responsible for maintenance of transcriptional regulation and provide a cellular memory mechanism throughout development. Studies in fly, yeast, mouse, and human have implicated modulation of higher-order chromatin structure as an important component in this process. Specifically, connections between SWI/SNF complexes and trx-G genes have provided a mechanistic link between chromatin remodeling and transcriptional regulation. Here we discuss recent genetic and biochemical data that has shed light on the molecular mechanisms and pathways associated with Pc-G and trx-G function in developmental processes such as cell cycle control and hematopoiesis. genesis 26:189-197, 2000.

Animals↗