Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression最新文献

Modification of the histone proteins that form the core around which chromosomal DNA is looped has profound epigenetic effects on the accessibility of the associated DNA for transcription, replication and repair. The SET domain is now recognized as generally having methyltransferase activity targeted to specific lysine residues of histone H3 or H4. There is considerable sequence conservation within the SET domain and within its flanking regions. Previous reviews have shown that SET proteins from Arabidopsis and maize fall into five classes according to their sequence and domain architectures. These classes generally reflect specificity for a particular substrate. SET proteins from rice were found to fall into similar groupings, strengthening the merit of the approach taken. Two additional classes, VI and VII, were established that include proteins with truncated/ interrupted SET domains. Diverse mechanisms are involved in shaping the function and regulation of SET proteins. These include protein–protein interactions through both intra- and inter-molecular associations that are important in plant developmental processes, such as flowering time control and embryogenesis. Alternative splicing that can result in the generation of two to several different transcript isoforms is now known to be widespread. An exciting and tantalizing question is whether, or how, this alternative splicing affects gene function. For example, it is conceivable that one isoform may debilitate methyltransferase function whereas the other may enhance it, providing an opportunity for differential regulation. The review concludes with the speculation that modulation of SET protein function is mediated by antisense or sense–antisense RNA.

The transition from vegetative to reproductive development is a highly regulated process that, in many plant species, is sensitive to environmental cues that provide seasonal information to initiate flowering during optimal times of the year. One environmental cue is the cold of winter. Winter annuals and biennials typically require prolonged exposure to the cold of winter to flower rapidly in the spring. This process by which flowering is promoted by cold exposure is known as vernalization. The winter-annual habit of Arabidopsis thaliana is established by the ability of FRIGIDA to promote high levels of expression of the potent floral repressor FLOWERING LOCUS C (FLC). In Arabidopsis, vernalization results in the silencing of FLC in a mitotically stable (i.e., epigenetic) manner that is maintained for the remainder of the plant life cycle. The repressed “off” state of FLC has features characteristic of facultative heterochromatin. Upon passing to the next generation, the “off” state of FLC is reset to the “on” state. The environmental induction and mitotic stability of vernalization-mediated FLC repression as well as the subsequent resetting in the next generation provides a system for studying several aspects of epigenetic control of gene expression.

RNA-directed DNA methylation, which is one of several RNAi-mediated pathways in the nucleus, has been highly elaborated in the plant kingdom. RNA-directed DNA methylation requires for the most part conventional DNA methyltransferases, histone modifying enzymes and RNAi proteins; however, several novel, plant-specific proteins that are essential for this process have been identified recently. DRD1 (defective in RNA-directed DNA methylation) is a putative SWI2/SNF2-like chromatin remodelling protein; DRD2 and DRD3 (renamed NRPD2a and NRPD1b, respectively) are subunits of Pol IVb, a putative RNA polymerase found only in plants. Interestingly, DRD1 and Pol IVb appear to be required not only for RNA-directed de novo methylation, but also for full erasure of methylation when the RNA trigger is withdrawn. These proteins thus have the potential to facilitate dynamic regulation of DNA methylation. Prominent targets of RNA-directed DNA methylation in the Arabidopsis thaliana genome include retrotransposon long terminal repeats (LTRs), which have bidirectional promoter/enhancer activities, and other types of intergenic transposons and repeats. Intergenic solitary LTRs that are targeted for reversible methylation by the DRD1/Pol IVb pathway can potentially act as switches or rheostats for neighboring plant genes. The resulting alterations in gene expression patterns may promote physiological flexibility and adaptation to the environment.

Cytosine bases are extensively methylated in the DNA of plant genomes. DNA methylation has been implicated in the silencing of transposable elements and genes, and loss of methylation can have severe consequences for the organism. The recent methylation profiling of the entire Arabidopsis genome has provided insight into the extent of DNA methylation and its functions in silencing and gene transcription. Patterns of DNA methylation are faithfully maintained across generations, but some changes in DNA methylation are observed in terminally differentiated tissues. Demethylation by a DNA glycosylase is required for the expression of imprinted genes in the endosperm and de novo methylation might play a role in the selective silencing of certain self-incompatibility alleles in the tapetum. Because DNA methylation patterns are faithfully inherited, changes in DNA methylation that arise somatically during the plant life cycle have the possibility of being propagated. Therefore, epimutations might be an important source of variation during plant evolution.

Citrus are natural hosts of several viroids, which are plant pathogens composed exclusively of a non-protein-coding, small single-stranded circular RNA that is able to replicate autonomously in susceptible hosts. They are responsible for symptoms such as stunting, leaf epinasty, and chlorosis. Citrus viroid III (CVd-III) has been long regarded as a possible dwarfing agent of citrus grafted on trifoliate orange and its hybrids. To investigate molecular mechanisms involved in pathogenesis, the messenger RNA (mRNA) differential display technique was here applied to identify genes whose transcription was significantly altered in leaves of Etrog citron (Citrus medica) infected by CVd-III (variant b). Of eighteen genes identified, thirteen were up-regulated by viroid infection, while five were down-regulated. Except for two genes that encode proteins of unknown function, the remaining genes are mainly involved in plant defence/stress responses, signal transduction, amino acid transport, and cell wall structure. Among the up-regulated genes, it is noteworthy a suppressor of RNA silencing that might be involved in viroid and virus pathogenicity. The functions of these genes are discussed.

The tumor suppressor p53 regulates diverse biological processes primarily via activation of downstream target genes. Even though many p53 target genes have been described, the precise mechanisms of p53 biological actions are uncertain. In previous work we identified by microarray analysis a candidate p53 target gene, FLJ11259/DRAM. In this report we have identified three uncharacterized human proteins with sequence homology to FLJ11259, suggesting that FLJ11259 is a member of a novel family of proteins with six transmembrane domains. Several lines of investigation confirm FLJ11259 is a direct p53 target gene. p53 siRNA prevented cisplatin-mediated up-regulation of FLJ11259 in NT2/D1 cells. Likewise in HCT116 p53+/+ cells and MCF10A cells, FLJ11259 is induced by cisplatin treatment but to a much lesser extent in isogenic p53-suppressed cells. A functional p53 response element was identified 22.3 kb upstream of the first coding exon of FLJ11259 and is shown to be active in reporter assays. In addition, chromatin immunoprecipitation assays indicate that p53 binds directly to this element in vivo and that binding is enhanced following cisplatin treatment. Confocal microscopy showed that an FLJ–GFP fusion protein localizes mainly in a punctate pattern in the cytoplasm. Overexpression studies in Cos-7, Saos2, and NT2/D1 cells suggest that FLJ11259 is associated with increased clonal survival. In summary, we have identified FLJ11259/DRAM as a p53-inducible member of a novel family of transmembrane proteins. FLJ11259/DRAM may be an important modulator of p53 responses in diverse tumor types.

E2F and FOXO transcription factors both play a role in neuronal apoptosis. In addition, both E2F-induced apoptosis and FOXO function are inhibited by the kinase Akt. We therefore tested whether FOXO is downstream of E2F-1 during neuronal apoptosis. We found that expression of endogenous FOXO1 and FOXO3a is induced by E2F-1. The presence of putative E2F binding sites in the promoters of both genes suggested that FOXO genes are direct targets of E2F-1. Indeed, a 4-hydroxytamoxifen activated E2F-1-ER fusion protein induced FOXO expression in the presence of cycloheximide. Moreover, E2F-1 activated the FOXO1 promoter in transient reporter assays, and E2F-1-ER as well as endogenous E2F bound to the FOXO1 promoter in vivo. Yet, E2F-1-mediated apoptosis of differentiated PC12 cells after withdrawal of NGF was not accompanied by changes in FOXO expression, indicating that no transcriptional induction of FOXO occurs during E2F-1-dependent neuronal apoptosis. In summary, our data identify E2F-1 as a first transcription factor regulating FOXO expression, providing a link between E2F and FOXO proteins in the control of cell fate.

The insulin receptor (InR) signaling pathway is largely conserved in metazoans and it is required for normal growth and development in Drosophila. Despite the importance of this pathway in regulating growth, development and metabolism in Drosophila, little is known about how dInR expression is controlled in flies. Here we report the characterization of the dInR gene promoter and the analysis of its expression during embryo development. Drosophila InR gene has three promoters spanning 40 kb in the genome. These promoters direct the expression of three distinct mRNA transcripts that share common exons downstream of the initiator codon ATG but have different 5′UTRs. All three promoters are differentially regulated, spatially and temporally, contributing to a very complex pattern of expression in the developing embryo. Our results indicate that dInR expression in Drosophila displays an intricate pattern of regulation that assures an adequate control of growth, development and metabolism.

A cDNA for the gene ZFP182, encoding a C2H2-type zinc finger protein, was cloned from rice by RT-PCR. ZFP182 codes an 18.2 kDa protein with two C2H2-type zinc finger motifs, one nuclear localization signal and one Leu-rich domain. The DLN-box/EAR-motif, which exists in most of plant C2H2-type zinc finger proteins, does not exist in ZFP182. The expression analysis showed that ZFP182 gene was constitutively expressed in leaves, culms, roots and spikes at the adult rice plants, and markedly induced in the seedlings by cold (4 °C), 150 mM NaCl and 0.1 mM ABA treatments. The approximate 1.4 kb promoter region of ZFP182 gene was fused into GUS reporter gene and transformed into tobacco. The histochemical analysis revealed that GUS expression could not be detected in transformed tobacco seedlings under normal conditions, but strongly observed in tobacco leaf discs and the vascular tissue of roots treated with NaCl or KCl. Expression of ZFP182 in transgenic tobacco and overexpression in rice increased plant tolerance to salt stress. These results demonstrated that ZFP182 might be involved in plant responses to salt stress.