Current Genomics - Volume 5, Issue 3, 2004

Nonsense-mediated mRNA decay (NMD) functions to ensure quality gene expression by degrading mRNAs that prematurely terminate translation. By so doing, it eliminates the production of potentially deleterious truncated proteins. NMD also degrades certain naturally occurring transcripts as a means of achieving proper levels of gene expression. With the exception of prokaryotes, NMD typifies all organisms that have been examined. As an example of its importance, NMD is required for the viability of mammalian blastocysts in culture as well as mammalian embryos in utero. The repertoire of factors that mediate NMD is larger in C. elegans, D. melanogaster, mammalian cells and, possibly, A. thaliana, than it is in S. cerevisiae and S. pombe. NMD requires not only a premature termination codon but also a downstream element. Whereas this element in S. cerevisiae, S. pombe, C. elegans, D. melanogaster and plants is debatably either a short cis-acting mRNA sequence or an abnormal 3' untranslated region, it is a splicing-generated exon junction complex of proteins in mammalian cells. In fact, NMD may have provided a selective pressure for where introns colonize within mammalian genes. There also appear to be differences among different eukaryotes as to whether NMD is restricted to newly synthesized mRNA or can also target steady-state mRNA. In summary, despite the conservation of NMD in eukaryotes, different mechanisms have evolved to define those premature termination codons that elicit NMD.

The notion that protein-coding genes are the only biologically significant moieties in the genome is revolutionarized by the discovery of non-coding RNAs. Among them is a group of small non-coding RNAs termed microRNAs (miRNAs) that has recently been brought to the limelight. Their presence in the genome was only realized after the identification of their founders lin-4 and let-7 in C. elegans through genetic screens. To date, several hundreds of microRNAs have been identified. They are single-stranded RNA molecules of ∼21-22 nucleotides long, excised from precursors of ∼70 nucleotides predicted in silico to from imperfect stem-loop structures. Many of these miRNAs are evolutionarily conserved, implicating important biological functions. Emerging data points to an important role of these tiny RNA molecules in regulating gene expression of target RNAs by at least two post-transcriptional mechanisms: binding to imperfect complementary sequence of the 3' untranslated region (3'UTR) and repressing translation; and endonucleolytic cleavage by a double-stranded RNA-mediated interference (RNAi) mechanism through base-pairing with perfect or near-perfect complementary sequence. Studies in several miRNAs in plants and animals illustrate that these small riboregulators can play critical roles in developmental timing and spatial control of cell fate decisions, cell proliferation, apoptosis, cell differentiation and cell metabolism. Developmental defects and tumorigenesis can be a consequence of abnormal expression of miRNAs. This review discusses the biological functions, mechanisms of action, biogenesis and regulation of miRNAs, as well as identification of their target genes, highlighting the potential diversity of this novel class of gene regulators.

Forkhead box (FOX) proteins are modulator proteins that belong to a large transcription factor family, characterized by specific functions such as DNA binding, trans-activation or trans-repression. FOX DNA-binding domains, composed of evolutionarily well-conserved 100 amino acids essential for DNA recognition, a prerequisite for transcription initiation. In eukaryotic cells, FOX proteins play essential roles in a wide range of cellular and developmental processes. Recent experiments indicate that several FOX genes are mutated in ocular diseases. Ocular tissues including the lashes, eyelids, cornea, iris and lens, are affected as a result of mutations in FOXC1, FOXC2, FOXE3, FOXL2 and FOXN4. Moreover, alterations in Foxg1 and Foxd1, new emerging FOX genes, can compromise a proper projection of visual information to the brain. In addition to their role in different organ development, FOX proteins are also involved in cell cycle regulation and in signal transduction by interacting with key molecules in different pathways. This review will focus on the FOX genes directly related to the developmental genetic disorders of the eye.

Cells often respond to viral infection by activating a cellular suicide process, limiting viral replicative potential and hence minimising the spread of the infection. This cellular self-destruction, termed apoptosis, occurs in a tightly regulated, morphologically and biochemically defined manner. To counter this host response to infection, some viruses have evolved molecular strategies to evade apoptosis by encoding proteins that inhibit components of the host's apoptotic machinery. The first identified member of the p35 family, encoded by an insect virus genome, was cloned by virtue of its ability to inhibit insect cell death induced by viral infection. Many insect viruses carry p35 genes and numerous studies have indicated that p35 proteins can suppress a wide variety of cell death stimuli in cells of evolutionarily divergent organisms. A second member of the p35 family, p49, has also recently been cloned and characterised. Like p35, p49 was originally isolated as an inhibitor of infection mediated insect cell death but can also suppress other apoptotic stimuli. Members of the p35 family suppress apoptosis by inhibiting caspases, a family of cysteine proteases that constitute the effector arm of cell death pathways, through a substrate-inhibitor mechanism. This article reviews the anti-apoptotic capacities of members of the p35 family and the mechanism of action underlying their pro-survival activity. Insights into the molecular regulation of apoptosis gained through experimental approaches exploiting p35 family members are also discussed.

Global or selective alterations in gene expression patterns and / or post-translational modifications in protein profiles underlie the genesis of potentially all physiological or pathological processes. Unraveling the complexities of these events requires in-depth analysis of intracellular changes at the molecular level. The present review describes some of the techniques employed to identify novel genes, to determine changes in global gene expression patterns and to evaluate qualitative and quantitative changes at the level of encoded proteins. The successful application of these approaches has revolutionized our knowledge and understanding of many fatal diseases and is also facilitating the development of novel and specific therapeutic modalities for improving treatment.

The oxidation of catechol metabolites (2-OH-E1 / 2 / 3 and 4-OH-E1 / 2 / 3) of the endogenous estrogen, i.e. estrone (E1), 17 beta-estradiol (E2), estriol (E3), gives rise to corresponding estrogen-2,3-quinone (E-2,3-Q) and estrogen-3,4- quinone (E-3,4-Q). These reactive estrogen metabolites form covalent adducts with DNA and quinone, and semi-quinone forms of catechol estrogens -induced DNA adducts are found in various target tissues of cancer. Catecholestrogen through redox cycling produce free radicals that also generate various forms of free radical-induced DNA damage. Interaction of estrogen-induced oxidants and estrogen metabolites with DNA has been shown to generate mutations in genes. Hypermethylation at CpG sites in specific regions of the genome coupled with estrogen-induced oxidative damage at CpG sites, predominantly in the hypermethylated regions, could also cause alterations in the genome of cells of estrogen target organs that lead to mutation of genes. Increasing evidence shows that estrogen through oxidative stress and / or its metabolic products induce genetic alteration affecting both the structural as well as function of the genes. Presence of multiple forms of genetic alterations such as chromosomal aberrations, gene amplifications, DNA sequence variations, and DNA microsatellite instability in estrogen-related cancers and induction of similar genetic events by estrogen both in vivo and in vitro indicate that genetic alterations play an important role in estrogen-related carcinogenesis. This review highlights the current understanding of the estrogen-induced genetic alterations and their significance in estrogen-related carcinogenesis.

Understanding of the full potential of the genome coding capacity demands a deep knowledge of the different pathways that control gene expression. Translation initiation in eukaryotic mRNAs is a highly regulated process that accounts for the last step of gene expression control. While most mRNAs initiate translation using the AUG triplet closest to the 5'end, a growing number of mRNAs appear to follow different rules, giving rise to proteins that differ in their amino terminus. Internal ribosome entry site (IRES) elements provide an alternative to initiate translation that allow the use of internal start codons, sometimes located several hundred of residues away from the 5'end of the mRNA, bypassing strong RNA structures. Therefore, they represent a strategy to increase genetic diversity without increasing genome length. The IRES sequences found in viral and cellular mRNAs do not show overall sequence similarity, albeit they perform a similar function. IRES elements in viral mRNAs constitute an efficient method to distinguish its own mRNA from that of the host, and thus facilitate its survival when cellular protein synthesis is impaired. Viral IRES exploit different strategies to recruit the translational machinery, including direct ribosome binding, eIF3 or eIF4G-mediated mechanism. Cellular IRES mediated-translation represents a regulatory mechanism that helps the cell to cope with transient stress. They may be grouped according to common tropism, stimulation by similar situations and expression of specific targets in differentiated cells. Protein mediated-ribosome binding is likely to enhance the efficiency of cellular IRES sequences under specific environments. This review is focused to discuss recent advances on functional IRES elements.

Small supernumerary marker chromosomes (sSMC) in human are present in 0.043% of newborn children. They can be defined as additional centric chromosome fragments smaller than chromosome 20. sSMC include cases with the i(18p)-, the i(12p)- (i.e. Pallister Killian-) or the inv dup(22)- (i.e. cat-eye-) syndrome. However, about 30% of the remaining sSMC are not yet correlated with clinical syndromes, mostly due to problems in comprehensive characterisation of the sSMC. Here we present an overview of the approaches for sSMC characterisation and suggest a strategy for a straightforward and comprehensive characterisation of the marker chromosomes in question.