RNA processing and human disease

Gene expression involves multiple regulated steps leading from gene to active protein. Many of these steps involve some aspect of RNA processing. Diseases caused by mutations that directly affect RNA processing are relatively rare compared with mutations that disrupt protein function. The vast majority of diseases of RNA processing result from loss of function of a single gene due to mutations in cis-acting elements required for pre-messenger RNA (mRNA) splicing. However, a few diseases are caused by alterations in the trans-acting factors required for RNA processing and in the vast majority of cases it is the pre-mRNA splicing machinery that is affected. Clearly, alterations that disrupt splicing of pre-mRNAs from large numbers of genes would be lethal at the cellular level. A common theme among these diseases is that only subsets of genes are affected. This is consistent with an emerging view that different subsets of exons require different sets of cis-acting elements and trans-acting factors.     

Prediction of protein function and pathways in the genome era

The growing number of completely sequenced genomes adds new dimensions to the use of sequence analysis to predict protein function. Compared with the classical knowledge transfer from one protein to a similar sequence (homology-based function prediction), knowledge about the corresponding genes in other genomes (orthology-based function prediction) provides more specific information about the proteins function, while the analysis of the sequence in its genomic context (context-based function prediction) provides information about its functional context. Whereas homology-based methods predict the molecular function of a protein, genomic context methods predict the biological process in which it plays a role. These complementary approaches can be combined to elucidate complete functional networks and biochemical pathways from the genome sequence of an organism. Here we review recent advances in the field of genomic-context based methods of protein function prediction. Techniques are highlighted with examples, including an analysis that combines information from genomic-context with homology to predict a role of the RNase L inhibitor in the maturation of ribosomal RNA.Received 16 October 2003; received after revision 25 November 2003; accepted 26 November 2003     

U7 snRNAs induce correction of mutated dystrophin pre-mRNA by exon skipping

Most cases of Duchenne muscular dystrophy are caused by dystrophin gene mutations that disrupt the mRNA reading frame. Artificial exclusion (skipping) of a single exon would often restore the reading frame, giving rise to a shorter, but still functional dystrophin protein. Here, we analyzed the ability of antisense U7 small nuclear (sn)RNA derivatives to alter dystrophin pre-mRNA splicing. As a proof of principle, we first targeted the splice sites flanking exon 23 of dystrophin pre-mRNA in the wild-type muscle cell line C2C12 and showed precise exon 23 skipping. The same strategy was then successfully adapted to dystrophic immortalized mdx muscle cells where exon-23-skipped dystrophin mRNA rescued dystrophin protein synthesis. Moreover, we observed a stimulation of antisense U7 snRNA expression by the murine muscle creatine kinase enhancer. These results demonstrate that alteration of dystrophin pre-mRNA splicing could correct dystrophin gene mutations by expression of specific U7 snRNA constructs.     

The special Sm core structure of the U7 snRNP: far-reaching significance of a small nuclear ribonucleoprotein

The polypeptide composition of the U7 small nuclear ribonucleoprotein (snRNP) involved in histone messenger RNA (mRNA) 3' end formation has recently been elucidated. In contrast to spliceosomal snRNPs, which contain a ring-shaped assembly of seven so-called Sm proteins, in the U7 snRNP the Sm proteins D1 and D2 are replaced by U7-specific Sm-like proteins, Lsm10 and Lsm11. This polypeptide composition and the unusual structure of Lsm11, which plays a role in histone RNA processing, represent new themes in the biology of Sm/Lsm proteins. Moreover this structure has important consequences for snRNP assembly that is mediated by two complexes containing the PRMT5 methyltransferase and the SMN (survival of motor neurons) protein, respectively. Finally, the ability to alter this polypeptide composition by a small mutation in U7 snRNA forms the basis for using modified U7 snRNA derivatives to alter specific pre-mRNA splicing events, thereby opening up a new way for antisense gene therapy.     

基因功能注释——后基因组时代面临的挑战

在已经解序的、数以百计的生物基因组中,存在大量编码未知功能蛋白的基因序列。同时,众多已知功能的酶蛋白在解序的基因组中找不到对应的基因。确定未知功能基因的功能和寻找孤儿酶对应的基因是后基因组时代面临的极具挑战性的科学任务。本文综合讨论了目前基因组中基因功能注释存在的问题及解决这些问题的策略与方法。     

Molecular cloning of a cDNA encoding alpha-glucosidase in the digestive gland of the shrimp, Litopenaeus vannamei

The complete sequence of the 3-kb cDNA and the 5' genomic structure are reported for the gene encoding the shrimp alpha-glucosidase. Alpha-glucosidase cDNA was isolated from a shrimp digestive gland cDNA library. The 2830-base pair cDNA contains an open reading frame that encodes 919 amino acids. The shrimp alpha-glucosidase cDNA shows a high level of identity with that of the human sucrase-isomaltase, human maltase-glucoamylase, and human acid lysosomal alpha-glucosidase, indicating that the protein shares the same structural domains. The similarities among these proteins are found as clusters and characterize the glycosyl hydrolase family 31. To our knowledge, this is the first report to describe a satellite sequence in the 5' genomic structure before the TATA box in an invertebrate sequence.     

The mutator phenotype theory of carcinogenesis and the complex histopathology of tumours: support for the theory from the independent occurrence of nuclear abnormality,loss of specialisation and invasiveness among occasional neoplastic lesions

The mutator phenotype theory of carcinogenesis suggests that genetic instability is an early and essential part of tumour development. This instability provides for substantially random cell-to-cell genomic variation (genomic heterogeneity) to arise among cells of individual tumours. Genetically unstable cells then produce 'successful' clones of cells with the necessary mutations for malignant behaviour. In a previous paper (Bignold L. P., Cell. Mol. Life Sci. 2002; 59: 950-958), it was pointed out that a population of cells which is heterogeneous for behaviour-related genes may well also be heterogeneous for morphology-related genes. This would result in cellular pleomorphism among cells of individual tumours, and so explain this almost universal characteristic of solid malignancies. paragraph sign If the concept of random genomic variability applies fully to the histopathology of tumours, then most tumours should show a mixture of neoplastic features, especially nuclear atypia, loss of specialised function (such as loss of production of mucus by glandular cells) and invasiveness. However, occasional lesions might be expected to occur which show these characteristics independently. That is, lesions should exist which exhibit one or two of the three characteristics of neoplasms without the other(s). paragraph sign This paper identifies, among human tumours, lesions which show independence of these characteristics. Two of the examples discussed are a Bowenoid solar keratosis that shows severe nuclear atypia, but no apparent loss of specialisation and no invasiveness. On the other hand, anaplastic small cell carcinoma of the lung often exhibits marked loss of differentiation, very aggressive invasion and metastasis, but little nuclear pleomorphism. paragraph sign These examples are considered to provide further support for the importance of the mutator phenotype to the pathogenesis of neoplasia.     

“Whatever happened to the Genomatron?” Documenting a 21st century science

With notable exceptions, specialist museums have generally failed to collect an adequate record of the material culture of post-war science and technology. Some reasons for this failure are identified, and some suggestions for remedying this situation are made with the help of a specific example: genomic science and medicine. Genomics is a quintessentially 21st-century science: data-rich, digital, and technique-and technology-driven. As such, it presents particular challenges and opportunities to museums wishing to improve their performance in collecting recent and contemporary science and technology. The paper explores different dimensions of this challenge through the attempt to establish a Museum Genomics Initiative, an international group of museum professionals who are committed to collaborating around the documentation of genomic science and medicine.     

Prospects for NMR imaging in the study of biological morphogenesis

Small objects can be visualised with a spatial resolution that approaches microscopic dimensions using the technique of high resolution nuclear magnetic resonance (NMR) imaging. Some important features of the method are described and the prospects for using the technique to study morphogenesis are discussed. It is concluded that NMR imaging, in conjunction with the related method of localised spectroscopy, is capable of producing novel structural information.     

Prospects for NMR imaging in the study of biological morphogenesis

Summary Small objects can be visualised with a spatial resolution that approaches microscopic dimensions using the technique of high resolution nuclear magnetic resonance (NMR) imaging. Some important features of the method are described and the prospects for using the technique to study morphogenesis are discussed. It is concluded that NMR imaging, in conjunction with the related method of localised spectroscopy, is capable of producing novel structural information.     

The Dim protein family: from structure to splicing

The spliceosome is a dynamic macromolecular machine that catalyzes pre-mRNA splicing through a mechanism controlled by several accessory proteins, including the Dim proteins. The Dim protein family is composed of two classes, Dim1 and Dim2, which share a common thioredoxin-like fold. They were originally identified for their role in cell cycle progression and have been found to interact with Prp6, an essential component of the spliceosome, which forms the bridge of U4/U6.U5-tri-snRNP. In spite of their biological and structural similarities, Dim1 and Dim2 proteins differ in many aspects. Dim1 bears distinctive structural motifs responsible for its interaction with other spliceosome components. Dim2 forms homodimers and contains specific domains required for its interactions with partners. This originality suggests that although both proteins are involved in pre-mRNA splicing, they are likely to be involved in different biological pathways. In the present article we review the structure and function of the Dim proteins.     

Homing endonucleases: from basics to therapeutic applications

Homing endonucleases (HE) are double-stranded DNAses that target large recognition sites (12–40 bp). HE-encoding sequences are usually embedded in either introns or inteins. Their recognition sites are extremely rare, with none or only a few of these sites present in a mammalian-sized genome. However, these enzymes, unlike standard restriction endonucleases, tolerate some sequence degeneracy within their recognition sequence. Several members of this enzyme family have been used as templates to engineer tools to cleave DNA sequences that differ from their original wild-type targets. These custom HEs can be used to stimulate double-strand break homologous recombination in cells, to induce the repair of defective genes with very low toxicity levels. The use of tailored HEs opens up new possibilities for gene therapy in patients with monogenic diseases that can be treated ex vivo. This review provides an overview of recent advances in this field.     

RNA and protein-dependent mechanisms in tauopathies: consequences for therapeutic strategies

Tauopathies are a group of neurodegenerative diseases characterised by intracellular deposits of the microtubule-associated protein tau. The most typical example of a tauopathy is Alzheimer’s disease. The importance of tau in neuronal dysfunction and degeneration has been demonstrated by the discovery of dominant mutations in the MAPT gene, encoding tau, in some rare dementias. Recent developments have shed light on the significance of tau phosphorylation and aggregation in pathogenesis. Furthermore, emerging evidence reveals the central role played by tau pre-mRNA processing in tauopathies. The present review focuses on the current understanding of tau-dependent pathogenic mechanisms and how realistic therapies for tauopathies can be developed. Received 3 December 2006; received after revision 23 February 2007; accepted 20 March 2007     

Average conditional correlation and tree structures for multivariate GARCH models

We propose a simple class of multivariate GARCH models, allowing for time‐varying conditional correlations. Estimates for time‐varying conditional correlations are constructed by means of a convex combination of averaged correlations (across all series) and dynamic realized (historical) correlations. Our model is very parsimonious. Estimation is computationally feasible in very large dimensions without resorting to any variance reduction technique. We back‐test the models on a six‐dimensional exchange‐rate time series using different goodness‐of‐fit criteria and statistical tests. We collect empirical evidence of their strong predictive power, also in comparison to alternative benchmark procedures. Copyright © 2006 John Wiley & Sons, Ltd.     

Nuclear transport mechanisms

The term nuclear transport, refers to the movement of a large variety of macromolecules both into and out of the nucleus. Transport must be extremely selective, yet also very efficient. A single type of channel, the nuclear pore complex, mediates all movement across the nuclear envelope. Selectivity is achieved through the use of families of soluble factors that target substrates for import and export and deliver them to their appropriate intracellular destinations. We now have a fairly detailed understanding of the basic mechanisms of protein import into the nucleus. Many of these same principles can be applied to protein export and perhaps RNA export. This review will summarize the current status of what is known about various transport pathways and highlight the questions that remain to be answered.     

DNA sequence organisation in relation to genome size in birds

Summary DNA sequence interspersion was investigated in pheasant and pelican nuclear DNA. As is typical for birds, these genomes are organized in a long period pattern. Altogether, 5 bird species with genome sizes between 1.6 and 1.9 pg DNA are compared with regard to the extent of repetitive and single copy sequence interspersion. The result indicates that the average length of interspersed repetitive sequences increases with genome size.Acknowledgment. This work was supported by the Deutsche Forschungsgemeinschaft. Mrs H. Tuczynski and Mr J. S. Jackson are thanked for editorial assistance.