Sex differentiation: the role of alternative splicing.

Sex differentiation in Drosophila is controlled by a regulatory cascade with at least three regulated alternative RNA-processing events. The results of recent work have verified much of the earlier molecular and genetic work in this field and have provided a demonstration that both positive and negative regulatory mechanisms are involved.     

Sex determination: a hypothesis based on steroid ratios

This paper presents a hypothesis for sex determination based on the ratio of androgen to estrogen in the gonad during sexual differentiation. In vertebrates the ratio of these steroids, and therefore, the sex of an individual is controlled by the quantity of the enzyme aromatase. For animals with a ZZ, ZW sex determining mechanism, such as birds, in which the heterogametic sex is female, an inducer for the aromatase gene is postulated to be on the W chromosome. In animals with an XX, XY system in which the heterogametic sex is male, such as mammals, the Y chromosome is postulated to code for a repressor of the aromatase gene. This hypothesis can account for naturally occurring sex reversal such as seen in some fish and amphibians, experimentally induced sex reversal by administration of steroids in birds, reptiles, fish and amphibians, and temperature-dependent sex determination as in reptiles. For invertebrates the same hypothetical model applies though the specific androgenic and estrogenic steroids differ. Both the X-to-autosome ratio method of sex determination typified by fruit flies and the haplodiploid method of bees as well as hormonal control of sexual differentiation in crustaceans are accounted for by this hypothesis.     

Sex,AGility, and the regulation of alternative splicing

Alternative splicing is an important means of regulating the expression of eukaryotic genes and enhancing protein diversity. A detailed examination of the Drosophila Sex-lethal gene has led to two significant discoveries-the role of the splicing factor SPF45 in defining the site of exon ligation, and that alternative splicing can be regulated at the second step.     

Understanding alternative splicing: towards a cellular code

In violation of the 'one gene, one polypeptide' rule, alternative splicing allows individual genes to produce multiple protein isoforms - thereby playing a central part in generating complex proteomes. Alternative splicing also has a largely hidden function in quantitative gene control, by targeting RNAs for nonsense-mediated decay. Traditional gene-by-gene investigations of alternative splicing mechanisms are now being complemented by global approaches. These promise to reveal details of the nature and operation of cellular codes that are constituted by combinations of regulatory elements in pre-mRNA substrates and by cellular complements of splicing regulators, which together determine regulated splicing pathways.     

Ethyl acetate: a possible alternative for anaesthetizing insects

In order to anaesthetize insects in a laboratory, chilling and application of diethyl ether and carbon dioxide are commonly used. However none of the above methods is problem free. In particular, the use of diethyl ether, despite its simplicity, is now limited due to its poor safety. In our research, we evaluated ethyl acetate as an alternative anaesthetic substance. The effects of ethyl acetate anaesthesia were compared with those produced by carbon dioxide on adult green lacewings (Neuroptera: Chrysopidae). The biological parameters measured were longevity and fecundity. No significant differences appeared between the two treatments and the control. Although further research is necessary, the use of ethyl acetate proves to be very promising and presents a valid alternative to the use of diethyl ether and, in many cases, also to carbon dioxide and chilling.     

Rbm20 regulates titin alternative splicing as a splicing repressor

Titin, a sarcomeric protein expressed primarily in striated muscles, is responsible for maintaining the structure and biomechanical properties of muscle cells. Cardiac titin undergoes developmental size reduction from 3.7 megadaltons in neonates to primarily 2.97 megadaltons in the adult. This size reduction results from gradually increased exon skipping between exons 50 and 219 of titin mRNA. Our previous study reported that Rbm20 is the splicing factor responsible for this process. In this work, we investigated its molecular mechanism. We demonstrate that Rbm20 mediates exon skipping by binding to titin pre-mRNA to repress the splicing of some regions; the exons/introns in these Rbm20-repressed regions are ultimately skipped. Rbm20 was also found to mediate intron retention and exon shuffling. The two Rbm20 speckles found in nuclei from muscle tissues were identified as aggregates of Rbm20 protein on the partially processed titin pre-mRNAs. Cooperative repression and alternative 3′ splice site selection were found to be used by Rbm20 to skip different subsets of titin exons, and the splicing pathway selected depended on the ratio of Rbm20 to other splicing factors that vary with tissue type and developmental age.     

可变剪接调控植物开花的作用机制进展

开花是植物生长发育的关键转折,与种子生产和作物产量密切相关。开花转变受到复杂的基因网络调控,许多开花相关基因通过可变剪接产生多种转录本,调控开花时间。文中从多个角度系统地综述了可变剪接调控植物开花的分子机制,并对将来的研究进行了展望。     

Epigenetics in alternative pre-mRNA splicing

Alternative splicing plays critical roles in differentiation, development, and disease and is a major source for protein diversity in higher eukaryotes. Analysis of alternative splicing regulation has traditionally focused on RNA sequence elements and their associated splicing factors, but recent provocative studies point to a key function of chromatin structure and histone modifications in alternative splicing regulation. These insights suggest that epigenetic regulation determines not only what parts of the genome are expressed but also how they are spliced.     

Half-pint: alternative splicing in the Drosophila ovary

A new study from the Schüpbach lab implicates a splicing factor, Half-pint, in the regulation of oogenesis in Drosophila. Through processing of the otu mRNA, Hfp appears to control both mitosis and RNA localization in the germline.     

Genome wide identification and classification of alternative splicing based on EST data

MOTIVATION: Alternative splicing is currently seen to explain the vast disparity between the number of predicted genes in the human genome and the highly diverse proteome. The mapping of expressed sequences tag (EST) consensus sequences derived from the GeneNest database onto the genome provides an efficient way of predicting exon-intron boundaries, gene structure and alternative splicing events. However, the alternative splicing events are obscured by a large number of putatively artificial exon boundaries arising due to genomic contamination or alignment errors. The current work describes a methodology to associate quality values to the predicted exon-intron boundaries. High quality exon-intron boundaries are used to predict constitutive and alternative splicing ranked by confidence values, aiming to facilitate large-scale analysis of alternative splicing and splicing in general. RESULTS: Applying the current methodology, constitutive splicing is observed in 33,270 EST clusters, out of which 45% are alternatively spliced. The classification derived from the computed confidence values for 17 of these splice events frequently correlate (15/17) with RT-PCR experiments performed for 40 different tissue samples. As an application of the confidence measure, an evaluation of distribution of alternative splicing revealed that majority of variants correspond to the coding regions of the genes. However, still a significant fraction maps to non-coding regions, thereby indicating a functional relevance of alternative splicing in untranslated regions. AVAILABILITY: The predicted alternative splice variants are visualized in the SpliceNest database at http://splicenest.molgen.mpg.de     

Comparative cross-species alternative splicing in plants

Alternative splicing (AS) can add significantly to genome complexity. Plants are thought to exhibit less AS than animals. An algorithm, based on expressed sequence tag (EST) pairs gapped alignment, was developed that takes advantage of the relatively small intron and exon size in plants and directly compares pairs of ESTs to search for AS. EST pairs gapped alignment was first evaluated in Arabidopsis (Arabidopsis thaliana), rice (Oryza sativa), and tomato (Solanum lycopersicum) for which annotated genome sequence is available and was shown to accurately predict splicing events. The method was then applied to 11 plant species that include 17 cultivars for which enough ESTs are available. The results show a large, 3.7-fold difference in AS rates between plant species with Arabidopsis and rice in the lower range and lettuce (Lactuca sativa) and sorghum (Sorghum bicolor) in the upper range. Hence, compared to higher animals, plants show a much greater degree of variety in their AS rates and in some plant species the rates of animal and plant AS are comparable although the distribution of AS types may differ. In eudicots but not monocots, a correlation between genome size and AS rates was detected, implying that in eudicots the mechanisms that lead to larger genomes are a driving force for the evolution of AS.     

Visualization of alternative splicing in vivo

The analysis of sequences required for alternative splicing of mRNA has predominantly been performed using cell culture systems. However, the phenotype of cultured cells is almost invariably different from that of cells in the intact animal. It is therefore possible that there are significant differences in the regulation of specific splicing reactions in vivo compared to in cell culture. Here, we describe methods for the visualization and analysis of alternative splicing in vivo using transgenic mice. These methods allow for the analysis of the temporal and tissue-specific regulation of alternative splicing both visually and quantitatively.