Alternative splicing in individual Aplysia neurons generates neuropeptide diversity

The neuron R15 is a peptidergic cell within the abdominal ganglion of Aplysia that participates in two neural circuits governing physiological and behavioral programs. We have cloned and characterized the major gene product expressed in this neuron. The R15 cDNA encodes a polyprotein precursor that is cleaved to yield a set of small neuropeptides. One peptide, R15 alpha 1, may act on different target cells to generate distinct but complementary physiological alterations that contribute to a program of cardiovascular changes in Aplysia. We have found that the RNA encoding the R15 polyprotein is spliced differently in different neurons. Our results suggest that alternative splicing of RNAs encoding polyproteins may provide a mechanism to generate distinct but overlapping sets of peptides that govern distinct but related physiological or behavioral programs.     

Alternative splicing and proteome diversity in plants: the tip of the iceberg has just emerged

Alternative splicing has recently emerged as one of the most significant generators of functional complexity in several relatively well-studied animal genomes, but little is known about the extent of this phenomenon in higher plants. However, recent computational and experimental studies discussed here suggest that alternative splicing probably plays a far more significant role in the generation of proteome diversity in plants than was previously thought.     

Alternative splicing in the testes

Germ-cell differentiation is an ideal process for studying the effects of alternative splicing and there are examples of alternative splicing of genes involved in gene regulation and signal transduction at every stage of the spermatogenic pathway. A network of testes-specific splicing factor interactions has been uncovered and combining our knowledge of these RNAs and proteins should lead to an understanding of the regulation of alternative splicing and male fertility.     

Alternative splicing in ascomycetes

Alternative splicing is a complex and regulated process, which results in mRNA with different coding capacities from a single gene. Extend and types of alternative splicing vary greatly among eukaryotes. In this review, I focus on alternative splicing in ascomycetes, which in general have significant lower extend of alternative splicing than mammals. Yeast-like species have low numbers of introns and consequently alternative splicing is lower compared to filamentous fungi. Several examples from single studies as well as from genomic scale analysis are presented, including a survey of alternative splicing in Neurospora crassa. Another focus is regulation by riboswitch RNA and alternative splicing in a heterologous system, along with putative protein factors involved in regulation.     

Alternative splicing and disease

Almost all protein-coding genes are spliced and their majority is alternatively spliced. Alternative splicing is a key element in eukaryotic gene expression that increases the coding capacity of the human genome and an increasing number of examples illustrates that the selection of wrong splice sites causes human disease. A fine-tuned balance of factors regulates splice site selection. Here, we discuss well-studied examples that show how a disturbance of this balance can cause human disease. The rapidly emerging knowledge of splicing regulation now allows the development of treatment options.     

Alternative pre-mRNA splicing: the logic of combinatorial control

Alternative splicing of mRNA precursors is a versatile mechanism of gene expression regulation that accounts for a considerable proportion of proteomic complexity in higher eukaryotes. Its modulation is achieved through the combinatorial interplay of positive and negative regulatory signals present in the RNA, which are recognized by complexes composed of members of the hnRNP and SR protein families.     

Alternative splicing in disease and therapy

Alternative splicing is the major source of proteome diversity in humans and thus is highly relevant to disease and therapy. For example, recent work suggests that the long-sought-after target of the analgesic acetaminophen is a neural-specific, alternatively spliced isoform of cyclooxygenase 1 (COX-1). Several important diseases, such as cystic fibrosis, have been linked with mutations or variations in either cis-acting elements or trans-acting factors that lead to aberrant splicing and abnormal protein production. Correction of erroneous splicing is thus an important goal of molecular therapies. Recent experiments have used modified oligonucleotides to inhibit cryptic exons or to activate exons weakened by mutations, suggesting that these reagents could eventually lead to effective therapies.     

Alternative splicing: a paradoxical qudo in eukaryotic genomes

One of the most remarkable observations stemming from the sequencing of genomes of diverse species is that the number of protein-coding genes in an organism does not correlate with its overall cellular complexity. Alternative splicing, a key mechanism for generating protein complexity, has been suggested as one of the major explanation for this discrepancy between the number of genes and genome complexity. Determining the extent and importance of alternative splicing required the confluence of critical advances in data acquisition, improved understanding of biological processes and the development of fast and accurate computational analysis tools. Although many model organisms have now been completely sequenced, we are still very far from understanding the exact frequency of alternative splicing from these sequenced genomes.This paper will highlight some recent progress and future challenges for functional genomics and bioinformatics in this rapidly developing area.