Alternative splicing

About: Alternative splicing is a research topic. Over the lifetime, 20764 publications have been published within this topic receiving 1113366 citations. The topic is also known as: alternative nuclear mRNA splicing, via spliceosome & GO:0000380.

Antisense-Mediated RNA Targeting: Versatile and Expedient Genetic Manipulation in the Brain

Abstract: A limiting factor in brain research still is the difficulty to evaluate in vivo the role of the increasing number of proteins implicated in neuronal processes. We discuss here the potential of antisense-mediated RNA targeting approaches. We mainly focus on those that manipulate splicing (exon skipping and exon inclusion), but will also briefly discuss mRNA targeting. Classic knockdown of expression by mRNA targeting is only one possible application of antisense oligonucleotides (AON) in the control of gene function. Exon skipping and inclusion are based on the interference of AONs with splicing of pre-mRNAs. These are powerful, specific and particularly versatile techniques, which can be used to circumvent pathogenic mutations, shift splice variant expression, knock down proteins, or to create molecular models using in-frame deletions. Pre-mRNA targeting is currently used both as a research tool, e.g. in models for motor neuron disease, and in clinical trials for Duchenne muscular dystrophy and amyotrophic lateral sclerosis. AONs are particularly promising in relation to brain research, as the modified AONs are taken up extremely fast in neurons and glial cells with a long residence, and without the need for viral vectors or other delivery tools, once inside the blood brain barrier. In this review we cover 1. The principles of antisense-mediated techniques, chemistry and efficacy. 2. The pros and cons of AON approaches in the brain compared to other techniques of interfering with gene function, such as transgenesis and short hairpin RNAs, in terms of specificity of the manipulation, spatial and temporal control over gene expression, toxicity and delivery issues. 3. The potential applications for Neuroscience. We conclude that there is good evidence from animal studies that the CNS can be successfully targeted, but the potential of the diverse AON-based approaches appears to be under-recognized.

Cloning and expression of chicken p54c-ets cDNAs: the first p54c-ets coding exon is located into the 40.0 kbp genomic domain unrelated to v-ets.

Abstract: We have isolated cDNA clones of chicken c-ets mRNA the longest of which, designated pCk E54A, contained approximately 2.0 kb of a c-ets mRNA species. Nucleotide sequencing of this clone revealed a single long open reading frame, extending from the first ATG codon (nucleotide +1) to a TGA termination codon at nucleotide 1324. The predicted translation product contains 441 amino acid residues and its molecular weight is 48 kd. Expression in COS-1 cells of this clone resulted in the synthesis of polypeptides immunologically indistinguishable from the authentic p54c-ets after one-dimensional gel electrophoresis. Comparison of the nucleotide sequence of this cDNA to that of v-ets of avian acute leukemia virus E26 showed that both sequences are almost colinear with the exception of five point mutations but present striking differences in their 5' and 3' parts. 79 nucleotides downstream of the first ATG codon in c-ets cDNA are not found in the 5' part of v-ets where they are replaced by 223 different nucleotides. The 3' parts of v-ets and the coding region of the chicken c-ets cDNAs are also different: the last 13 codons of the cDNA are replaced by 16 different codons in v-ets. Thus our results precisely define the structural differences between the ets encoded domain of E26 viral transforming protein (P135 gag-myb-ets) and the normal cellular protein p54c-ets expressed at high levels in chicken thymocytes and bursal lymphocytes. They also suggest the possibility of alternative splicing of different 5' exons to a common set of 3' exons.

Exon and junction microarrays detect widespread mouse strain- and sex-bias expression differences

Abstract: Studies have shown that genetic and sex differences strongly influence gene expression in mice. Given the diversity and complexity of transcripts produced by alternative splicing, we sought to use microarrays to establish the extent of variation found in mouse strains and genders. Here, we surveyed the effect of strain and sex on liver gene and exon expression using male and female mice from three different inbred strains. 71 liver RNA samples from three mouse strains – DBA/2J, C57BL/6J and C3H/HeJ – were profiled using a custom-designed microarray monitoring exon and exon-junction expression of 1,020 genes representing 9,406 exons. Gene expression was calculated via two different methods, using the 3'-most exon probe ("3' gene expression profiling") and using all probes associated with the gene ("whole-transcript gene expression profiling"), while exon expression was determined using exon probes and flanking junction probes that spanned across the neighboring exons ("exon expression profiling"). Widespread strain and sex influences were detected using a two-way Analysis of Variance (ANOVA) regardless of the profiling method used. However, over 90% of the genes identified in 3' gene expression profiling or whole transcript profiling were identified in exon profiling, along with 75% and 38% more genes, respectively, showing evidence of differential isoform expression. Overall, 55% and 32% of genes, respectively, exhibited strain- and sex-bias differential gene or exon expression. Exon expression profiling identifies significantly more variation than both 3' gene expression profiling and whole-transcript gene expression profiling. A large percentage of genes that are not differentially expressed at the gene level demonstrate exon expression variation suggesting an influence of strain and sex on alternative splicing and a need to profile expression changes at sub-gene resolution.

Differential Expression of a Human Kallikrein 5 (KLK5) Splice Variant in Ovarian and Prostate Cancer

Abstract: The presence of more than one mRNA form is common among kallikrein genes. We identified an mRNA transcript of the human kallikrein gene 5 (KLK5) , denoted KLK5 spl