Alternative splicing (AS) can regulate gene expression by introducing premature termination codons (PTCs) into spliced mRNA that subsequently elicit transcript degradation by the nonsense-mediated mRNA decay (NMD) pathway. However, the range of cellular functions controlled by this process and the factors required are poorly understood. By quantitative AS microarray profiling, we find that there are significant overlaps among the sets of PTC-introducing AS events affected by individual knockdown of the three core human NMD factors, Up-Frameshift 1 (UPF1), UPF2, and UPF3X/B. However, the levels of some PTC-containing splice variants are less or not detectably affected by the knockdown of UPF2 and/or UPF3X, compared with the knockdown of UPF1. The intron sequences flanking the affected alternative exons are often highly conserved, suggesting important regulatory roles for these AS events. The corresponding genes represent diverse cellular functions, and surprisingly, many encode core spliceosomal proteins and assembly factors. We further show that conserved, PTC-introducing AS events are enriched in genes that encode core spliceosomal proteins. Where tested, altering the expression levels of these core spliceosomal components affects the regulation of PTC-containing splice variants from the corresponding genes. Together, our results show that AS-coupled NMD can have different UPF factor requirements and is likely to regulate many general components of the spliceosome. The results further implicate general spliceosomal components in AS regulation.The production of multiple mRNA variants through alternative splicing (AS) represents a widespread mechanism for the expansion of proteomic diversity, and regulated AS plays important roles in many physiological processes (for reviews, see references 4, 5, and 34). However, sequence-based predictions have revealed that approximately one-third or more of AS events have the potential to introduce a premature termination codon (PTC) that could target the resulting spliced transcript for nonsense-mediated mRNA decay (NMD) (32). While many predicted PTC-introducing AS events do not appear to be conserved or subject to regulation by NMD, AS microarray profiling experiments have revealed that approximately 10 to 20% of these events display substantial changes when NMD is disrupted (42). AS microarray profiling (40, 42) thus provides a basis for identifying new genes and functional processes regulated by AS-coupled NMD and for elucidating the factor requirements for this mode of gene regulation on a large scale.In mammals, NMD is generally, though not always (6, 35), dependent on a splicing event sufficiently downstream of a termination codon. Termination codons are usually recognized as premature when they occur more than 50 to 55 nucleotides upstream of a final splice junction (39), which is "marked" by the deposition a postsplicing exon junction complex (EJC) (30). NMD is believed to require three core UPF factors which are conserved from yeast to humans, namely, UPF1 (also kno...

Alternative splicing in the central nervous system

A microarray analysis provides new evidence suggesting that specific cellular processes in the mammalian CNS are coordinated at the level of alternative splicing, and that a complex splicing code underlies CNS-specific alternative splicing regulation.