As crafty as its animal namesake, the cell-type-specific RNA splicing regulator FOX2 slips in and out of the transcriptome, causing the inclusion of one exon here or the exclusion of another there, with no apparent rhyme or reason.
However, researchers at the Salk Institute and the University of California, San Diego recently outsmarted FOX2 by elucidating a code for FOX2-regulated RNA splicing in human embryonic stem cells (hESCs). Their findings are certain to increase our understanding of cell-type-specific alternative splicing.
The team combined a modified cross-linking immunoprecipitation assay with high-throughput sequencing (HITS-CLIP) to map RNA targets of FOX2. The method revealed thousands of FOX2 pre-mRNA targets, representing 7% of hESC genes. FOX2 bound preferentially near alternative splice sites. When bound upstream of an alternative exon, FOX2 repressed exon usage, whereas downstream FOX2 binding enhanced exon inclusion.
Many FOX2 targets were themselves splicing regulators, and FOX2 was found to autoregulate its own splicing. FOX2 depletion led to rapid cell death in hESCs but not in other cell types that express FOX2, which suggests that FOX2 has distinct RNA targets in different cell types. Get all the details at Nature Structural & Molecular Biology, February 2009.