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Pauses to POL II elongation affect splicing
Even if the elongation rates of pol II were not regulatable, experiments with slow polymerases in mammalian cells and yeast put into the scene the importance of the presence of pauses for pol II transcription on splicing. Pauses for pol II have been found in the 3'-flanking regions of genes regulating termination and polyadenylation (Enriquez-Harris et al. 1991), between closely spaced genes (Ashfield et al. 1991), and at several internal sites in the c and N-myc genes (Keene et al. 1999). Artificial arrests (ARTAR) to pol II elongation have been created and shown to be effective in pausing pol II at positions far downstream from the promoter (Kulish and Struhl 2001). The effect of a MAZ-type pol II pause on the alternative splicing of the tropomyosin gene has been commented on above (Roberts et al. 1998). Insertions of MAZ pauses at certain positions of the fibro-blast growth factor receptor 2 gene deeply affect alternative splicing of its mutually exclusive exons IIIb and IIIc when minigenes are transfected into cells in culture. However, the effects on splicing are not observed when in vitro transcribed pre-RNAs, containing similar pauses, are directly transfected into the cells, strongly demonstrating the co-transcriptional nature of the MAZ effects (Robson-Dixon and García-Blanco 2004). Most importantly, a natural pol II pause was shown to contribute to the regulation of the alternative processing of immunoglobulin µ RNA, where a combination of alternative polyadenylation and splicing determine the switch from membrane to soluble immunoglobulin synthesis. The pause site, located between a poly(A) and a splicing site enhances the use of the upstream poly(A) site, which leads to the soluble form of IgM. Interestingly, nuclear run-ons demonstrated a stalling of RNA polymerase just downstream from the soluble µ poly(A) site (Peterson et al. 2002).
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