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Genomic mRNA profiling reveals compensatory mechanisms for the requirement of the essential splicing factor U2AF.
Mol Cell Biol. 2010 Dec 13;
Authors: Sridharan V, Heimiller J, Singh R
The large subunit of the U2 auxiliary factor (U2AF) recognizes the polypyrimidine-tract (Py-tract) located adjacent to the 3' splice site to facilitate U2 snRNP recruitment. While U2AF is considered essential for pre-mRNA splicing, its requirement for splicing on a genome-wide level has not been analyzed. Using Solexa sequencing, we performed mRNA profiling for splicing in the fission yeast U2AF(59) (prp2.1) temperature-sensitive mutant. Surprisingly, our analysis reveals that introns show a range of splicing defects in the mutant strain. While U2AF(59)-inactivation (non-permissive) conditions inhibit splicing of some introns, others are spliced apparently normally. Bioinformatics analysis indicates that U2AF(59)-insensitive introns have stronger 5' splice sites and higher A/U content. Most importantly, features that contribute to U2AF(59) insensitivity of an intron unexpectedly reside in its 5'-most 30 nucleotides. These include the 5' splice site, a guanosine at position 7, and the 5' splice site to branchpoint sequence context. A differential requirement (similar to U2AF(59)) for introns may also apply to other general splicing factors (e.g. prp10). Our combined results indicate that U2AF insensitivity is a common phenomenon and that varied intron features warrant existence of unrecognized aspects of spliceosome assembly.
PMID: 21149581 [PubMed - as supplied by publisher]
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Genomic mRNA profiling reveals compensatory mechanisms for the requirement of the essential splicing factor U2AF.
Mol Cell Biol. 2010 Dec 13;
Authors: Sridharan V, Heimiller J, Singh R
The large subunit of the U2 auxiliary factor (U2AF) recognizes the polypyrimidine-tract (Py-tract) located adjacent to the 3' splice site to facilitate U2 snRNP recruitment. While U2AF is considered essential for pre-mRNA splicing, its requirement for splicing on a genome-wide level has not been analyzed. Using Solexa sequencing, we performed mRNA profiling for splicing in the fission yeast U2AF(59) (prp2.1) temperature-sensitive mutant. Surprisingly, our analysis reveals that introns show a range of splicing defects in the mutant strain. While U2AF(59)-inactivation (non-permissive) conditions inhibit splicing of some introns, others are spliced apparently normally. Bioinformatics analysis indicates that U2AF(59)-insensitive introns have stronger 5' splice sites and higher A/U content. Most importantly, features that contribute to U2AF(59) insensitivity of an intron unexpectedly reside in its 5'-most 30 nucleotides. These include the 5' splice site, a guanosine at position 7, and the 5' splice site to branchpoint sequence context. A differential requirement (similar to U2AF(59)) for introns may also apply to other general splicing factors (e.g. prp10). Our combined results indicate that U2AF insensitivity is a common phenomenon and that varied intron features warrant existence of unrecognized aspects of spliceosome assembly.
PMID: 21149581 [PubMed - as supplied by publisher]
More...