University of Maryland
Overview: Splicing Signals
Research in the Mount lab is devoted to understanding how multicellular organisms accomplish the correct processing of RNA from protein-coding genes. This involves identifying the elements of primary sequence information that determine where (and whether or not) splicing will occur, determining which components of the splicing machinery play especially salient roles in recognizing those signals, and determining how those factors act.
Auxiliary splicing signals in Arabidopsis thaliana
In addition to the core splicing signals, which are located at splice sites, auxiliary splicing signals at variable distances from splice sites are required for faithful splice site selection, both in vivo and in vitro. In particular, exonic splicing enhancers (ESEs) activate nearby splice sites (both 5' and 3' splice sites) and promote the inclusion (vs. skipping) of exons in which they reside. We have developed an exon inclusion assay in the model plant Arabidopsis thaliana. We find that exon inclusion in this assay is ESE-dependent; lines differing only within a short region centrally located within an exon can show either nearly complete skipping or complete inclusion. We are using this assay to understand the sequences that contribute to splice site selection.
SR protein genes in Arabidopsis thaliana
The serine-arginine-rich (SR) proteins constitute a conserved family of pre-mRNA splicing factors. In Arabidopsis thaliana, they are encoded by 19 genes, most of which are themselves alternatively spliced. We have been studying the effect of mutations in several SR protein genes. In particular, Xiao-Ning Zhang, a postdoc in the laboratory has found evidence that the two alternatively spliced isoforms of SR45 have distinct biological functions in plant development.
Intron evolution and the minor spliceosome
The existing structure of genes is produced by processes of intron gain, intron loss and intron type switching. We have investigated minor (U12-type) introns in collaboration with the group of Wojciech Makalowski at the Institute of Bioinformatics at the University of Münster. The evolution of U12-type introns in Drosophila, where they are significantly reduced in number, is of special interest. Undergraduate researchers Ian Henderson and Karishma Dagar have been investigating the splicing of U12 introns, including a twintron in the CG3294 gene.
Low complexity protein sequence
Low-complexity (repetitive) regions are typically not included in queries used by alignment-based tools for the identification of similar proteins. Nevertheless, such low-complexity regions, including arginine-serine-rich domains in splicing proteins, play important biological roles. We have developed a non-alignment approach for identifying and evaluating similar low-complexity regions based on shared repeated dipeptides and implemented in the program LOCST (Low Complexity Sequence Search Tool). This is work was performed with Nicolas Tilmans and Stephen Fiorelli.