The effect of mug174 deletion or red1 deletion mutation on gene expression in the fission yeast Schizosaccharomyces pombe
Our characterization of Mug174 using genetic and biochemical approaches revealed that Mug174 is the Coilin (an integral component of the Cajal body in multicellular organisms) ortholog in the fission yeast S. pombe. To investigate the Mug174 role in shaping transcriptome, we delete the mug174 gene and performed RNA-seq. We found that intron and exon-intron junction reads were elevated in mug174?, indicating that pre-mRNA splicing is compromised in the absence of Mug174. Red1 is not a splicing factor, but it promotes the degradation of unspliced mRNAs. By comparing the RNA-seq data from mug174? and red1?, we found that Mug174 and Red1 share the target introns. Our analyses are consistent with the previous finding that the Cajal body is required for proper pre-mRNA splicing, thereby supporting our idea that Mug174 is indeed the ortholog of Coilin. Overall design: We constructed mug174? or red1? cells using the standard gene replacement method in a parental wild-type S. pombe strain. We then isolated total RNA from vegetative wild-type, mug174?, and red1? cells twice (two biological replicates) and performed gene expresssion profiling analyses using data obtained from two independent RNA-seq of the three S.pombe strains.