The effect of pab2 deletion or clr4-1 mutation on gene expression in the fission yeast Schizosaccharomyces japonicus

Pab2/PABPN1 is a nuclear poly(A)-binding protein, but its function is not fully understood yet. To investigate the Pab2 role in shaping transcriptome, we delete the pab2 gene in S. japonicus and characterize it. We found that meiosis-related genes are increased in pab2∆. Surprisingly, we observed the increases in transcripts derived from constitutive heterochromatin. Moreover, the upregulated and downregulated genes in pab2∆ and clr4 (the ortholog of the histone H3 Lys9 methyltransferase SUV39) mutant cells were significantly overlapped. Besides, constitutive heterochromatin is adversely affected in pab2∆. Our analyses demonstrate that Pab2 is required for the assembly of constitutive heterochromatin, and this finding provides a new insight into the Pab2 function(s). We constructed pab2∆ cells using the standard gene replacement method and clr4-1 mutant cells using the PCR-based random mutagenesis of the clr4 gene. We then isolated total RNA from vegetative wild-type, pab2∆, and clr4-1 cells twice (two biological replicates) and performed gene expresssion profiling analyses using data obtained from two independent RNA-seq of the three S. japonicus strains.