Regulation of gene expression by the BLM helicase correlates with the presence of G-quadruplex DNA motifs

Abstract

Bloom syndrome is a rare autosomal recessive disorder characterized by genetic instability and cancer predisposition, and caused by mutations in the gene encoding the Bloom syndrome, RecQ helicase-like (BLM) protein. To determine whether altered gene expression might be responsible for pathological features of Bloom syndrome, we analyzed mRNA and microRNA (miRNA) expression in fibroblasts from individuals with Bloom syndrome and in BLM-depleted control fibroblasts. We identified mRNA and miRNA expression differences in Bloom syndrome patient and BLM-depleted cells. Differentially expressed mRNAs are connected with cell proliferation, survival, and molecular mechanisms of cancer, and differentially expressed miRNAs target genes involved in cancer and in immune function. These and additional altered functions or pathways may contribute to the proportional dwarfism, elevated cancer risk, immune dysfunction, and other features observed in Bloom syndrome individuals. BLM binds to G-quadruplex (G4) DNA, and G4 motifs were enriched at transcription start sites (TSS) and especially within first introns (false discovery rate ≤ 0.001) of differentially expressed mRNAs in Bloom syndrome compared with normal cells, suggesting that G-quadruplex structures formed at these motifs are physiologic targets for BLM. These results identify a network of mRNAs and miRNAs that may drive the pathogenesis of Bloom syndrome.

Fig. 1.

mRNA and miRNA expression patterns distinguish BS and BLM-depleted cells from comparable controls. PCAs of mRNA expression (A) and miRNA expression in BS (orange) and NM (blue) cells (B) by using average distance and linkage measures. Percentages indicate the portion of expression differences that can be attributed to specific principal components. (C) Differentially expressed mRNAs identified in BS versus NM cells, and in BLM versus control fibroblasts treated with a nonspecific shRNA. (D) Differentially expressed miRNAs identified in BS versus NM cells, and in BLM versus control fibroblasts treated with a nonspecific shRNA. A total of 34,933 probes were present on mRNA arrays, whereas 149 miRNAs were represented in common on the array and Nanostring platforms used for miRNA expression profiling.

Fig. 2.

G4 motif frequencies and enrichment near transcription start sites and intron 1 boundaries of genes with altered expression in BS cells. (A) G4 motif frequencies as a function of location in genes up- and down-regulated in BS patient cells. G4 motif counts are shown for NT and TS over the 250 bp ± gene TSSs and exon 1/intron 1 5′ boundaries for genes expression of which was up- or down-regulated (red and blue curves, respectively) versus the comparable distributions for 1,000 randomly selected gene sets of equal size drawn from the pool of all genes on expression arrays. Gray areas indicate average G4 motif frequencies among all genes surveyed on expression arrays. (B) FDR of observed G4 motif frequencies compared with 1,000 randomly selected gene sets of equal size. ns, nonsignificant (FDR > 0.05).