Altered gene expression in the Werner and Bloom syndromes is associated with sequences having G-quadruplex forming potential

Abstract

The human Werner and Bloom syndromes (WS and BS) are caused by deficiencies in the WRN and BLM RecQ helicases, respectively. WRN, BLM and their Saccharomyces cerevisiae homologue Sgs1, are particularly active in vitro in unwinding G-quadruplex DNA (G4-DNA), a family of non-canonical nucleic acid structures formed by certain G-rich sequences. Recently, mRNA levels from loci containing potential G-quadruplex-forming sequences (PQS) were found to be preferentially altered in sgs1Delta mutants, suggesting that G4-DNA targeting by Sgs1 directly affects gene expression. Here, we extend these findings to human cells. Using microarrays to measure mRNAs obtained from human fibroblasts deficient for various RecQ family helicases, we observe significant associations between loci that are upregulated in WS or BS cells and loci that have PQS. No such PQS associations were observed for control expression datasets, however. Furthermore, upregulated genes in WS and BS showed no or dramatically reduced associations with sequences similar to PQS but that have considerably reduced potential to form intramolecular G4-DNA. These findings indicate that, like Sgs1, WRN and BLM can regulate transcription globally by targeting G4-DNA.

Figure 1.

Multivariate analyses of gene expression data. (A) Principle component analyses. Two-dimensional visualization of samples by the first two principal components (PC1 and PC2). (B) Average linkage clustering of samples by Euclidean distance. The vertical axis (Height) indicates the similarity between the clusters.

Figure 2.

Differentially expressed gene probes in RecQ helicase-deficient fibroblast cell strains. (A) upregulated genes and (B) downregulated genes. Indicated values are subsets of a total 22277 gene probes.

Figure 3.

Combined analysis of overlap significance in the indicated subgenic locations between differentially expressed genes and genes with PQS or PQS-related motifs having much lower G4-DNA forming potential (pPQS or pPQS-mut2). Values are given for associations with PQS (A), pPQS (B) and pPQS-mut2 (C). Significance is computed by one-sided Fisher’s test. Categorized by region, P-values are colored to highlight significant overlaps: white text within a black background indicates a P-value lower than 10⁻⁴. Black text within a gray background indicates a P-value of intermediate significance, between 10⁻⁴ and 10⁻³.