Transcriptome guided identification of novel functions of RECQ1 helicase

Abstract

Gene expression changes in the functional absence of a specific RecQ protein, and how that relates to disease outcomes including cancer predisposition and premature aging in RecQ helicase associated syndromes, are poorly understood. Here we describe detailed experimental strategy for identification of RECQ1-regulated transcriptome that led us to uncover a novel association of RECQ1 in regulation of cancer cell migration and invasion. We initiated a focused study to determine whether RECQ1, the most abundant RecQ protein in humans, alters gene expression and also investigated whether RECQ1 binds with G4 motifs predicted to form G-quadruplex structures in the target gene promoters. Rescue of mRNA expression of select RECQ1-downregulated genes harboring G4 motifs required wild-type RECQ1 helicase. However, some RECQ1-regulated genes are also regulated by BLM and WRN proteins regardless of the presence or absence of G4 motifs. The approach described here is applicable for systematic comparison of gene expression signatures of individual RecQ proteins in isogenic background, and to elucidate their participation in transcription regulation through G-quadruplex recognition and/or resolution. Such strategies might also reveal molecular pathways that drive the pathogenesis of cancer and other diseases in specific RecQ deficiency.

Clinicopathological and Functional Significance of RECQL1 Helicase in Sporadic Breast Cancers

“…A novel observation in the current study is that low RECQL1 also influenced survival in ER+ cohorts that received endocrine therapy implying that RECQL1 could also have predictive significance. Given the recent evidence that RECQL1 may modulate gene expression (26, 28), we speculate that ER and/or ER mediated gene expression could be influenced by low RECQL1 in tumours. To explore this hypothesis we investigated ERα protein levels in control and RECQL1-depleted breast cancer cells.…”

“…Given the recent evidence that RECQL1 may modulate gene expression (26, 28), we conducted preliminary studies to explore if RECQL1 may impact upon ERα expression in breast cancer cell lines. In control cells, as expected, ERα expression was not detectable in MDA-MB-468 cells and MCF-7 cells have proficient ERα expression.…”

Mechanistic and biological considerations of oxidatively damaged DNA for helicase-dependent pathways of nucleic acid metabolism

“…In the future, it will be important to assess RECQL1’s role in modulating gene expression in cancer cells exposed to agents that induce DNA damage, particularly oxidative stress given the observations that RECQL1 deficiency sensitizes cells to ionizing radiation or H 2 O 2 . Co-regulation of gene expression by RECQL1 and the sequence-related WRN and BLM helicases suggests that the potentially overlapping roles of human RecQ helicases in gene expression [95] may contribute to the complexity of the DNA damage response.…”

RecQ and Fe–S helicases have unique roles in DNA metabolism dictated by their unwinding directionality, substrate specificity, and protein interactions

“…WRN is also likely to regulate expression of genes with enriched G4 motifs at these locations, only in a different set compared with BLM, suggesting distinct roles of the two RecQ helicases in disease pathogenesis [156]. Other studies that included chromatin immunoprecipitation experiments suggested that RECQL1 [157], XPB, and the Fe–S helicase XPD [147] regulate gene expression directly through their interactions with predicted G4-forming sequences in promoters. Certain RecQ and Fe–S helicases also preferentially interact with and resolve unusual DNA structures in the G-rich telomeric repeats (see Telomeres ) (Figure 2).…”