Transcriptional regulation by a RecQ helicase

Abstract

RecQ helicases participate in a variety of DNA metabolic processes through their multiple biochemical activities. In vitro characterization and cellular studies have suggested that RECQ1 (also known as RECQL or RECQL1) performs its diverse functions through specific interactions with DNA and protein partners. We have taken an unbiased approach to determine the contribution of RECQ1 in genome maintenance and as a putative susceptibility factor in breast cancer. Here, we provide methodology to map the genome-wide binding sites of RECQ1 together with the profiling of RECQ1-dependent transcriptome to investigate its role in gene regulation. The described approach will be helpful to develop a mechanistic framework for elucidating critical functions of RECQ1 and other RecQ homologs in distinct chromatin and biological contexts.

Keywords: ChIP-seq; Genomic stability; Helicase; RNA-seq; RecQ; Transcription.

Figure 1.

Schematic of experimental workflow for unbiased investigation of genome-wide roles of RECQ1 (and in principle, other RecQ helicases) in transcriptional regulation. Methodology for ChIP-seq (A) and RNA-seq (B) are outlined in this chapter.

Figure 2.

Elucidating gene regulatory mechanisms of RECQ1 by integrating ChIP-seq and RNA-seq data. Determination of the genomic landscape of RECQ1 binding and integrating that with the transcriptomic changes in RECQ1-deficient cells allows identification of genome-wide regions where RECQ1 functions, in cooperation with other transcription factors and co-factors to regulate transcriptional outcomes. RecQ helicases likely employ their catalytic activities and structure specific DNA binding in regulating gene expression. We recently employed this approach to uncover a new role of RECQ1 in regulation of estrogen response pathway. TSS denotes transcriptional start site.