Identification of SLIRP as a G Quadruplex-Binding Protein

• Published in: Journal of the American Chemical Society Vol. 139; no. 36; pp. 12426 - 12429
• Main Authors: Williams, Preston, Li, Lin, Dong, Xiaoli, Wang, Yinsheng
• Format: Journal Article
• Language: English
• Published: United States American Chemical Society 13.09.2017
• Subjects: Chromatin Immunoprecipitation; Clustered Regularly Interspaced Short Palindromic Repeats; DNA; DNA replication; G-Quadruplexes; genes; Genome, Human; genomics; guanine; Humans; Mass Spectrometry; Microscopy, Fluorescence; nucleotide sequences; Protein Binding; Proteome; RNA-Binding Proteins - chemistry; telomeres; transcription (genetics)
• ISSN: 0002-7863; 1520-5126; 1520-5126
• DOI: 10.1021/jacs.7b07563

The guanine quadruplex (G4) structure in DNA is a secondary structure motif that plays important roles in DNA replication, transcriptional regulation, and maintenance of genomic stability. Here, we employed a quantitative mass spectrometry-based approach to profile the interaction proteomes of three well-defined G4 structures derived from the human telomere and the promoters of cMYC and cKIT genes. We identified SLIRP as a novel G4-interacting protein. We also demonstrated that the protein could bind directly with G4 DNA with K d values in the low nanomolar range and revealed that the robust binding of the protein toward G4 DNA requires its RRM domain. We further assessed, by using CRISPR-Cas9-introduced affinity tag and ChIP-Seq analysis, the genome-wide occupancy of SLIRP, and showed that the protein binds preferentially to G-rich DNA sequences that can fold into G4 structures. Together, our results uncovered a novel cellular protein that can interact directly with G4 DNA, which underscored the complex regulatory networks involved in G4 biology.