Side-by-side comparison of G-quadruplex (G4) capture efficiency of the antibody BG4 versus the small-molecule ligands TASQs

• Published in: iScience Vol. 26; no. 6; p. 106846
• Main Authors: Feng, Yilong, He, Zexue, Luo, Zhenyu, Sperti, Francesco Rota, Valverde, Ibai E., Zhang, Wenli, Monchaud, David
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 16.06.2023; Elsevier
• Subjects: biochemistry; Biochemistry, Molecular Biology; chemistry; Genetics; Genomics; Life Sciences; Medical biochemistry; Plants genetics; chemistry; Medical biochemistry; biochemistry
• ISSN: 2589-0042; 2589-0042
• DOI: 10.1016/j.isci.2023.106846

The search for G-quadruplex (G4)-forming sequences across the genome is motivated by their involvement in key cellular processes and their putative roles in dysregulations underlying human genetic diseases. Sequencing-based methods have been developed to assess the prevalence of DNA G4s genome wide, including G4-seq to detect G4s in purified DNA (in vitro) using the G4 stabilizer PDS, and G4 chromatin immunoprecipitation and sequencing (G4 ChIP-seq) to detect G4s in in situ fixed chromatin (in vivo) using the G4-specific antibody BG4. We recently reported on G4-RNA precipitation and sequencing (G4RP-seq) to assess the in vivo prevalence of RNA G4 landscapes transcriptome wide using the small molecule BioTASQ. Here, we apply this technique for mapping DNA G4s in plants (rice) and compare the efficiency of this new technique, G4-DNA precipitation and sequencing, G4DP-seq, to that of BG4-DNA-IP-seq that we developed for mapping of DNA G4s in rice using BG4. By doing so, we compare the G4 capture ability of small-sized ligands (BioTASQ and BioCyTASQ) versus the antibody BG4. [Display omitted] •Sequencing-based techniques are pivotal to understand G-quadruplex-DNA biology•Prior to sequencing, G4s must be isolated by affinity capture in vitro or in vivo•We compare here G4 chemoprecipitation by TASQs and immunoprecipitation by BG4•G4DP-seq (TASQ) and BG4-DNA-IP-seq (BG4) offer complementary views on G4 landscapes Biochemistry; Chemistry; Medical biochemistry