Conformation Selective Antibody Enables Genome Profiling and Leads to Discovery of Parallel G-quadruplex in Human Telomeres

We report the application of an parallel specific antibody, D1, for high-throughput profiling of genomic parallel G-quadruplexes in mammalian cells.ChIP-seq data together with a bioinformatic analysis revealed that parallel quadruplexes were largely presented in gene regions. Besides, consensus sequences for parallel quadruplex formation were characterized, which is presented as a G-rich sequence with a short loop size (<3nt). These results indicated that the G-rich sequences with short loops (N1-3: 55.2%) tended to form parallel G-quadruplexes in cells.Furtherly, we analyzed the association between D1 and the telomeric G-quadruplex in vivo. Here, reads consisting of more than 3 TTAGGG/CCCTAA occurrences were defined as telomeric reads. In D1 ChIP sample, the abundance of telomeric reads was 4.18-fold higher than input (Figure 3A), indicating the formation of parallel G-quadruplex at telomeres in living cells.