Environmental Toxicology Graduate Program, University of California, Riverside, Riverside, CA 92521-0403, USA.
Department of Chemistry, University of California, Riverside, Riverside, CA 92521-0403, USA.
Nucleic Acids Res. 2023 Sep 8;51(16):8434-8446. doi: 10.1093/nar/gkad588.
High-order chromatin organization plays an important role in biological processes and disease development. Previous studies revealed a widespread occurrence of guanine quadruplex (G4) structures in the human genome, with enrichment in gene regulatory regions, especially in promoters. However, it remains unclear whether G4 structures contribute to RNA polymerase II (RNAPII)-mediated long-range DNA interactions and transcription activity. In this study, we conducted an intuitive overlapping analysis of previously published RNAPII ChIA-PET (chromatin interaction analysis with paired-end tag) and BG4 ChIP-seq (chromatin immunoprecipitation followed by sequencing using a G4 structure-specific antibody) data. We observed a strong positive correlation between RNAPII-linked DNA loops and G4 structures in chromatin. Additionally, our RNAPII HiChIP-seq (in situ Hi-C followed by ChIP-seq) results showed that treatment of HepG2 cells with pyridostatin (PDS), a small-molecule G4-binding ligand, could diminish RNAPII-linked long-range DNA contacts, with more pronounced diminutions being observed for those contacts involving G4 structure loci. RNA sequencing data revealed that PDS treatment modulates the expression of not only genes with G4 structures in their promoters, but also those with promoters being connected with distal G4s through RNAPII-linked long-range DNA interactions. Together, our data substantiate the function of DNA G4s in RNAPII-associated DNA looping and transcription regulation.
高级染色质组织在生物过程和疾病发展中起着重要作用。先前的研究表明，在人类基因组中广泛存在鸟嘌呤四链体（G4）结构，其在基因调控区域富集，特别是在启动子中。然而，G4 结构是否有助于 RNA 聚合酶 II（RNAPII）介导的长距离 DNA 相互作用和转录活性仍不清楚。在这项研究中，我们对先前发表的 RNAPII ChIA-PET（通过末端配对标签进行染色质相互作用分析）和 BG4 ChIP-seq（使用 G4 结构特异性抗体进行染色质免疫沉淀测序）数据进行了直观的重叠分析。我们观察到 RNAPII 相关 DNA 环与染色质中的 G4 结构之间存在强烈的正相关。此外，我们的 RNAPII HiChIP-seq（原位 Hi-C 后进行 ChIP-seq）结果表明，用小分子 G4 结合配体吡啶并[4,3-d]嘧啶（PDS）处理 HepG2 细胞可以减少 RNAPII 相关的长距离 DNA 接触，而涉及 G4 结构位点的接触减少更为明显。RNA 测序数据表明，PDS 处理不仅调节了启动子中具有 G4 结构的基因的表达，还调节了通过 RNAPII 相关的长距离 DNA 相互作用与远端 G4 相连的启动子的基因表达。总之，我们的数据证实了 DNA G4 在 RNAPII 相关的 DNA 环化和转录调控中的作用。
