Identification of endogenous G-quadruplexes (G4s) in human, mouse, and pig (ATAC-Seq)

G4s are non-canonical four-stranded structures and emerge as novel genetic regulatory elements. Endogenous G4s (eG4s) can form quadruplex structures and induce double strand breaking during DNA replication, and thus contributing to genomic instability and genome evolution. Besides, eG4s are closely associated with gene expression regulation, and both their stimulative and repressive roles in the genome have been elucidated. Although functions of several specific G4s have been reported, a systematical identification and characterization of eG4s is still unconducted. Here we applied Cleavage Under Targets and Tagmentation (CUT&Tag) for mapping eG4s across human, mouse, and pig at high resolution and low background. We analyzed their genomics distribution, evolutionary conservation, dynamics, regulation, and impacts on gene expression in a single framework. ATAC-seq Overall design: We conducted ATAC-seq experiment on genomic DNA extracted from human (SW620) and pig (PK15 and ST) cells in two biological replicates.

G四链体（G4s）是一类非经典的四链核酸结构，现已成为新兴的基因调控元件。内源G四链体（eG4s）可在DNA复制过程中形成四链体结构并诱导双链断裂，进而参与基因组不稳定与基因组演化进程。此外，eG4s与基因表达调控密切相关，其在基因组中兼具激活与抑制基因表达的功能已得到系统阐明。尽管已有数种特定G4s的功能被报道，但目前仍未开展针对eG4s的系统性鉴定与表征工作。本研究借助靶标切割与标签化测序（Cleavage Under Targets and Tagmentation, CUT&Tag）技术，以高分辨率、低背景的方式在人类、小鼠及猪的全基因组范围内绘制eG4s的分布图谱。我们在统一分析框架下，对eG4s的基因组分布、进化保守性、动态变化、调控机制及其对基因表达的影响开展了全面分析。
转座酶可及性测序（ATAC-seq）实验设计：我们对从人类（SW620）及猪（PK15、ST）细胞中提取的基因组DNA开展了ATAC-seq实验，每组设置2次生物学重复。