PDF(Pubmed)
Abstract：
Cis-regulatory elements (CREs) are pivotal in orchestrating gene expression throughout diverse biological systems. Accurate identification and in-depth characterization of functional CREs are crucial for decoding gene regulation networks during cellular processes. In this study, we develop Kethoxal-Assisted Single-stranded DNA Assay for Transposase-Accessible Chromatin with Sequencing (KAS-ATAC-seq) to quantitatively analyze the transcriptional activity of CREs. A main advantage of KAS-ATAC-seq lies in its precise measurement of ssDNA levels within both proximal and distal ATAC-seq peaks, enabling the identification of transcriptional regulatory sequences. This feature is particularly adept at defining Single-Stranded Transcribing Enhancers (SSTEs). SSTEs are highly enriched with nascent RNAs and specific transcription factors (TFs) binding sites that define cellular identity. Moreover, KAS-ATAC-seq provides a detailed characterization and functional implications of various SSTE subtypes. Our analysis of CREs during mouse neural differentiation demonstrates that KAS-ATAC-seq can effectively identify immediate-early activated CREs in response to retinoic acid (RA) treatment. Our findings indicate that KAS-ATAC-seq provides more precise annotation of functional CREs in transcription. Future applications of KAS-ATAC-seq would help elucidate the intricate dynamics of gene regulation in diverse biological processes.
摘要：
顺式调节元件（CREs）在协调整个生物系统中的基因表达方面至关重要。功能CRE的准确识别和深入表征对于在细胞过程中解码基因调控网络至关重要。在这项研究中,我们开发了用于转座酶可访问染色质的Kethoxal辅助单链DNA分析测序（KAS-ATAC-seq），以定量分析CREs的转录活性。KAS-ATAC-seq的主要优势在于其在近端和远端ATAC-seq峰内的ssDNA水平的精确测量，能够识别转录调控序列。该特征特别擅长定义单链转录增强子(SSTE)。SSTE高度富含新生RNA和定义细胞同一性的特异性转录因子(TF)结合位点。此外，KAS-ATAC-seq提供了各种SSTE亚型的详细表征和功能含义。我们对小鼠神经分化过程中的CRE的分析表明，KAS-ATAC-seq可以有效地识别响应于视黄酸（RA）治疗的立即早期激活的CRE。我们的发现表明KAS-ATAC-seq提供了转录中功能CRE的更精确注释。KAS-ATAC-seq的未来应用将有助于阐明不同生物过程中基因调控的复杂动力学。
