Quantitative analysis of cis-regulatory elements in transcription with KAS-ATAC-seq

Ruitu Lyu (), Yun Gao, Tong Wu, Chang Ye, Pingluan Wang and Chuan He ()
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Ruitu Lyu: The University of Chicago
Yun Gao: The University of Chicago
Tong Wu: The University of Chicago
Chang Ye: The University of Chicago
Pingluan Wang: The University of Chicago
Chuan He: The University of Chicago

Nature Communications, 2024, vol. 15, issue 1, 1-17

Abstract: 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.

Date: 2024
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DOI: 10.1038/s41467-024-50680-8

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