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

Author

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  • Ruitu Lyu

    (The University of Chicago
    The University of Chicago
    The University of Chicago)

  • Yun Gao

    (The University of Chicago
    The University of Chicago
    The University of Chicago)

  • Tong Wu

    (The University of Chicago
    The University of Chicago
    The University of Chicago)

  • Chang Ye

    (The University of Chicago
    The University of Chicago
    The University of Chicago)

  • Pingluan Wang

    (The University of Chicago
    The University of Chicago
    The University of Chicago)

  • Chuan He

    (The University of Chicago
    The University of Chicago
    The University of Chicago
    The University of Chicago)

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.

Suggested Citation

  • Ruitu Lyu & Yun Gao & Tong Wu & Chang Ye & Pingluan Wang & Chuan He, 2024. "Quantitative analysis of cis-regulatory elements in transcription with KAS-ATAC-seq," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
  • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-50680-8
    DOI: 10.1038/s41467-024-50680-8
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