Single-nucleotide transcription start sites profiling via Nascent Strand-Specific RNA sequencing uncovers IFN-γ-induced promoter dynamics

Ke Sun; Luemou Shen; Junli Wang; Jiahao Zheng; Xu Zhang; Fucheng Luo; Kai Chen; Ning Song

doi:10.1016/j.jgg.2026.03.014

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Single-nucleotide transcription start sites profiling via Nascent Strand-Specific RNA sequencing uncovers IFN-γ-induced promoter dynamics

doi: 10.1016/j.jgg.2026.03.014

a. State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China;
b. Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, Guangdong 511458, China;
c. Archaeal Biology Center, Synthetic Biology Research Center, Shenzhen Key Laboratory of Marine Microbiome Engineering, Key Laboratory of Marine Microbiome Engineering of Guangdong Higher Education Institutes, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong 518060, China;
d. Shandong Provincial Key Laboratory of Development and Regeneration, School of Life Sciences, Shandong University, Qingdao, Shandong 266237, China

Funds:

This study was supported by the National Natural Science Foundation of China (32270560), the Principal Investigator Project of the Southern Marine Science and Engineering Guangdong Laboratory (YQ2024004), the Natural Science Foundation of Yunnan Province (202102AA100053), and the Natural Science Foundation of Shandong Province (ZR2023MC091).

Received Date: 2026-01-12
Accepted Date: 2026-03-16
Rev Recd Date: 2026-03-13

Available Online: 2026-03-24

Abstract

Abstract

Transcriptional regulation is a highly dynamic process in which nascent RNAs provide the most immediate readout of transcriptional activity. Precise mapping of transcription start sites (TSSs) is therefore critical for understanding promoter architecture and gene regulation, yet remains technically challenging. Here, we introduce Nascent Strand-Specific RNA sequencing (NSS-seq), a robust and streamlined method for genome-wide profiling of the capped 5′ ends of nascent RNAs. By directly capturing transcription initiation events, NSS-seq overcomes the temporal delay inherent to conventional RNA-seq and enables time-resolved interrogation of transcriptional dynamics. Applied to interferon-gamma (IFN-γ)-stimulation, NSS-seq uncovered previously unrecognized IFN-γ-responsive genes and transient transcription factor activation patterns underlying interferon-mediated tumor-suppressive functions. Together, NSS-seq provides a cost-effective and technically accessible platform for dissecting promoter-level regulatory dynamics during cellular responses.
- NSS-seq,
- Nascent RNA,
- Transcription start site (TSS),
- Transcription initiation,
- Interferon-γ signaling,
- Promoter dynamics

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References(55)

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