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<p>Single-cell sequencing has advanced our understanding of cell-type diversity and heterogeneity. However, existing single-cell multi-omics methods lack the ability to monitor gene expression dynamics during S-phase progression. Here, we introduce single-cell (sc)Repli-RamDA-seq (scRR-seq), a multi-omics method that enables high-resolution DNA replication profiling and full-length total RNA sequencing from the same single cell in a haplotype-specific manner. scRR-seq generates DNA replication and RNA sequencing data comparable to individually obtained scRepli-seq and scRamDA-seq data, respectively. Unlike other scDNA/RNA-seq methods, scRR-seq allows one to tell the S-phase stage of a given cell based on the percentage of the replicated genome derived from scRepli-seq data. This facilitates analysis&#xa0;of gene expression dynamics during S-phase progression, enabling the&#xa0;identification&#xa0;of S-phase progression markers. scRR-seq also detects copy-number variation in non-S-phase cells and outperforms other scDNA/RNA-seq methods in various measures. Taken together, scRR-seq is a robust single-cell multi-omics method with promising potential for comprehensive genome/transcriptome analysis.</p>

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scRepli-RamDA-seq: a multi-omics technology enabling the analysis of gene expression dynamics during S-phase

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2025年12月15日

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  • Rawin Poonperm,
  • Taiki Yoneda,
  • Taito Imada,
  • Saori Takahashi,
  • Takako Ichinose,
  • Hisashi Miura,
  • Tetsutaro Hayashi,
  • Mariko Kuse,
  • Mika Yoshimura,
  • Koji Nagao,
  • Chikashi Obuse,
  • Itoshi Nikaido,
  • Ichiro Hiratani,
  • Shin-ichiro Takebayashi

摘要

Single-cell sequencing has advanced our understanding of cell-type diversity and heterogeneity. However, existing single-cell multi-omics methods lack the ability to monitor gene expression dynamics during S-phase progression. Here, we introduce single-cell (sc)Repli-RamDA-seq (scRR-seq), a multi-omics method that enables high-resolution DNA replication profiling and full-length total RNA sequencing from the same single cell in a haplotype-specific manner. scRR-seq generates DNA replication and RNA sequencing data comparable to individually obtained scRepli-seq and scRamDA-seq data, respectively. Unlike other scDNA/RNA-seq methods, scRR-seq allows one to tell the S-phase stage of a given cell based on the percentage of the replicated genome derived from scRepli-seq data. This facilitates analysis of gene expression dynamics during S-phase progression, enabling the identification of S-phase progression markers. scRR-seq also detects copy-number variation in non-S-phase cells and outperforms other scDNA/RNA-seq methods in various measures. Taken together, scRR-seq is a robust single-cell multi-omics method with promising potential for comprehensive genome/transcriptome analysis.