Scholarlink

<p>Understanding genome regulation is limited by the complexity of molecular interactions in living cells. Cell-free systems provide a simplified platform for studying gene expression, but low mRNA levels have prevented RNA-seq. To address this, we develop an active learning workflow combining Bayesian optimization with automated high-throughput experimentation to systematically explore over 1.6 million buffer compositions, experimentally testing 653. We identify a “mRNA-optimized” buffer (20-fold increase in mRNA yield) and a “trade-off” buffer (13-fold increase while maintaining protein production). Using direct RNA-seq, we profile the T7 phage transcriptome in cell-free systems and compare it with a purified T7-RNAP transcription system and phage-infected bacteria. This comparative analysis reveals distinct regulatory layers: the T7-RNAP system captures promoter-strength hierarchies but lacks RNA degradation, whereas cell-free systems provide an accurate estimation of in vivo expression and reveal mRNA maturation sites. This work establishes cell-free transcriptomics as a controlled approach to study genome regulation.</p>

错误：搜索内容不能为空，请输入英文关键词
错误：关键词超出字数限制，请精简
高级检索

Active-learning-guided optimization of cell-free systems for genome-wide transcriptomic profiling reveals progressive layers of regulation

  • 期刊论文

  • 出版模式：

    开放获取

  • 发表日期：

    2026年6月27日

查看全文
  • Léa Wagner,
  • An Hoang,
  • Olivier Rue,
  • Olivier Delumeau,
  • Valentin Loux,
  • Gabin Derache,
  • Jean-Loup Faulon,
  • Matthieu Jules,
  • Olivier Borkowski

摘要

Understanding genome regulation is limited by the complexity of molecular interactions in living cells. Cell-free systems provide a simplified platform for studying gene expression, but low mRNA levels have prevented RNA-seq. To address this, we develop an active learning workflow combining Bayesian optimization with automated high-throughput experimentation to systematically explore over 1.6 million buffer compositions, experimentally testing 653. We identify a “mRNA-optimized” buffer (20-fold increase in mRNA yield) and a “trade-off” buffer (13-fold increase while maintaining protein production). Using direct RNA-seq, we profile the T7 phage transcriptome in cell-free systems and compare it with a purified T7-RNAP transcription system and phage-infected bacteria. This comparative analysis reveals distinct regulatory layers: the T7-RNAP system captures promoter-strength hierarchies but lacks RNA degradation, whereas cell-free systems provide an accurate estimation of in vivo expression and reveal mRNA maturation sites. This work establishes cell-free transcriptomics as a controlled approach to study genome regulation.