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<p>Characterizing shared patterns of RNA expression between genes across conditions has led to the discovery of regulatory networks and biological functions. However, it is unclear if such coordination extends to translation. In this study, we uniformly analyze 3,819 ribosome profiling datasets from 117 human and 94 mouse tissues and cell lines. We introduce the concept of translation efficiency covariation (TEC), identifying coordinated translation patterns across cell types. We nominate candidate mechanisms driving shared patterns of translation regulation. TEC is conserved across human and mouse cells and uncovers gene functions that are not evident from RNA or protein co-expression. Moreover, our observations indicate that proteins that physically interact are highly enriched for positive covariation at both translational and transcriptional levels. Our findings establish TEC as a conserved organizing principle of mammalian transcriptomes. TEC has potential as a predictive marker for gene function and may offer a framework for designing gene expression systems in synthetic biology and biotechnological applications.</p>

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Translation efficiency covariation identifies conserved coordination patterns across cell types

  • 期刊论文

  • 发表日期：

    2025年7月25日

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  • Yue Liu,
  • Shilpa Rao,
  • Ian Hoskins,
  • Michael Geng,
  • Qiuxia Zhao,
  • Jonathan Chacko,
  • Vighnesh Ghatpande,
  • Kangsheng Qi,
  • Logan Persyn,
  • Jun Wang,
  • Dinghai Zheng,
  • Yochen Zhong,
  • Dayea Park,
  • Elif Sarinay Cenik,
  • Vikram Agarwal,
  • Hakan Ozadam,
  • Can Cenik

摘要

Characterizing shared patterns of RNA expression between genes across conditions has led to the discovery of regulatory networks and biological functions. However, it is unclear if such coordination extends to translation. In this study, we uniformly analyze 3,819 ribosome profiling datasets from 117 human and 94 mouse tissues and cell lines. We introduce the concept of translation efficiency covariation (TEC), identifying coordinated translation patterns across cell types. We nominate candidate mechanisms driving shared patterns of translation regulation. TEC is conserved across human and mouse cells and uncovers gene functions that are not evident from RNA or protein co-expression. Moreover, our observations indicate that proteins that physically interact are highly enriched for positive covariation at both translational and transcriptional levels. Our findings establish TEC as a conserved organizing principle of mammalian transcriptomes. TEC has potential as a predictive marker for gene function and may offer a framework for designing gene expression systems in synthetic biology and biotechnological applications.