Systematic Identification of Post-Transcriptional Regulatory Modules
Systematic Identification of Post-Transcriptional Regulatory Modules
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DOI：
10.1101/2023.02.27.530345
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发表时间：
2023-03
期刊：
影响因子：
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通讯作者：
M. Khoroshkin;A. Buyan;Martin Dodel;A. Navickas;Johnny Yu;Fathima Trejo;Anthony Doty;Rithvik Baratam;S. Zhou;Tanvi Joshi;Kristle Garcia;B. Choi;S. Miglani;Vishvak Subramanyam;Hailey Modi;Daniel Markett;M. Corces;I. Kulakovskiy;F. Mardakheh;H. Goodarzi
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文献类型：
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作者：
M. Khoroshkin;A. Buyan;Martin Dodel;A. Navickas;Johnny Yu;Fathima Trejo;Anthony Doty;Rithvik Baratam;S. Zhou;Tanvi Joshi;Kristle Garcia;B. Choi;S. Miglani;Vishvak Subramanyam;Hailey Modi;Daniel Markett;M. Corces;I. Kulakovskiy;F. Mardakheh;H. Goodarzi
在我们的细胞中，有限数量的RNA结合蛋白（RBP）负责整个转录组中RNA代谢的所有方面。为了实现这一点，RBP形成作用于特定靶调节子的调节单元。然而，景观的RBP组合的相互作用仍然很少探索。在这里，我们进行了系统的注释RBP组合的相互作用，通过多模态数据集成。我们通过生成50个人类RBP的体内邻近依赖性生物素化数据集，构建了RBP蛋白邻域的大规模地图。同时，我们使用CRISPR干扰单细胞读数来捕获RBP敲低后的转录组学变化。通过将这些物理和功能相互作用读数与来自eCLIP测定的RBP mRNA靶点图谱沿着组合，我们生成了功能性RBP相互作用的整合图谱。然后，我们使用这个地图来匹配RBPs的上下文特定的功能，并验证了预测的功能生化四个RBPs。这项研究突出了以前未被充分认识的RBP间相互作用的规模，无论是遗传的还是物理的，并且是更全面地了解转录后调控过程及其潜在分子语法的第一步。
In our cells, a limited number of RNA binding proteins (RBPs) are responsible for all aspects of RNA metabolism across the entire transcriptome. To accomplish this, RBPs form regulatory units that act on specific target regulons. However, the landscape of RBP combinatorial interactions remains poorly explored. Here, we performed a systematic annotation of RBP combinatorial interactions via multimodal data integration. We built a large-scale map of RBP protein neighborhoods by generating in vivo proximity-dependent biotinylation datasets of 50 human RBPs. In parallel, we used CRISPR interference with single-cell readout to capture transcriptomic changes upon RBP knockdowns. By combining these physical and functional interaction readouts, along with the atlas of RBP mRNA targets from eCLIP assays, we generated an integrated map of functional RBP interactions. We then used this map to match RBPs to their context-specific functions and validated the predicted functions biochemically for four RBPs. This study highlights the previously underappreciated scale of the inter-RBP interactions, be it genetic or physical, and is a first step towards a more comprehensive understanding of post-transcriptional regulatory processes and their underlying molecular grammar.