A unified view of low complexity regions (LCRs) across species.
A unified view of low complexity regions (LCRs) across species.
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DOI：
10.7554/elife.77058
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发表时间：
2022-09-13
期刊：
影响因子：
7.7
通讯作者：
Calo, Eliezer
中科院分区：
文献类型：
--
作者：
Lee, Byron;Jaberi-Lashkari, Nima;Calo, Eliezer
关键词：
低复杂性区域(LCR)在许多重要的生物过程中发挥着作用，但我们对它们的序列、特征、关系和功能缺乏统一的看法。在这里，我们使用点图和降维来系统地定义LCR类型/复制关系，并创建能够整合LCR特征和功能的LCR序列空间图。通过定义蛋白质组中的LCR关系，我们深入了解了LCR类型和拷贝数如何有助于更高顺序的组装，例如富含K的LCR拷贝数对核仁蛋白RPA43在体内和体外组装的重要性。通过LCR图谱，我们揭示了LCR序列空间的潜在结构，并将该空间中的差异占据与包括后生动物细胞外基质和植物细胞壁在内的高阶组装的保守和出现联系起来。总之，LCR关系和图谱揭示和识别了核仁中富含E的LCR蛋白之间的支架-客户关系，并揭示了LCR序列空间中先前未描述的区域，具有更高阶组装的特征，包括硬骨特有的T/H丰富的序列空间。因此，LCRs的这种统一视图使得发现LCRs如何编码生物体的更高顺序组合成为可能。
Low complexity regions (LCRs) play a role in a variety of important biological processes, yet we lack a unified view of their sequences, features, relationships, and functions. Here, we use dotplots and dimensionality reduction to systematically define LCR type/copy relationships and create a map of LCR sequence space capable of integrating LCR features and functions. By defining LCR relationships across the proteome, we provide insight into how LCR type and copy number contribute to higher order assemblies, such as the importance of K-rich LCR copy number for assembly of the nucleolar protein RPA43 in vivo and in vitro. With LCR maps, we reveal the underlying structure of LCR sequence space, and relate differential occupancy in this space to the conservation and emergence of higher order assemblies, including the metazoan extracellular matrix and plant cell wall. Together, LCR relationships and maps uncover and identify scaffold-client relationships among E-rich LCR-containing proteins in the nucleolus, and revealed previously undescribed regions of LCR sequence space with signatures of higher order assemblies, including a teleost-specific T/H-rich sequence space. Thus, this unified view of LCRs enables discovery of how LCRs encode higher order assemblies of organisms.