Uncovering Transcriptional Regulators and Targets of sRNAs Using an Integrative Data-Mining Approach: H-NS-Regulated RseX as a Case Study.
Uncovering Transcriptional Regulators and Targets of sRNAs Using an Integrative Data-Mining Approach: H-NS-Regulated RseX as a Case Study.
复制标题
DOI：
10.3389/fcimb.2021.696533
复制
发表时间：
2021
影响因子：
5.7
通讯作者：
Contreras LM
中科院分区：
文献类型：
--
作者：
Mihailovic MK;Ekdahl AM;Chen A;Leistra AN;Li B;González Martínez J;Law M;Ejindu C;Massé É;Freddolino PL;Contreras LM
细菌小RNA(SRNAs)通过在感染过程中实现快速、有效的基因衰减网络，在发病机制中发挥重要作用。近几十年来，革兰氏阳性和革兰氏阴性病原体中建议的和生化确认的sRNAs的数量激增。然而，有限的同源性、网络复杂性和条件特异性阻碍了对这些RNA调节因子活性和调控的完整表征。为了简化sRNAs表达及其转录后活动的发现，我们提出了一种整合的体内数据挖掘方法，将DNA蛋白质占有率、RNA-SEQ和RNA可及性数据与基序识别和靶标预测算法相结合。我们以特征良好的大肠杆菌sRNA的子集为基准，其中一定程度的体内转录调控和转录后活性先前已被报道，并在该sRNA集的很大一部分中找到了对已知调控的支持。我们展示了我们的方法扩展对sna RseX的理解的能力，sna RseX是一种已知的包膜应力连锁sRNA，由于缺乏本地表达检测，其细胞角色一直难以捉摸。使用提出的方法，我们确定了一小部分假定的RseX调节器和靶标用于实验研究。这些发现使我们能够确认天然的RseX在消除H-NS抑制的条件下的表达，以及揭示RseX在菌毛调控中的转录后作用。除了RseX，我们还发现了163个推测的调控DNA结合蛋白位点，对应于62个sRNAs的调控，这可能会导致对sRNA转录调控的新理解。对于32个sRNA，我们还提出了一个子集的顶级靶点，通过参与筛选出在体内表现出结合位点可及性行为的区域。我们普遍预计，所提出的方法将有助于细菌中sRNA依赖的网络表征。在与发病机制相关的环境条件下进行这种研究，将使我们能够推断支持感染的复杂的快速调节方案。
Bacterial small RNAs (sRNAs) play a vital role in pathogenesis by enabling rapid, efficient networks of gene attenuation during infection. In recent decades, there has been a surge in the number of proposed and biochemically-confirmed sRNAs in both Gram-positive and Gram-negative pathogens. However, limited homology, network complexity, and condition specificity of sRNA has stunted complete characterization of the activity and regulation of these RNA regulators. To streamline the discovery of the expression of sRNAs, and their post-transcriptional activities, we propose an integrative in vivo data-mining approach that couples DNA protein occupancy, RNA-seq, and RNA accessibility data with motif identification and target prediction algorithms. We benchmark the approach against a subset of well-characterized E. coli sRNAs for which a degree of in vivo transcriptional regulation and post-transcriptional activity has been previously reported, finding support for known regulation in a large proportion of this sRNA set. We showcase the abilities of our method to expand understanding of sRNA RseX, a known envelope stress-linked sRNA for which a cellular role has been elusive due to a lack of native expression detection. Using the presented approach, we identify a small set of putative RseX regulators and targets for experimental investigation. These findings have allowed us to confirm native RseX expression under conditions that eliminate H-NS repression as well as uncover a post-transcriptional role of RseX in fimbrial regulation. Beyond RseX, we uncover 163 putative regulatory DNA-binding protein sites, corresponding to regulation of 62 sRNAs, that could lead to new understanding of sRNA transcription regulation. For 32 sRNAs, we also propose a subset of top targets filtered by engagement of regions that exhibit binding site accessibility behavior in vivo. We broadly anticipate that the proposed approach will be useful for sRNA-reliant network characterization in bacteria. Such investigations under pathogenesis-relevant environmental conditions will enable us to deduce complex rapid-regulation schemes that support infection.