Shared and organ-specific gene-expression programs during the development of the cochlea and the superior olivary complex

The peripheral and central auditory subsystems together form a complex sensory network that allows an organism to hear. The genetic programs of the two subsystems must therefore be tightly coordinated during development. Yet, their interactions and common expression pathways have never been systematically explored. MicroRNAs (miRNAs) are short non-coding RNAs that regulate gene expression and are essential for normal development of the auditory system. We performed mRNA and small-RNA sequencing of organs from both auditory subsystems at three critical developmental timepoints (E16, P0, P16) to obtain a comprehensive and unbiased insight of their expression profiles. Our analysis reveals common and organ-specific expression patterns for differentially regulated mRNAs and miRNAs, which could be clustered with a particular selection of functions such as inner ear development, Wnt signalling, K+ transport, and axon guidance, based on gene ontology. Bioinformatics detected enrichment of predicted targets of specific miRNAs in the clusters and predicted regulatory interactions by monitoring opposite trends of expression of miRNAs and their targets. This approach identified six miRNAs as strong regulatory candidates for both subsystems. Among them was miR-96, an established critical factor for proper development in both subsystems, demonstrating the strength of our approach. We suggest that other miRNAs identified by this analysis are also common effectors of proper hearing acquirement. This first combined comprehensive analysis of the developmental program of the peripheral and central auditory systems provides important data and bioinformatics insights into the shared genetic program of the two sensory subsystems and their regulation by miRNAs.

外周与中枢听觉亚系统共同构成了复杂的感觉网络，使生物体能够听见声音。因此，二者在发育过程中的遗传程序必须受到严格协调。然而，二者间的相互作用及共有表达通路尚未得到系统性探索。

微小RNA（miRNAs）是一类短链非编码RNA，可调控基因表达，对听觉系统的正常发育至关重要。我们针对两个听觉亚系统的器官，在三个关键发育时间点（E16、P0、P16）开展了mRNA与小RNA测序，以全面且无偏倚地解析其表达谱特征。分析结果揭示了差异调控的mRNA与miRNA的共有表达模式及器官特异性表达模式；基于基因本体（gene ontology）注释，可将这些分子聚类至特定功能类别，涵盖内耳发育、Wnt信号通路、钾离子转运及轴突导向等生物学过程。

生物信息学分析发现，上述聚类中富集了特定miRNA的预测靶基因，并通过监测miRNA与其靶基因的表达趋势负相关，预测了二者的调控相互作用。通过该方法，本研究筛选出6个可作为两个听觉亚系统关键调控候选因子的miRNA。其中miR-96便是其中之一，它是已被证实的、对两个亚系统正常发育至关重要的关键因子，这一结果验证了本研究方法的有效性。我们推测，本分析中筛选出的其他miRNA同样是听觉正常发育的共有效应因子。

这项针对外周与中枢听觉系统发育程序的首次联合全面分析，为两个感觉亚系统的共有遗传程序及其受miRNA调控的机制提供了重要数据与生物信息学研究视角。