Characterising the regulatory landscape during inner ear development

听力障碍是一种使人衰弱的状况，会影响正常生活的许多方面。听力在不同的环境中都很重要，包括对儿童语言和认知技能的发展，对成年人的工作表现和正常的社会互动。在世界范围内，大约每800名婴儿中就有一名患有听力问题，而60岁以上的成年人中有50%以上患有某种形式的听力缺陷。儿童的听力损失通常与内耳的缺陷有关，内耳是耳朵的一部分，容纳着感知声音和平衡的细胞（毛细胞），并产生向大脑传递信息的神经元。老年人的毛细胞是逐渐死亡的，既不能用耳内的其他细胞替代，也不能通过细胞疗法替代。这就使得对极度失聪的人使用助听器或植入人工耳蜗成为了唯一的解决办法。尽管我们在了解听力损失的遗传和其他原因方面取得了很大进展，但仍有许多情况的起源仍然未知。这主要是由于耳朵的复杂性，但也因为我们仍然没有完全了解控制胚胎耳朵形成的动态遗传程序。后者很重要，因为许多发育基因的突变与耳聋有关。另一方面，许多患有耳聋或与听力障碍相关综合征的患者在已知基因中没有任何突变。在这里，我们建议建立一个完整的路线图，祖细胞，有潜力贡献所有的感觉器官，是如何承诺耳朵的命运，并防止采取其他身份。换句话说，我们将产生一个包含耳朵形成“驱动指令”的遗传网络。我们已经在这个过程中定义了不同的步骤，以及所有帮助细胞在每个十字路口做出正确选择的参与者。然而，我们现在需要确定它们起作用的序列，它们是如何相互控制的，以及这个过程是如何在全基因组水平上被调节的。为此，我们将现代分子生物学技术应用于一个经过充分研究的羊膜模型系统——小鸡。鸡胚适合于实验操作，更重要的是可以在活胚中快速测试我们的发现。我们现在将确定：-指导何时何地使用每个参与者的基因组控制区-这些基因组控制区在内耳细胞中何时何地活跃-与这些基因组控制区相互作用的“主调节器”，从而在参与者的上游发挥作用-其中一个关键参与者，转录因子Six1与其基因组周围相互作用以控制通往耳朵的道路的方式。我们将把这些信息汇集到一个大型的互动网络中，并将对公众开放。这个网络将允许我们和其他研究人员1)通过提供基因组编码的详细指令来模拟细胞如何成为最终耳细胞的过程；Ii)预测由其任何成分的突变或缺失引起的功能结果（表型），反之亦然。此外，该项目还将确定人类耳聋的新候选基因和候选调节控制区及其潜在功能，为细胞重编程为耳祖细胞和老化耳细胞的再激活提供重要信息，并为诊断提供更好的工具。最后，由于遗传控制区的变化是进化变化和生物多样性的关键驱动因素，因此我们的数据也将被用于研究复杂感觉器官的进化。

Hearing impairment is a debilitating condition that influences many aspects of normal life. The ability to hear is important in different contexts including for the development of speech and cognitive skills in children, for performance at work and normal social interactions in adults. Worldwide, about one of every 800 babies is born with hearing problems, while more than 50% of adults over 60 suffer from some form of hearing deficit. Hearing loss in children is often associated with defects of the inner ear, the part of the ear that houses the cells that perceive sound and balance (hair cells) and generates the neurons that transmit information to the brain. In older people, hair cells die gradually, and cannot be replaced either from other cells within the ear or through cell-based therapies. This leaves hearing aids or cochlear implants in the profoundly deaf as the only solutions.Although we have made much progress in understanding the genetic and other causes for hearing loss, there are still many conditions where the origin remains unknown. This is largely due to the complexity of the ear, but also to the fact that we still do not fully understand the dynamic genetic programme that controls ear formation in the embryo. The latter is important because mutations in many developmental genes are associated with deafness. On the other hand, many patients that present with deafness or syndromes associated with hearing impairment do not have any mutations in known genes. Here we propose to establish a complete road map for how progenitor cells, which have the potential to contribute to all sense organs, are committed to ear fate and prevented from taking up other identities. In other words, we will produce a genetic network containing the 'driving instructions' for ear formation. We have already defined distinct steps during this process, and all the players that help cells to make the correct choice at each crossroad. However, we now need to establish the sequence in which they work, how they control each other and how this process is regulated on a genome-wide level. To this end we have adapted modern molecular biology techniques to a well-studied amniote model system, the chick. The chick embryo lends itself to experimental manipulation, and importantly to rapid testing of our findings in the living embryo. We will now determine:- the genomic control regions that direct when and where each of the players is used- where and when these genomic control regions are active in inner ear cells- the 'master regulators' that interact with these genomic control regions, and hence act upstream of the players- the way in which one of the key players, the transcription factor Six1, interacts with its genomic surrounding to control the road towards ear, but away from lens fateWe will assemble this information into a large interactive network, which will be made publicly available. This network will allow us and other researchers i) to model the process of how cells become definitive ear cells by providing the detailed instructions encoded in the genome; ii) to predict the functional outcome (phenotype) caused by mutation or deletion of any of its components and vice-versa.In addition, the project will identify new candidate genes and candidate regulatory control regions for human deafness and their potential functions, provide important information for reprogramming cells into ear progenitors and for re-activating cells in the ageing ear, and provide better tools for diagnosis. Finally, because changes in genetic control regions are the critical drivers of evolutionary change and therefore for biological diversity, our data will also be exploited to study the evolution of complex sense organs.