Deciphering the role of p63 in secondary palate development using systems biology

利用系统生物学解读 p63 在味觉二次发育中的作用

• 批准号: MR/M012174/1
• 负责人: Michael Dixon
• 金额: $ 88.56万
• 依托单位: University of Manchester
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2015
• 资助国家: 英国
• 起止时间: 2015 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=MR%2FM012174%2F1
• 关键词: Deciphering; role; p63; secondary; palate

Development of the palate, which ultimately separates the mouth from the nasal passages, involves a complex series of inter-dependent events that requires close co-ordination of cell growth, cell adhesion, cell migration, cellular differentiation, and cell death. Failure of these processes to occur correctly results in the birth defect cleft palate. Cleft palate, which has an incidence of approximately 1 in 2500 live births, results in considerable problems to affected individuals as they may experience problems with eating, speaking and psychosocial adjustment due to the altered facial appearance. The frequent occurrence and major healthcare burden imposed by cleft palate highlight the need to dissect the fundamental mechanisms that underlie normal development of the palate and how these are disturbed in cleft palate. As a result of ethical concerns, these studies cannot be performed in humans. In mice palate development mirrors that occurring in humans and the mouse is, therefore, the major animal model used in the study of palatogenesis. Although the descriptive embryology of mouse palate development is well-established, the underlying genetic events are poorly characterised.Recently, we have generated compelling evidence that the transcription factor p63, which is a master control gene, plays a central role in the genetic events driving palatal development. We have generated a complete profile of the genes expressed in the developing palate at the critical time-points in its development by using high-throughput sequencing of RNA (RNA-seq) isolated from carefully dissected mouse palates. In parallel, we have identified all the regions of the genome to which p63 binds in the developing palate using the ChIP-seq technique. Despite the generation of these genome-wide datasets and the confirmation of a large number of p63 transcriptional targets in the secondary palate, the gene regulatory networks controlled by p63 have not been elucidated. The behaviour of these complex networks cannot be predicted by simple intuitive approaches but requires sophisticated computational methods. In this project, we will firstly apply time-course methods to analyse RNA-seq data generated from cells and from palatal shelves dissected from mice in which the function of p63 has been disrupted. By combining the results from these two distinct but complementary systems, we will identify the direct and biologically-relevant early regulatory links in the p63-controlled developmental regulatory network which will facilitate our understanding of the role of p63 in secondary palate development. Secondly, we will use the data generated on the gene regulatory networks controlled by p63 to analyse a mouse which exhibits cleft palate as the result of increased p63 signalling. These experiments will allow us to determine why it is essential that the level of p63 signalling is reduced in a specific subset of cells during normal development of the palate. Finally, to facilitate collaborative working, we will ensure that all the data generated during the project are freely available via the World-Wide Web.Ultimately, the project will provide crucial information about a developmental process of major significance and serve as a test case for using systems-level developmental genetics to dissect the gene regulatory networks that are disrupted in congenital human malformations more widely.

腭的发育最终将口腔与鼻腔通道分开，涉及一系列复杂的相互依赖的事件，需要细胞生长、细胞粘附、细胞迁移、细胞分化和细胞死亡的密切协调。这些过程的失败发生正确的结果在出生缺陷腭裂。腭裂的发病率约为2500活产婴儿中的1例，会给受影响的个体带来相当大的问题，因为他们可能会因面部外观的改变而出现进食、说话和心理社会调整方面的问题。腭裂的频繁发生和重大的医疗负担突出了需要解剖的基本机制，腭的正常发育的基础，以及这些是如何在腭裂干扰。由于伦理问题，这些研究不能在人类中进行。在小鼠中，腭发育反映了在人类中发生的情况，因此小鼠是腭发生研究中使用的主要动物模型。虽然小鼠腭发育的描述性胚胎学是建立良好的，基本的遗传事件的characterized.Recently，我们已经产生了令人信服的证据表明，转录因子p63，这是一个主控制基因，在驱动腭发育的遗传事件中起着核心作用。我们已经产生了一个完整的档案中表达的基因在其发展中的关键时间点，通过使用高通量测序的RNA（RNA-seq）从仔细解剖的小鼠腭分离。与此同时，我们使用ChIP-seq技术鉴定了发育中腭中p63结合的所有基因组区域。尽管这些全基因组数据集的产生和大量的p63转录靶点在次级腭的确认，由p63控制的基因调控网络尚未阐明。这些复杂网络的行为无法通过简单的直观方法预测，而是需要复杂的计算方法。在这个项目中，我们将首先应用时间过程方法来分析从细胞和从p63功能被破坏的小鼠解剖的腭架产生的RNA-seq数据。通过结合这两个不同但互补的系统的结果，我们将确定直接的和生物学相关的早期监管环节的p63控制的发育调控网络，这将有助于我们的理解p63的作用，在次生腭发育。其次，我们将使用由p63控制的基因调控网络上产生的数据来分析由于p63信号传导增加而表现出腭裂的小鼠。这些实验将使我们能够确定为什么在腭的正常发育过程中，p63信号传导的水平在特定的细胞亚群中降低是至关重要的。最后，为了促进协作，我们将确保项目期间生成的所有数据都可以通过万维网免费获取。最终，该项目将提供有关具有重大意义的发育过程的关键信息，并作为使用系统水平的测试案例。发育遗传学来剖析更广泛地破坏人类先天性畸形的基因调控网络。

项目成果

Expanding the genetic and phenotypic spectrum of popliteal pterygium disorders.

• DOI: 10.1002/ajmg.a.36896
• 发表时间: 2015-03
• 期刊: AMERICAN JOURNAL OF MEDICAL GENETICS PART A
• 影响因子: 2
• 作者: Leslie, Elizabeth J.;O'Sullivan, James;Cunningham, Michael L.;Singh, Ankur;Goudy, Steven L.;Ababneh, Faroug;Alsubaie, Lamia;Ch'ng, Gaik-Siew;van der Laar, Ingrid M. B. H.;Hoogeboom, A. Jeannette M.;Dunnwald, Martine;Kapoor, Seema;Jiramongkolchai, Pawina;Standley, Jennifer;Manak, J. Robert;Murray, Jeffrey C.;Dixon, Michael J.
• 通讯作者: Dixon, Michael J.

PEGS: An efficient tool for gene set enrichment within defined sets of genomic intervals.

• DOI: 10.12688/f1000research.53926.2
• 发表时间: 2021
• 期刊: F1000Research
• 作者: Briggs P;Hunter AL;Yang SH;Sharrocks AD;Iqbal M
• 通讯作者: Iqbal M

Revisiting the embryogenesis of lip and palate development.

• DOI: 10.1111/odi.14174
• 发表时间: 2022-07
• 期刊: ORAL DISEASES
• 影响因子: 3.8
• 作者: Hammond, Nigel L.;Dixon, Michael J.
• 通讯作者: Dixon, Michael J.

Efficient inference for sparse latent variable models of transcriptional regulation.

• DOI: 10.1093/bioinformatics/btx508
• 发表时间: 2017-12-01
• 期刊: Bioinformatics (Oxford, England)
• 作者: Dai Z;Iqbal M;Lawrence ND;Rattray M
• 通讯作者: Rattray M

Predicting stimulation-dependent enhancer-promoter interactions from ChIP-Seq time course data.

• DOI: 10.7717/peerj.3742
• 发表时间: 2017
• 期刊: PeerJ
• 影响因子: 2.7
• 作者: Dzida T;Iqbal M;Charapitsa I;Reid G;Stunnenberg H;Matarese F;Grote K;Honkela A;Rattray M
• 通讯作者: Rattray M