Characterisation of a novel NANOG / KDM4B complex to regulate heterochromatin function and chromosome stability in pluripotent stem cells

调节多能干细胞异染色质功能和染色体稳定性的新型 NANOG / KDM4B 复合物的表征

• 批准号: BB/M022285/1
• 负责人: Peter Rugg-Gunn
• 金额: $ 43.44万
• 依托单位: Babraham Institute
• 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=BB%2FM022285%2F1
• 关键词: Characterisation; novel; NANOG; KDM4B; complex

Pluripotent stem cells (PSC) are unspecialised cells that can form any cell type of the body. There is currently much hope that PSC could be used for cell-based therapies for the treatment of diseases, replacement for worn out tissues as we age, and for better understanding of human development, but there are still several hurdles that must be overcome before these goals are achieved. One of the hurdles is the appearance of genetic instability, and in particular the accumulation of too many chromosomes, that can affect PSC. How these unwanted changes arise remains poorly understood, but scientists are trying to prevent the changes from occurring in order to produce safer and better quality PSC.We have chosen to study an exciting and mysterious part of our genome called constitutive heterochromatin. In many different cell types, heterochromatin is important for key cellular processes, including the maintenance of genetic stability and control of chromosome number, although it has been relatively poorly studied in PSC so far. In our recent work, we have identified a new pathway through which heterochromatin is controlled in PSC. Unexpectedly, this new pathway uses several well-known stem cell factors but we are now able to assign new functions to them. Importantly, we when use genetic tricks to prevent these factors from functioning in PSC, it leads to defects in heterochromatin organisation, to the associated loss of genetic stability, and to the accumulation of additional chromosomes in the cells. This unanticipated connection between stem cell factors, heterochromatin organisation and the control of chromosome stability is important because it could provide an explanation for how genetic changes appear in PSC and would potentially allow researchers to prevent this from occurring. Our research has led us to form the hypothesis that heterochromatin is involved directly in the genetic instability of PSC. The overall aim in this research proposal, therefore, is to determine how heterochromatin is controlled in PSC, and what happens when this level of control goes wrong. We have carefully planned three main objectives to test our hypothesis.The first objective is to define how the stem cell factors control heterochromatin in PSC. Our research strongly suggests the involvement of an additional factor, KDM4B, and so we would like to examine this factor in more detail. We will achieve this by asking whether KDM4B localises to heterochromatin in PSC, and then measure what happens to heterochromatin when we remove Kdm4b from PSC. We predict that heterochromatin will show defects and possibly the appearance of chromosome instability in the PSC.The second objective is to investigate how defects in heterochromatin lead to chromosome instability in PSC. Previous research from many laboratories has shown that the particular signals that mark and define heterochromatin are required to prevent genetic instability, and we want to take this forward by investigating how these signals are controlled in PSC, especially in light of the new mode of heterochromatin regulation that we have now identified.The third objective is to use the knowledge that we generate to improve the quality and genetic stability of PSC so that we can remove one of the current hurdles to future applications. We anticipate that if we can understand how heterochromatin organisation is connected to chromosome instability in PSC, then we can, in future, devise ways to prevent this from happening. Understanding the detailed mechanism of how this occurs may lead to improved use of stem cells for regenerative medicine. This knowledge is also important in research outside of PSC, especially in ageing and cancer for example, where the normal process of heterochromatin regulation is disrupted. By better understanding how heterochromatin is controlled in general, we may be able to develop strategies to detect early changes and also to prevent them from happening.

多能干细胞(PSC)是一种未特化的细胞，可以形成身体的任何细胞类型。目前，PSC可以用于基于细胞的疗法，用于疾病的治疗，随着我们年龄的增长替换磨损的组织，以及更好地了解人类发育，目前很有希望，但在实现这些目标之前，仍有几个障碍必须克服。障碍之一是出现遗传不稳定，特别是过多的染色体积累，这可能会影响PSC。这些不必要的变化是如何发生的仍然知之甚少，但科学家们正在努力阻止这些变化的发生，以便生产出更安全、质量更好的PSC。我们选择研究我们基因组中一种令人兴奋和神秘的部分，称为构成异染色质。在许多不同类型的细胞中，异染色质对关键的细胞过程非常重要，包括维持遗传稳定性和控制染色体数量，尽管迄今为止在PSC中对异染色质的研究相对较少。在我们最近的工作中，我们发现了一条在PSC中控制异染色质的新途径。出乎意料的是，这一新途径使用了几种众所周知的干细胞因子，但我们现在能够为它们赋予新的功能。重要的是，当我们使用遗传技巧来阻止这些因子在PSC中发挥作用时，它会导致异染色质组织的缺陷，相关的遗传稳定性的丧失，并导致细胞中额外的染色体积累。干细胞因子、异染色质组织和染色体稳定性控制之间这种意想不到的联系是重要的，因为它可以为PSC中如何出现遗传变化提供解释，并可能使研究人员防止这种情况发生。我们的研究使我们形成了一个假设，即异染色质直接参与了PSC的遗传不稳定性。因此，这项研究提案的总体目标是确定PSC中异染色质是如何控制的，以及当这种控制水平出错时会发生什么。我们仔细计划了三个主要目标来验证我们的假设。第一个目标是确定干细胞因子如何控制PSC中的异染色质。我们的研究有力地表明了另一个因素KDM4B的参与，因此我们想更详细地研究这个因素。我们将通过询问KDM4B是否定位于PSC中的异染色质来实现这一点，然后测量当我们从PSC中移除KDM4B时异染色质会发生什么。我们预测，在PSC中，异染色质将出现缺陷，并可能出现染色体不稳定的现象。第二个目标是研究异染色质缺陷如何导致PSC中的染色体不稳定。许多实验室以前的研究表明，标记和定义异染色质的特定信号是防止遗传不稳定性所必需的，我们希望通过研究这些信号在PSC中是如何控制的，特别是考虑到我们现在已经识别的异染色质调节的新模式来推进这一点。第三个目标是利用我们产生的知识来提高PSC的质量和遗传稳定性，以便我们能够消除当前应用的障碍之一。我们预计，如果我们能够理解异染色质组织是如何与PSC中的染色体不稳定联系在一起的，那么我们就可以在未来设计出防止这种情况发生的方法。了解这种情况发生的详细机制可能会导致干细胞更好地用于再生医学。这一知识在PSC以外的研究中也很重要，特别是在衰老和癌症方面，在这些领域，异染色质调节的正常过程被打乱。通过更好地了解异染色质一般是如何控制的，我们可能能够制定策略来检测早期变化并防止它们发生。

项目成果

Promoter interactome of human embryonic stem cell-derived cardiomyocytes connects GWAS regions to cardiac gene networks.

• DOI: 10.1038/s41467-018-04931-0
• 发表时间: 2018-06-28
• 期刊: Nature communications
• 影响因子: 16.6
• 作者: Choy MK;Javierre BM;Williams SG;Baross SL;Liu Y;Wingett SW;Akbarov A;Wallace C;Freire-Pritchett P;Rugg-Gunn PJ;Spivakov M;Fraser P;Keavney BD
• 通讯作者: Keavney BD

Illuminating chromatin compaction in live cells and fixed tissues using SiR-DNA fluorescence lifetime

使用 SiR-DNA 荧光寿命照亮活细胞和固定组织中的染色质压缩

• DOI: 10.1101/2020.05.02.073536
• 发表时间: 2020
• 作者: Hockings C

Genome-wide analysis of DNA replication and DNA double-strand breaks using TrAEL-seq.

• DOI: 10.1371/journal.pbio.3000886
• 发表时间: 2021-03
• 期刊: PLoS biology
• 影响因子: 9.8
• 作者: Kara N;Krueger F;Rugg-Gunn P;Houseley J
• 通讯作者: Houseley J

Global reorganisation of cis-regulatory units upon lineage commitment of human embryonic stem cells.

• DOI: 10.7554/elife.21926
• 发表时间: 2017-03-23
• 期刊: eLife
• 影响因子: 7.7
• 作者: Freire-Pritchett P;Schoenfelder S;Várnai C;Wingett SW;Cairns J;Collier AJ;García-Vílchez R;Furlan-Magaril M;Osborne CS;Fraser P;Rugg-Gunn PJ;Spivakov M
• 通讯作者: Spivakov M

Molecular profiling of aged neural progenitors identifies Dbx2 as a candidate regulator of age-associated neurogenic decline.

• DOI: 10.1111/acel.12745
• 发表时间: 2018-06
• 期刊: Aging cell
• 影响因子: 7.8
• 作者: Lupo G;Nisi PS;Esteve P;Paul YL;Novo CL;Sidders B;Khan MA;Biagioni S;Liu HK;Bovolenta P;Cacci E;Rugg-Gunn PJ
• 通讯作者: Rugg-Gunn PJ