Novel role of non-coding RNAs in regulating genomic DNA methylation

通过基因组测序的出现，揭示了人类基因组的独特性，98.5%的基因组编码非蛋白质编码的DNA。大约75%的人类基因组被转录成不编码蛋白质的非编码RNA(NcRNAs)。自从这一发现以来，主要的问题之一是，在我们的细胞中，ncRNAs是否在功能上扮演着重要的角色？越来越明显的是，几个ncRNA具有功能作用，起着细胞特性和组织内稳的调节作用。近年来，对ncRNAs以及RNA结合蛋白(RBPs)的定位和功能表征有所增加。研究表明，RNA在几乎所有与健康和疾病有关的细胞生物学元素中都具有巨大的潜力。因此，对非编码RNA的进一步研究有可能有助于更全面地了解与基因组稳定性、细胞周期控制和细胞分化相关的途径。因此，ncRNA代表了一个未被开发的治疗靶点，用于重新编程应用程序和衰老相关疾病。最近的研究表明，ncRNAs参与调节表观遗传修饰，如改变细胞质mRNA的加工，调节染色质功能，以及基因组DNA的甲基化。最终，这些功能会影响基因表达和细胞功能。DNA甲基化的表观遗传调控是动态的，并随着环境应激源的变化而变化。在癌症等疾病的发生和衰老等生物过程中，DNA甲基化模式可能会发生异常变化，导致基因的不正确表达。因此，为什么了解DNA甲基化是如何协调的背后的基本调控机制是重要的。这个项目主要集中在cncRNA，CCDC26，对人类基因组DNA甲基化变化的影响。Kanhere小组已经证明，CCDC26与DNA甲基转移酶(DNMT1)结合，该酶是已知的催化和维持基因组DNA甲基化的酶。CRISPR-Cas9介导的CCDC26的移除显示了抑制DNMT1与基因组DNA结合的效果，导致低甲基化，降低基因组稳定性，进而导致细胞死亡(Jones等人，2021)。本项目旨在进一步阐明这些发现，目的是全面了解ncRNA：DNMT1相互作用背后的机制，帮助我们推测这种相互作用在衰老和疾病发展中的作用和功能意义。这项工作将通过分子和细胞生物学方法来研究调控ncRNA介导的DNA甲基化的分子机制。以及转录学和CRISPR-Cas9介导的基因组工程等现代技术的应用。该项目的目的是通过可应用于更广泛的ncRNA研究领域的方法，更好地表征ncRNA CCDC26的功能意义。通过扩大我们对ncRNAs的了解及其与健康和疾病表观遗传调控的关联，ncRNAs未来有可能在临床环境中用作预后或诊断生物标记物，以及新疗法的靶标。琼斯，R.，Wijesinghe，S.，Wilson，C.，Halsall，J.，Liloglou，T.，&Kanhere，A.(2021)。一个长的基因间非编码RNA调节DNA甲基转移酶-1的核定位。《科学》，24(4)，102273。网址：10.1016/j.isci.2021.102273

Through the advent of genomic sequencing it was revealed that the human genome is unique in that 98.5% encodes for non-protein coding DNA. Approximately 75% of the human genome is transcribed into non-coding RNA (ncRNAs) that do not code for proteins. Since this discovery one of the main questions has been, is there a functionally significant role that ncRNAs play in our cells?It is becoming clear that several ncRNA hold functional roles, acting as regulators of cell identity, and tissue homeostasis. In recent years, mapping and functional characterisation of ncRNAs, as well as RNA-binding proteins (RBPs) has increased. Research has shown there to be great potential for RNA in virtually all elements of cell biology relating to health and disease. Therefore, further investigation into non-coding RNAs has the potential to aid in a more comprehensive understanding of pathways relating to genomic stability, cell cycle control, and cell differentiation. Thus, ncRNA represents an unexploited therapeutic target for reprogramming applications and aging-related diseases. Recent studies have indicated that ncRNAs are involved in regulating epigenetic modifications such as, altering the processing of cytoplasmic mRNA, modulating chromatin function, and methylation of genomic DNA. Ultimately these functions affect gene expression and cell function. The epigenetic regulation of DNA methylation is dynamic and changes in response to environmental stressors. Upon the development of diseases such as, cancer and during biological processes such as, ageing DNA methylation patterns can undergo aberrant changes resulting in the incorrect expression of genes. Hence why an understanding of the fundamental regulatory mechanisms behind how DNA methylation is coordinated is important. This project has been set out to focus primarily on the effects of the lncRNA, CCDC26, on DNA methylation changes in the human genome. It has been demonstrated by the Kanhere group that CCDC26 binds to the enzyme DNA methyltransferase (DNMT1) which is known for catalysing and maintaining methylation of genomic DNA. CRISPR-Cas9 mediated removal of CCDC26 showed the effects of inhibiting the binding of DNMT1 to genomic DNA, resulting in hypomethylation, reduction in genomic stability and subsequently leading to increase cell death (Jones et al., 2021). This project aims to further elucidate these findings, with the goals of gaining a comprehensive understanding of the mechanisms behind ncRNA:DNMT1 interactions, helping us to speculate the role and functional significance of this interplay in ageing and development of disease. This work will be achieved through molecular and cell biology approaches to investigate the molecular mechanisms governing ncRNA mediated regulation of DNA methylation. As well as employment of modern technologies such as transcriptomics and CRISPR-Cas9 mediated genomic engineering. The aim of this project is to better characterise the functional significance of ncRNA, CCDC26, through methods that can be applied within the wider field of ncRNA research. By expanding our knowledge of ncRNAs and their association with epigenetic regulation in health and disease, there is future potential for ncRNAs to be used in clinical setting as prognostic or diagnostic biomarkers, as well as targets for novel therapies. Jones, R., Wijesinghe, S., Wilson, C., Halsall, J., Liloglou, T., & Kanhere, A. (2021). A long intergenic non-coding RNA regulates nuclear localization of DNA methyl transferase-1. iScience, 24(4), 102273. doi:10.1016/j.isci.2021.102273