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之处在于98.5%的非蛋白质编码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，一个主要的问题是，ncrna在我们的细胞中是否具有重要的功能作用？越来越清楚的是，几种ncRNA具有功能作用，作为细胞身份和组织稳态的调节剂。近年来，对ncrna以及rna结合蛋白（rbp）的定位和功能表征有所增加。研究表明，RNA在与健康和疾病有关的几乎所有细胞生物学要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代表了重编程应用和衰老相关疾病尚未开发的治疗靶点。最近的研究表明，ncrna参与调控表观遗传修饰，如改变细胞质mRNA的加工，调节染色质功能和基因组DNA的甲基化。这些功能最终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，并在环境胁迫下发生变化。在诸如癌症等疾病的发展和诸如诸如此类的生物过程中，老化的DNA甲基化模式可能发生异常变化，导致基因的不正确表达。因此，了解DNA甲基化协调背后的基本调控机制是很重要的。该项目主要关注lncRNA 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，DNMT1是催化和维持基因组DNA甲基化的酶。CRISPR-Cas9介导的CCDC26的去除显示出抑制DNMT1与基因组DNA结合的作用，导致低甲基化，基因组稳定性降低，随后导致细胞死亡增加（Jones et al., 2021）。该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控制ncRNA介导的DNA甲基化调节的分子机制。以及使用现代技术，如转录组学和CRISPR-Cas9介导的基因组工程。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及其在健康和疾病中与表观遗传调控的关联的认识，未来ncRNAs有可能在临床环境中用作预后或诊断生物标志物，以及新疗法的靶点。Jones， R., Wijesinghe， S., Wilson， C., Halsall， J., Liloglou， T., & Kanhere， A.（2021）。长基因间非编码RNA调控DNA甲基转移酶-1的核定位。科学通报，24(4),102273。doi: 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