Differentiated normal cell identity and epigenetic barriers to trans-differentiation and reprogramming

细胞身份是由某些基因的表达决定的，这些基因会产生特定的蛋白质。通常，基因表达是由表观遗传机制调节的。多能干细胞可以在分化过程中转化为特殊的细胞身份。相反，体细胞可以通过使用一组转录因子被重新编程为具有干细胞样身份的细胞，也称为诱导多能干细胞（iPSCs）。因此存在一定程度的可塑性，允许细胞在细胞身份之间切换。控制这一过程仍然具有挑战性，因为细胞通常保留其先前起源的一些表观遗传记忆，因此可能会抵制任何改变其身份或恢复到其原始细胞起源。因此，目前iPSCs技术的局限性包括重编程效率低、肿瘤发展和自发分化。阐明表观遗传机制在控制细胞身份和提供细胞记忆中的作用将有助于推进干细胞研究在再生医学、疾病建模和药物发现方面的应用。此前已有研究表明，10 - 11易位（TET）酶将5-甲基胞嘧啶（5mC）转化为5-羟甲基胞嘧啶（5hmC）与活跃的基因转录有关，在细胞转化过程中起着重要作用。也就是说，在iPSC重编程过程中，5hmC富集和TET活性促进了DNA去甲基化和多能性的转录再激活。因此，缺乏TET表达的细胞不能被重编程为iPSCs。此外，已确定5hmC的全球水平在不同的组织和细胞类型之间存在差异。因此，5hmC可能是决定细胞身份的关键中间体。因此，基因组的5hmC分布可能被用作细胞转化过程中细胞身份的标志。这个项目的总体目标是研究细胞如何知道自己是什么。更具体地说，目的是阐明5hmC在细胞重编程过程中建立和维持细胞身份的表观遗传机制中的作用。这将通过确定5hmC介导的DNA去甲基化在驱动细胞身份中的作用，确定组蛋白修饰和5hmC如何共同实现细胞重编程，以及通过建立数学模型来描述细胞转化过程中基因表达、DNA甲基化和组蛋白修饰之间的相互作用来实现。

Cellular identity is defined by the expression of certain genes that result in the production of specific proteins. Typically, gene expression is known to be regulated by epigenetic mechanisms. Pluripotent stem cells can be converted to a specialised cell identity in a process known as differentiation. Contrariwise, somatic cells can be reprogrammed back to cells with a stem-like identity, also called induced pluripotent stem cells (iPSCs), by using a subset of transcription factors. A degree of plasticity thus exists that allows cells to switch between cell identities. Controlling this process remains challenging as cells often retain some epigenetic memory of their previous origin, and therefore may resist any change to their identity or revert to their original cell origin. Therefore, current limitations of iPSCs technology include low reprogramming efficiency, tumour development and spontaneous differentiation. Elucidating the role of epigenetic mechanisms in governing cell identity and providing a cell with its memory will help advance the applications of stem cell research in regenerative medicine, disease modelling and drug discovery. Previously, it has been shown that the conversion of 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC) by ten-eleven translocation (TET) enzymes is associated with active gene transcription and plays an essential role during cell conversion. Namely, during iPSC reprogramming, 5hmC enrichment and TET activity facilitate DNA demethylation and transcriptional reactivation of pluripotency. Consequently, cells that lack TET expression cannot be reprogrammed to iPSCs. Additionally, global levels of 5hmC have been identified to differ between distinct tissue and cell types. Thus, 5hmC might act as a key intermediate essential to determining cell identity. It is therefore likely that genomic 5hmC distributions could be used as signatures of cell identity during cell conversion. The general objective of this project is to investigate how a cell knows what it is. More specifically, the aim is to elucidate the role of 5hmC in the epigenetic mechanism that establishes and maintains cell identity during cellular reprogramming. This will be achieved by identifying the role of 5hmc-mediated DNA demethylation in driving cell identity, determining how histone modifications and 5hmC come together to enable cell reprogramming and by establishing mathematical models to describe the interplay between gene expression, DNA methylation and histone modifications during cell conversion.