Epigenetic control of nuclear chromatin organisation in cardiac development

许多哺乳动物的组织和器官在发育后逐渐失去再生能力，导致晚年的退行性疾病。在成人器官中，各种细胞类型执行其基本功能，只有有限的细胞替代用于组织维护和愈合。在细胞核中，组蛋白和DNA上的表观遗传标记有助于建立活性和抑制性染色质状态，这被认为是维持细胞谱系中的基因活性模式，但也调节整体核和染色体功能。使用先进的显微镜，核蛋白的免疫检测和染色质免疫沉淀（ChIP），我们已经确定了小鼠心脏发育的特定表观遗传特征。我们假设，在这些细胞中的染色质的重组有助于有丝分裂后的非再生状态的成人心脏。我们将使用各种实验和计算方法来探索这一点。该项目旨在：（i）确定小鼠胚胎心脏发育过程中蛋白质组成的变化，表观遗传标记和浓缩染色质的核定位。比较胚胎心脏组织和体外培养的心肌细胞的实验将用于测试表观遗传标记和染色质组成的改变是否会影响它们在细胞核和有丝分裂活性中的空间关联。(ii)通过生成新的染色质构象捕获（CCC）数据，然后进行生物信息学分析，发现染色体和染色质如何从小鼠心脏祖细胞重组为分化的心脏细胞。(iii)将这些CCC分析与这些组织的未发表的互补基因表达数据和ChIP表观基因组图谱数据以及公开的全基因组数据集相结合，以评估改变的核组织的功能影响。(iv)利用人类成年和胎儿心脏组织样本的大量公开可用的染色质基因组数据来检查小鼠和人类细胞之间这种影响的一致性。这个博士项目将涉及两个合作研究小组，将核组织动力学的专业知识与先进的生物信息学相结合，以揭示心脏细胞有丝分裂后状态的表观遗传信号传导机制和途径。研究结果将提供更多关于表观遗传学在心脏发育和成熟中的作用的知识，这可能导致更好地保存成年心脏的再生能力。博士研究将通过染色质和基因表达的基因组分析，免疫荧光共聚焦显微镜和图像分析提供表观遗传学，发育生物学，分子生物学和生物信息学方面的知识和可转移技能。

Many mammalian tissues and organs gradually lose their regenerative capacities after development, leading to degenerative diseases in later life. In adult organs, various cell types perform their essential functions with only limited cell replacement for tissue maintenance and healing. In the cell nucleus, epigenetic marks on the histones and DNA help to set up active and repressive chromatin states, which are thought to maintain gene activity patterns in cell lineages but also regulate overall nuclear and chromosome function. Using advanced microscopy, immunodetection of nuclear proteins and chromatin immunoprecipitation (ChIP), we have identified specific epigenetic signatures of mouse cardiac development. We hypothesise that the reorganisation of chromatin in these cells contributes to the post-mitotic non regenerative state of the adult heart. We will explore this using a variety of experimental and computational approaches.The project aims to: (i) determine changes in protein composition, epigenetic marks and nuclear localisation of condensed chromatin during mouse embryonic heart development. Experiments comparing embryonic heart tissue and in vitro cultured cardiomyocytes will then be used to test whether alterations in epigenetic markers and chromatin composition can affect their spatial associations in the nucleus and mitotic activity. (ii) discover how chromosomes and chromatin are reorganised from murine cardiac progenitors to differentiated heart cells by generating novel chromatin conformation capture (CCC) data followed by bioinformatics analysis.(iii) integrate these CCC analyses with unpublished complementary gene expression data and ChIP epigenomic mapping data for these tissues, as well as publicly available genome-wide data sets, to assess the functional impacts of altered nuclear organisation.(iv) exploit the large volumes of publicly available chromatin genomic data for human adult and fetal heart tissue samples to examine the consistency of such impacts between mouse and human cells.This PhD project will involve two collaborating research groups, combining expertise in nuclear organisation dynamics with advanced bioinformatics, to reveal the epigenetic signalling mechanisms and pathways contributing to the post-mitotic state of cardiac cells. The research outcomes will provide more knowledge on the role of epigenetics in heart development and maturation, which could lead to better preservation of regenerative capacity in the adult heart. The PhD study will provide knowledge and transferrable skills in epigenetics, developmental biology, molecular biology and bioinformatics through genomic analysis of chromatin and gene expression, immunofluorescence confocal microscopy and image analysis.