An integrative epigenomic approach to discover small RNA mediated regulatory programs in Paramecium tetraurelia

一种综合表观基因组方法来发现草履虫中小 RNA 介导的调控程序

• 批准号: 292631656
• 负责人: Professor Dr. Marcel Schulz
• 金额: --
• 依托单位: Institut für Kardiovaskuläre Regeneration
• 依托单位国家: 德国
• 项目类别: Research Grants
• 财政年份: 2016
• 资助国家: 德国
• 起止时间: 2015-12-31 至 2020-12-31
• 项目状态: 已结题
• 来源: https://gepris.dfg.de/gepris/projekt/292631656?language=en
• 关键词: integrative; epigenomic; approach; discover; small

Recent advances in RNA Biology show that small RNA molecules control phenotypic variation at the epigenetic level either by post-transcriptional or transcriptional inactivation of gene expression. However, the ongoing work mostly focuses on individual loci and individual mechanisms rather than estimating the extent to which such mechanisms contribute to transcriptome dynamics, and as a consequence, to phenotypic plasticity or phenotypic robustness. The epigenetic model organism Paramecium allows us to study genome wide RNA and chromatin dynamics to get an insight into small RNA controlled short-term regulation of gene expression and long-term manifestation of gene expression patterns by epigenetic mechanisms. Recently, we described different RNA-mediated silencing pathways acting at different levels. Now, we will analyse genome wide small RNA/chromatin associations in different metabolic states dissecting post-transcriptional and transcriptional silencing pathways. This will be achieved by an integrative approach using bioinformatics to differentiate between newly identified siRNA clusters associated or not associated with heterochromatin formation, as well as biochemical analysis of siRNAs and dissection of their genetic requirements such as RNAi components involved in post-transcriptional or transcriptional silencing. Further, a new integrative analysis approach will be used to associate short RNA abundance and chromatin modifications with gene expression. We will model trans acting siRNA networks enabling coordinated activation and silencing of gene groups, as well as identification of trans acting RNAs derived from gene duplicates. As a consequence, we will not only be able to describe the extent of epigenetic pathways controlling gene expression and adaptation of this unicellular organism during vegetative growth, we will moreover analyse which of these epigenetic characters can be passed on to sexual progeny. This will be done by crosses of genetically identical but epigenetically different individuals and subsequent analysis of F1 clones. We will thus identify genetic requirements for epigenetic inheritance, which will allow for brand new conclusions on the possibilities for inheritance of gene expression: manifestation of positively selected gene expression patterns by small RNAs, which are mobile elements between generations, will be the key to understand short-time Lamarckian adaptation in contrast to long-term Darwinian evolution.

RNA生物学的最新进展表明，小RNA分子通过基因表达的转录后或转录失活在表观遗传水平上控制表型变异。 然而，正在进行的工作主要集中在单个基因座和单个机制，而不是估计这些机制在多大程度上有助于转录组动态，因此，表型可塑性或表型鲁棒性。表观遗传模式生物草履虫允许我们研究全基因组RNA和染色质动力学，以了解小RNA控制的基因表达的短期调控和表观遗传机制的基因表达模式的长期表现。最近，我们描述了不同的RNA介导的沉默途径在不同的水平上发挥作用。现在，我们将分析全基因组小RNA/染色质协会在不同的代谢状态解剖转录后和转录沉默途径。这将通过使用生物信息学的综合方法来实现，以区分与异染色质形成相关或不相关的新鉴定的siRNA簇，以及siRNA的生物化学分析和其遗传要求的解剖，如参与转录后或转录沉默的RNAi组分。此外，一种新的综合分析方法将用于关联短RNA丰度和染色质修饰与基因表达。我们将模拟反式作用siRNA网络，使协调激活和沉默的基因组，以及识别来自基因重复的反式作用RNA。因此，我们不仅能够描述在营养生长过程中控制这种单细胞生物的基因表达和适应的表观遗传途径的程度，我们还将分析这些表观遗传特征中的哪些可以传递给有性后代。这将通过遗传上相同但表观遗传上不同的个体的杂交和随后的F1克隆分析来完成。因此，我们将确定表观遗传的遗传要求，这将允许对基因表达的遗传可能性的全新结论：小RNA的正选择基因表达模式的表现，这是几代之间的移动的元素，将是理解短期拉马克适应与长期达尔文进化的关键。