Characterization of silencer element-associated chromatin

沉默元件相关染色质的表征

基本信息

批准号：
10381796
负责人：
Julian Andrew Segert
金额：
$ 4.03万
依托单位：
HARVARD MEDICAL SCHOOL
依托单位国家：
美国
项目类别：
财政年份：
2022
资助国家：
美国
起止时间：
2022-03-01 至 2025-02-28
项目状态：
未结题

来源：
https://reporter.nih.gov/project-details/10381796
关键词：
3-Dimensional Address Affinity Architecture Attention Binding Binding Proteins Biological Assay Biology Cells Cellular Assay ChIP-seq Characteristics Chemicals Chromatin Collection Complex DNA DNA Binding DNA-Binding Proteins Data Development Developmental Process Disease Drosophila genus Elements Embryo Enhancers Ensure Epigenetic Process Experimental Designs Fluorescent in Situ Hybridization Future Gene Expression Gene Expression Regulation Genes Genetic Genetic Transcription Genome Genomics Histone Code Histones Investigation Label Lead Maps Mass Spectrum Analysis Mesoderm Methods Modeling Modification Molecular Conformation Nature Pathway interactions Positioning Attribute Post-Translational Protein Processing Process Proteomics Regulation Regulatory Element Reporter Repressor Proteins Research Research Personnel Research Project Grants Role Snails Statistical Models Surveys System Techniques Testing Time Transcriptional Silencer Elements Validation Variant Visualization Western Blotting base career cell type chromatin modification cofactor combinatorial design experience experimental analysis falls genome wide association study high throughput screening histone modification human disease improved insight morphogens mutant prevent promoter protein protein interaction recruit spatiotemporal tool transcription factor

项目摘要

Abstract Spatio-temporal control of gene expression is a fundamental process in biology. While the role of enhancers to positively regulate gene expression has been appreciated for decades, silencers are conspicuously absent from most models. A recent string of high-throughput screens in multiple systems has identified thousands of silencers. Strikingly, a large number of these silencers fall within bifunctional cis-regulatory elements that also act as enhancers in other cell types or developmental times. Silencers are also enriched for eQTLs and GWAS hits, suggesting they are essential for understanding the genetics of complex disease. Silencers are distinct from insulators, which prevent enhancer-promoter interactions. Silencers actively dampen expression of their target genes and, like enhancers, act independently of position and orientation. Even though a large number of silencers have been functionally identified in reporter assays, it is still difficult to predict new silencer elements. While enhancers, promoters, and insulators can be predicted by ChIP-seq for specific histone post- translational modifications, no chromatin modifications are known to be predictive of silencers. Additionally, the set of DNA binding proteins and their cofactors at silencers is largely unknown. Identification of ChIP-seq target that are highly predictive of silencers would vastly improve the ability of researchers to study these fundamental elements in new contexts and can give insights into silencing mechanisms. In order to address fundamental lingering questions regarding silencers, I will perform a proteomic survey to identify factors that distinguish silencer and enhancer states of bifunctional cis-regulatory elements in Drosophila mesoderm. This will give key insights into the mechanisms of silencer elements. I will also investigate the three-dimensional contacts formed between silencers and their targets. It has already been observed that silencers bound by Snail do not contact TSSs, but instead disrupt normal enhancer-promoter contacts, a process known as anti- looping. Completion of this project will fill address many of the outstanding questions regarding silencer elements, including the factors responsible for silencing and the effect they have on their target genes. This project will uncover specific markers of silencers that will allow future investigators to identify them via ChIP- seq similar to how other functional elements can be annotated. This research project will give valuable experience in experimental design and analysis that I hope to carry with me into a career as an academic investigator.

抽象的基因表达的时空控制是生物学的基本过程。而增强剂的作用几十年来，积极调节基因表达已被人们赞赏，消音器显然不存在来自大多数型号。最近在多个系统中的一连串的高通量屏幕已经确定了数千个消音器。令人惊讶的是，许多这些消音器属于双功能的顺式调节元素充当其他细胞类型或发育时间的增强子。消音器也用于EQTL和GWAS 热门歌曲，表明它们对于理解复杂疾病的遗传学至关重要。消音器是不同的从绝缘子，可以防止增强子促进剂相互作用。消音器积极抑制其表达靶基因且像增强子一样，独立于位置和方向行动。即使大量消音器在报告基因测定中已在功能上鉴定出来，仍然很难预测新的消音器元素。虽然可以通过CHIP-SEQ预测增强子，启动子和绝缘子，以预测特定的组蛋白。翻译修饰，没有染色质修饰可以预测消音器。另外，在消音器处的DNA结合蛋白及其辅助因子的集合在很大程度上是未知的。鉴定芯片序列目标高度预测消音器的人将大大提高研究人员研究这些的能力在新环境中的基本要素，可以深入了解沉默机制。为了解决关于消音器的基本挥之不去的问题，我将进行蛋白质组学调查，以确定因素区分果蝇中胚层中双功能顺式调节元件的消音器和增强态。这将对消音器元素的机制提供关键的见解。我还将调查三维消音器及其目标之间形成了联系。已经观察到，消音器受到约束蜗牛不要与TSSS接触，而是破坏正常增强剂促进触点，这一过程称为抗循环。该项目的完成将填补有关消音器的许多未出现的问题要素，包括负责沉默的因素及其对目标基因的影响。这项目将发现消音器的特定标记，这将使未来的调查人员能够通过芯片识别它们 SEQ类似于如何注释其他功能元素。该研究项目将提供宝贵的我希望随身携带实验设计和分析的经验研究者。