RESEARCH-PGR: Impact of Transposable Element Bursts on the Rice Genome and Epigenome

研究-PGR：转座元件爆发对水稻基因组和表观基因组的影响

• 批准号: 2134912
• 负责人: Susan Wessler
• 金额: $ 230万
• 依托单位: University of California-Riverside
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2022
• 资助国家: 美国
• 起止时间: 2022-05-01 至 2026-04-30
• 项目状态: 未结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=2134912&HistoricalAwards=false
• 关键词: RESEARCH; PGR; Impact; Transposable; Element

Mechanisms that diversify genomes, at both the sequence and epigenetic levels, underlie phenotypic variation. With accelerated climate change, it is essential that mechanisms diversifying crop genomes be understood and applied to feed future generations. Most plant and animal genomes are derived from transposable elements (TEs), mobile fragments of DNA that often increase in copy number as they transpose from one genomic locus to another. The ability of TEs to insert near genes and alter their regulation and to promote genomic rearrangements and epigenetic changes has recently been recognized as a significant contributor to adaptive evolution. Stated simply, TEs can shake up otherwise (structurally) conservative genomes. This project exploits long read DNA sequencing technology and single cell epigenetic analyses to reveal how the rapidly amplifying TE called mPing alters, in real time, the rice genome, while avoiding host (epigenetic) silencing and mutagenic insertions. With respect to broader impacts, this project also addresses a crisis in the agricultural workforce, which is the oldest and least diverse among the sciences, by introducing undergraduates at a Hispanic Serving Institution to the excitement of plant genomics through authentic research experiences for up to 2000 incoming students/year. The research goals of this project are two-fold. The first is to understand the totality of structural genomic variation generated in three recombinant inbred (RI) populations by the massive amplification of the rice TE family Ping/mPing. Based on prior results, it is anticipated that at least 50,000 additional mPing insertion sites [with ~15% in accessible chromatin regions (ACRs)] and numerous structural variants (SVs) including copy number and presence absence variants and inversions will be identified. The second goal is to determine the consequences of a subset of these lesions on epigenetic regulation and reproductive isolation by generating a rice single cell cis-regulatory atlas and assessing the impact of mPing inserts in targeted RI lines. While the vast majority of the ~50,000 de novo mPing insertions may be neutral or eliminated by selection over evolutionary time, in the short term they will provide an invaluable tool to evaluate the function of ACRs more quickly and for far less cost than any other method currently available. Results of this project will reveal the potential of rapid TE amplification to reshape the epigenome, lead to reproductive isolation, and, for SVs, to rapidly generate the genomic variation that underlies pangenomes. All data generated by this project will be made available through deposition at established long-term sequence repositories such as the NCBI Short Read Archive (SRA) and Gene Expression Omnibus (GEO).This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

在序列和表观遗传水平上使基因组多样化的机制是表型变异的基础。 随着气候变化的加速，必须了解作物基因组多样化的机制，并将其用于养活后代。大多数植物和动物基因组来自转座因子（TE），即DNA的移动的片段，当它们从一个基因组位点转座到另一个基因组位点时，拷贝数通常会增加。TE插入附近基因并改变其调节以及促进基因组重排和表观遗传变化的能力最近被认为是适应性进化的重要贡献者。简单地说，TE可以动摇原本（结构上）保守的基因组。该项目利用长读段DNA测序技术和单细胞表观遗传分析来揭示快速扩增的TE（称为mPing）如何在真实的时间内改变水稻基因组，同时避免宿主（表观遗传）沉默和诱变插入。关于更广泛的影响，该项目还解决了农业劳动力的危机，这是科学中最古老和最不多样化的，通过向西班牙裔服务机构的本科生介绍植物基因组学的兴奋，通过真实的研究经验，每年有2000名新生。 该项目的研究目标是双重的。首先是了解水稻TE家族Ping/mPing的大量扩增在三个重组近交（RI）群体中产生的结构基因组变异的总体。基于先前的结果，预计将鉴定至少50，000个额外的mPing插入位点[约15%在可接近的染色质区域（ACR）中]和许多结构变体（SV），包括拷贝数和存在不存在变体和倒位。第二个目标是通过产生水稻单细胞顺式调节图谱和评估mPing插入物在靶向RI系中的影响来确定这些病变的子集对表观遗传调节和生殖隔离的后果。虽然约50，000个从头mPing插入中的绝大多数可能是中性的或通过进化时间的选择而被消除，但在短期内，它们将提供一种宝贵的工具，可以更快地评估ACR的功能，并且成本比任何其他方法都低得多。可用的。该项目的结果将揭示快速TE扩增重塑表观基因组的潜力，导致生殖隔离，并为SV快速产生泛基因组基础的基因组变异。该项目产生的所有数据将通过沉积在已建立的长期序列存储库（如NCBI Short Read Archive（SRA）和Gene Expression Omnibus（GEO））中提供。该奖项反映了NSF的法定使命，并通过使用基金会的知识价值和更广泛的影响审查标准进行评估，被认为值得支持。