BRC-BIO: Epigenetic Regulation of Transposable Elements in Maize

基因组学时代的一个令人惊讶的发现是真核生物基因组，特别是植物基因组，通常主要由转座因子（te）组成。这些元素复制并整合到不同的基因组位点，导致基因突变和显著的染色体改变。了解沉默的机制，这是通过世代开始和维持的，对于掌握TE沉默和转位之间的动态相互作用是重要的，转位塑造了基因组结构并影响了基因调控。然而，由于古代事件之外的新事件有限，对沉默起始的研究具有挑战性。本研究提出利用玉米独有的两种天然沉默基因（杀手等位基因），通过简单杂交可以主动启动TE沉默，而不是使用转基因构建体。本研究旨在探讨玉米表观遗传TE沉默的启动和后果，重点关注响应发育线索的复杂调控机制。此外，该提案优先考虑学生参与、多样性支持和教育推广。通过促进主要本科院校（PUIs）和研究密集型大学（R1）之间的合作，它旨在提高PI的研究生产力，同时解决资源不足环境中学生面临的挑战。结合合作本科生研究经验（CURE）的组成部分，可以使更多来自PUIs的本科生从事真正的研究。此外，还提出了为服务不足的学生量身定制的夏季研究奖学金计划，旨在克服因缺乏研究机会和与学术界联系有限而产生的障碍，从而促进他们在STEM领域的成功。本研究旨在对植物发育过程中表观遗传机制与转座子沉默之间复杂的相互作用获得有价值的见解。具体目标包括：1)研究玉米杀伤等位基因诱导的rna定向DNA甲基化（RdDM）。初步数据表明，ackiller衍生的小rna利用RdDM沉默活性Ac转座子，这为通过该途径沉默Ac提供了第一个证据。本研究拟通过研究Ack-small RNA在全基因组范围内对Ds的影响，以全面了解TE沉默过程中小RNA的靶向、起始和维持，并深入了解基因组进化过程中对Ds的古老沉默事件。2)基于杀伤小rna诱导RdDM受发育阶段严格调控的初步数据，探讨沉默机制的调控。这种调节可能涉及不同沉默机制之间的交替，包括RdDM、组蛋白修饰和翻译抑制。通过研究相同的小rna在不同组织中激活不同沉默途径的能力，本研究为探索TE沉默响应发育线索的动态调控提供了独特的机会。该奖项反映了美国国家科学基金会的法定使命，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。

One surprising discovery of the genomics era is that eukaryotic genomes, particularly plant genomes, often consist largely of transposable elements (TEs). These elements replicate and integrate into various genomic sites, causing genetic mutations and significant chromosomal alterations. Understanding the mechanism of silencing, which is initiated and then maintained through generations, is important to grasp the dynamic interplay between TE silencing and transpositions that shapes genome structure and influences gene regulation. However, studying the silencing initiation is challenging due to the limited novel occurrence beyond ancient events. This study proposes utilizing two naturally occurring silencers (killer alleles) exclusive to maize, which can actively initiate TE silencing through simple crosses instead of using transgenic constructs. The research aims to investigate the initiation and consequences of epigenetic TE silencing in maize, with a focus on the sophisticated regulated mechanisms responding to developmental cues. Moreover, the proposal prioritizes student engagement, diversity support, and educational outreach. By fostering collaborations between Primarily Undergraduate Institutions (PUIs) and research-intensive (R1) universities, it seeks to enhance the PI's research productivity while addressing challenges faced by students in under-resourced environments. Incorporating a Collaborative Undergraduate Research Experience (CURE) component enables more undergraduate students from PUIs to engage in authentic research. Additionally, a summer research fellowship program tailored for underserved students is proposed, aiming to overcome barriers arising from their lack of research access and limited connections with the academic community, thereby promoting their success in STEM fields.This research aims to gain valuable insights into the intricate interplay between epigenetic mechanisms and transposon silencing during plant development. Specific goals include: 1) Studying the RNA-directed DNA methylation (RdDM) induced by maize killer alleles. Preliminary data indicate that Ackiller-derived small RNAs utilize RdDM to silence active Ac transposons, providing the first evidence of Ac silencing through this pathway. The study proposes to examine the genome-wide effects on Ds from the Ack-small RNAs to gain a comprehensive understanding of small RNA targeting, initiation, and maintenance during TE silencing, and obtain insights into the ancient silencing events on Ds during genome evolution. 2) Investigating the regulation of the silencing mechanisms based on the preliminary data that killer- small RNAs induced RdDM is tightly regulated by developmental stages. This regulation may involve alternating among different silencing mechanisms including RdDM, histone modification, and translation inhibition. By studying the ability of the same small RNAs to activate distinct silencing pathways in different tissues, this research provides a unique opportunity to explore the dynamic regulation of TE silencing in response to developmental cues.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.