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，真核基因组，特别是植物基因组，往往主要由转座元件(TES)组成。这些元素复制并整合到不同的基因组位置，导致基因突变和显著的染色体变化。了解沉默的机制对于掌握TE沉默和转位之间的动态相互作用非常重要，TE沉默和转位塑造基因组结构并影响基因调控。然而，由于古代事件以外的小说发生的数量有限，对沉默起源的研究是具有挑战性的。本研究建议利用玉米特有的两种自然产生的沉默基因(杀手等位基因)，可以通过简单的杂交而不是使用转基因构建物来主动地启动TE沉默。本研究旨在研究玉米表观遗传TE沉默的开始和后果，重点是复杂的调控机制对发育线索的反应。此外，该提案将学生参与、多样性支持和教育推广列为优先事项。通过促进主要是本科院校(PUI)和研究密集型(R1)大学之间的合作，它试图提高PI的研究生产率，同时解决学生在资源不足的环境中面临的挑战。结合协作本科生研究体验(CURE)的组成部分，使更多来自PUI的本科生能够从事真实的研究。此外，还提出了一个为服务不足的学生量身定做的暑期研究奖学金计划，旨在克服他们缺乏研究机会和与学术界联系有限的障碍，从而促进他们在STEM领域的成功。本研究旨在获得有价值的见解，了解表观遗传机制和转座子沉默在植物发育过程中的复杂相互作用。具体目标包括：1)研究玉米杀手等位基因诱导的RNA诱导的DNA甲基化(RdDM)。初步数据表明，Aciller衍生的小RNA利用RdDM来沉默活跃的ac转座子，提供了通过这一途径沉默ac的第一个证据。本研究旨在研究Ack-Small RNAs在全基因组范围内对D的影响，以全面了解在TE沉默过程中小RNA的靶向、启动和维持，并深入了解基因组进化过程中对D的古代沉默事件。2)基于杀手-小RNA诱导的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的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激活不同组织中不同沉默途径的能力，这项研究提供了一个独特的机会来探索TE沉默对发育线索的动态调节。这一奖项反映了NSF的法定使命，并通过使用基金会的智力优势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.