BRC-BIO: Epigenetic Regulation of Transposable Elements in Maize

Hofstra University, Hempstead NY

Investigators

Abstract

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.