Overview:
Transposable element (TE) activity results in genome instability in a wide variety of organisms, including humans. This instability has been associated with several diseases, including neurofibromatosis, hemophilia, and cancer. Epigenetic silencing is an efficient mechanism for the initiation and maintenance of TE repression on a genome-wide scale in both plants and animals. My overarching research goal is to understand the dynamic epigenetic nature of TE silencing.
In my research, I adopt a novel model system in which active DNA transposons can be silenced by de novo silencing triggers that are sources of small RNAs in maize (Slotkin and Lisch, 2005 and 2006; Wang, et al., 2020). This system provides us with unique advantages to induce and monitor the initiation and maintenance of silencing in various tissues and at various time points during maize development.
Question 1. How the newly identified Ac killer kills an active Ac?
In a recent paper, we identified two independent “killer” alleles (Ack) that can induce the silencing of active maize Ac transposons (Wang et al. 2020). Ac killers represent the first case of TE silencing that can be attributable to self-initiated alternative transposition and demonstrate that Ac transposons silencing is initiated by small RNAs generated from the hairpin transcripts.
However, beyond this observation, the details of the silencing mechanism are not understood. Our working hypothesis is that Ack induces RNA-directed DNA methylation (RdDM) at all the small RNA targets genome-wide. We propose to perform next-generation sequencing experiments to identify the differentially methylated regions. Both the direct and indirect effects of Ack, both the initiation and maintenance of the silencing will be studied.
Question 2. How TE killing is regulated during plant development?
Recent papers have reported that the killing by some killers is precisely regulated by different signals, for example, developmental transitions (Li, et al., 2010) and abiotic stresses (Guo, et al., 2021). Our preliminary data show that the killing by Mu killer (Muk) in the germinating seeds employs different strategies between the embryo and endosperm. The same species of small RNA triggers a different silencing pathway in the germinating embryo. We plan to do the Bisulfite sequencing and ChIP experiment to identify the alternative silencing pathway in the embryo. This will help us understand how the initiation/maintenance of killing is regulated or enhanced.
Question 3. Why some macrotransposons do not jump?
In a recent paper that we published (Wang, et al., 2022), we documented ten jumping events of macrotransposons (two closely located transposons jumping together as a large transposon). An interesting observation is that all the jumping events are from two alleles. Another allele that shares a very similar structure and the same chromosomal location does not jump, in another word, is silenced. We plan to test the methylation status and histone markers for this allele to investigate the nature of the silencing. We are also interested to test if the silencing can be reversed by any development signals. This would help us understand how the ancient macrotransposons in the modern maize lines were silenced during maize domestication.
