Transposon control as a checkpoint during regeneration

PROJECT SUMMARY / ABSTRACT
Tissue regeneration is the process through which damaged tissue is restored to its original structure and
function. There is wide variation across species in their regenerative ability. For example, zebrafish can
regenerate all retinal neurons after injury while humans and mice cannot. Understanding the genetic basis and
molecular underpinnings of complex tissue regeneration in model species holds the promise to enhance human
regenerative medicine. Here I am using zebrafish to test the novel hypothesis that the control of transposable
elements (TEs) is a necessary checkpoint for complex tissue regeneration.
TEs are mobile DNA elements capable of self-replication that are ubiquitous and abundant in eukaryotes.
Uncontrolled TE activity leads to accumulation of TE-encoded nucleic acids and proteins that interfere with cell
homeostasis and can result in DNA damage, disrupting genome integrity. TE upregulation has been reported
during tissue regeneration in salamanders, sea cucumbers, and worms. I hypothesize that TE activation is a
hallmark of tissue injury that must be suppressed for successful regeneration, and an inability to suppress TEs
will stall regeneration. Supporting this hypothesis, my preliminary analyses of bulk RNA-seq data reveal TE
upregulation during early stages of eye regeneration that are later restored to control levels prior to tissue repair.
I predict that zebrafish and other organisms with a strong regenerative capacity deploy specific control systems
to suppress TE activity during regeneration. Here I will directly test the role of the Piwi pathway in suppressing
TE activity during zebrafish eye regeneration. The Piwi pathway is known to repress TEs in animal gonads,
including zebrafish, but there is growing evidence that the pathway is active in somatic tissues and required for
regeneration in planarians. Furthermore, I have detected piwil1 expression in the zebrafish eye, raising the
testable hypothesis that it functions during eye regeneration.
I will utilize a model of zebrafish retinal regeneration and a 2-pronged approach combining multimodal
genomics and manipulative experimentation. First, I will further establish that TE upregulation is a hallmark of
tissue injury by profiling TE expression changes across five regenerating tissues using publicly available single-
cell transcriptomic data. Second, I will generate a multi-omic single-cell dataset to assess TE expression changes
during cone regeneration from the onset of injury through to functional recovery. These data will provide the most
comprehensive and precise view of TE expression dynamics during regeneration for any species. Lastly, I will
directly test whether TE repression is required for regeneration by modulating TE activity using Piwi pathway
mutants and chemical inhibitors of TE activity. Together the outcomes of this project will be the first to directly
assess the role of TE activity and regulation during complex tissue regeneration. Moreover, these studies will
lay the foundation for new testable hypotheses surrounding differences between regeneratively competent
versus incompetent organisms and lead to the development of novel regenerative therapies.

Grant Number: 5F32EY034778-02
NIH Institute/Center: NIH
Principal Investigator: Krista Angileri