Developing genetically encoded intrabodies to define retrotransposon function in synaptic development - a vast portion of eukaryotic genomes is comprised of repetitive retrotransposons (rtes)-often…

The National Institute on Aging awarded the University of Massachusetts Medical School $452,783 on September 1, 2026, under the Aging Research program (CFDA 93.866) to develop genetically encoded intrabodies that inhibit individual enzymatic domains of retrotransposons in order to define retrotransposon function in synaptic development.

The project addresses a critical gap in functional genomics: traditional loss-of-function approaches such as gene knockout and RNA interference cannot decouple the distinct enzymatic activities of retrotransposons because these elements encode both enzymatic machinery—reverse transcriptase and integrase—and structural capsid proteins at high copy numbers. The recipient will develop and validate inhibitory nanobodies (intrabodies) targeting individual enzymatic domains of the Drosophila retrotransposon Copia, which the recipient has identified as a regulator of synaptic development. The project comprises two parallel aims: developing inhibitory intrabodies against Copia reverse transcriptase and developing inhibitory intrabodies against Copia integrase. Success will provide a generalizable toolkit for studying multi-functional genomic loci and advance understanding of retrotransposon roles in aging and neurodegeneration.

The period of performance runs from September 1, 2026, through August 31, 2028. Work is performed in Worcester, Massachusetts. This is a Project Grant, the assistance type used for discrete, time-limited research projects under the Aging Research program.

Developing genetically encoded intrabodies to define retrotransposon function in synaptic development - a vast portion of eukaryotic genomes is comprised of repetitive retrotransposons (rtes)-often dismissed as 'junk DNA'-that are emerging as powerful regulators of aging, neurodegeneration, and normal physiology. Their functional dissection is a major challenge; due to high copy numbers, traditional loss-of-function approaches like gene knockout are ineffective. The challenge is compounded by RTE complexity, as a single RTE encodes both enzymatic machinery- reverse transcriptase (rtase) and integrase (in)-and structural capsid proteins. An RTE's diverse roles may require distinct activities, but current tools like rnai or crispr cannot decouple these functions. This technological GAP is a critical barrier to understanding this enigmatic portion of the genome. To overcome this barrier, we propose a transformative technology: genetically encoded, inhibitory nanobodies ( intrabodies ) that neutralize individual retrotransposon enzymes in vivo. This unique approach allows for the dissection of distinct enzymatic activities of rtes, providing a generalizable tool for functional genomics. As a proof-of-principle, we will use the drosophila RTE copia, which we identified as a critical regulator of synaptic development. Our central hypothesis is that intrabodies can specifically inhibit individual enzymatic domains of copia in vivo, allowing for the dissection of their roles in neuronal biology. We will test this through two independent, parallel aims: (1) develop and validate inhibitory intrabodies against copia reverse transcriptase (rtase) and (2) develop and validate inhibitory intrabodies against copia integrase (in). This project develops parallel pipelines for generating inhibitory nanobodies against copia enzymes. Success will validate a transformative, generalizable toolkit for studying multi-copy, multi-functional genomic loci and provide the first direct evidence for the function of specific retrotransposon enzymatic activities in neuronal biology.