# Destruction of noncoding RNAs

> **NIH NIH R35** · WEILL MEDICAL COLL OF CORNELL UNIV · 2022 · $423,750

## Abstract

SUMMARY
Precise and dynamic control of gene expression is a balancing act between production and destruction. Although
noncoding RNAs are critical regulators of gene expression with important roles in development and disease, our
understanding of their destruction is still in its infancy. One of the reasons for this gap in knowledge is that some
noncoding RNAs, like microRNAs and circular RNAs, are resistant to the known pathways that destroy protein-
coding RNAs. Here I present my plan to identify how these two types of noncoding RNA are destroyed.
MicroRNAs (miRNAs) are protected from degradation by their effector protein Argonaute. One way to degrade
miRNAs is through target-directed miRNA degradation (TDMD), which occurs when a highly complementary
viral or artificial RNA interacts with the miRNA. My postdoctoral work identified two of the first examples of
endogenous targets that induce miRNA degradation, which also led to our discovery of an E3 ubiquitin ligase
that mediates TDMD and the identification of 48 additional miRNAs (likely an underestimate) subject to TDMD.
Our working model now is that the binding of highly complementary targets to the Argonaute–miRNA complex
leads to recruitment of the E3 ligase, ubiquitination and proteosomal degradation of Argonaute, and release and
degradation of the miRNA. With the discovery of TDMD effector proteins and the broad influence of TDMD on
miRNA stability, a major gap is identifying the target RNAs that induce TDMD. A related problem is understanding
why some targets are better than others. We will address these gaps by answering two questions: 1) Which
endogenous RNAs induce miRNA degradation? 2) What are the pairing rules and cis-acting elements that
promote TDMD? To do so, we will use transgenic mice, engineered cell lines, genome-wide approaches, and
classic molecular biology techniques. Our second area of research is understanding how circular RNAs
(circRNA) are degraded. The poster child of post-transcriptional circRNA regulation is Cdr1as, a conserved
circRNA that is highly expressed in neurons and limits spontaneous synaptic vesicle release. Cdr1as contains a
single near-perfect binding site that can be sliced by Ago2-loaded miR-671 and >70 seed sites for miR-7.
Previously, I showed that Cdr1as can be regulated by the independent and cooperative actions of miR-671 and
miR-7. How miR-7 induces destruction of Cdr1as is unclear as circRNAs should be resistant to miRNA-mediated
deadenylation and decapping. Here, we will answer two questions: 1) How is Cdr1as degraded? 2) How are
other unstable circRNAs degraded? The outcomes of our research will be the identification and improved
understanding of dedicated pathways for degrading noncoding RNAs. These pathways have potential for broad
impact as they are likely employed in diverse cell types and organisms and in response to a variety of stimuli.

## Key facts

- **NIH application ID:** 10501209
- **Project number:** 1R35GM147463-01
- **Recipient organization:** WEILL MEDICAL COLL OF CORNELL UNIV
- **Principal Investigator:** BENJAMIN MONTEVERDE KLEAVELAND
- **Activity code:** R35 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2022
- **Award amount:** $423,750
- **Award type:** 1
- **Project period:** 2022-08-01 → 2027-07-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10501209

## Citation

> US National Institutes of Health, RePORTER application 10501209, Destruction of noncoding RNAs (1R35GM147463-01). Retrieved via AI Analytics 2026-05-28 from https://api.ai-analytics.org/grant/nih/10501209. Licensed CC0.

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