# Developing a high-throughput method to validate microRNA biogenesis in vivo.

> **NIH NIH R21** · BOSTON UNIVERSITY MEDICAL CAMPUS · 2020 · $248,333

## Abstract

ABSTRACT: “Developing a high-throughput method to validate microRNA biogenesis in vivo”
 microRNAs (miRNAs) are a family of small regulatory RNAs involved in repression of gene expression. They
recognize their target mRNAs though base pairing and upon binding, trigger translational repression,
deadenylation and decay of the target mRNAs. Given that each miRNA has the potential to regulate hundreds
of genes, and several dozens of miRNAs are expressed in each cell type, miRNAs are one of the master
regulators of gene expression at post-transcriptional level in animals, plants and virus. Thus, the elucidation of
the miRNA complement is essential to understand gene regulation and mRNA turnover. The goal of this
project is to develop a high-throughput method for miRNA discovery and experimental validation in vivo.
 Current miRNA discovery methods heavily rely on providing sequencing evidence of a small RNA that fits into
a hairpin-like structure predicted bioinformatically. The problem is that sample availability or the abundance of a
specific cell type in a tissue may be limited and hamper the number of miRNAs that can be backed-up with
sequencing support. In these situations, the current solution is to sequence deeper, increasing overall costs. On
the other hand, the presence of a small RNA of ~22-nt does not guarantee the belonging to the miRNA family,
as random degradation of cellular RNAs also will produce small RNAs of this size and only tedious experimental
validation of their processing into intermediate species and mature miRNA can confirm their identity.
 A recent curation work found that of the over ~7,000 metazoan miRNAs in miRBase, the reference miRNA
database, only 1,175 fulfilled the features necessary to pass as miRNAs, directly rejected 3,470 as false positives
and lacked enough sequencing evidence to call another 2,105 miRNAs. Therefore, there is an unmet
technological need to develop a miRNA validation method that boosts the access to the miRNA candidates
even from limited samples and that allows rigorous multiplexed experimental validation of their processing.
 With the synergy of an interdisciplinary team that combines expertise in microRNAs and zebrafish
manipulation (Dr. Cifuentes, PI) and bioinformatics (Dr. Moxon, co-I), we will develop miRAGe (miRNA Analysis
Genome wide), a high-throughput method to integrate miRNA prediction and their experimental validation in
vivo. The fundamental concept behind miRAGe is the use of living cells as “organic computers” to analyze miRNA
processing. We will use massively parallel oligo pool synthesis to prepare the miRNA candidate precursors and
test their processing in injected zebrafish embryos. Small RNA sequencing will determine which candidates are
true microRNA by detecting their ~22-nucleotide mature product and their stereotypic intermediates.
 Overall, the results from this project will transform the access of the scientific community to high quality,
experimentally validated miRNA d...

## Key facts

- **NIH application ID:** 10043005
- **Project number:** 1R21GM138951-01
- **Recipient organization:** BOSTON UNIVERSITY MEDICAL CAMPUS
- **Principal Investigator:** Daniel Cifuentes
- **Activity code:** R21 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $248,333
- **Award type:** 1
- **Project period:** 2020-08-01 → 2022-07-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10043005

## Citation

> US National Institutes of Health, RePORTER application 10043005, Developing a high-throughput method to validate microRNA biogenesis in vivo. (1R21GM138951-01). Retrieved via AI Analytics 2026-05-22 from https://api.ai-analytics.org/grant/nih/10043005. Licensed CC0.

---

*[NIH grants dataset](/datasets/nih-grants) · CC0 1.0*