# Deep characterization of the biogenesis and function of Ebola virus microRNAs

> **NIH NIH R21** · BOSTON UNIVERSITY MEDICAL CAMPUS · 2020 · $206,974

## Abstract

PROJECT SUMMARY: “Deep characterization of the biogenesis and function of Ebola virus microRNAs”
 Ebola virus (EBOV) belongs to the group of hemorrhagic fever viruses and causes a severe disease in
humans with case fatality rates ranging from 40 to 90%. The devastating EBOV epidemic in West Africa
claimed at least 11,000 lives and resulted in billions of dollars of economic loss, highlighting the need for
early diagnostic and effective countermeasures.
 miRNAs are a family of small non-coding RNAs that regulate gene expression at post-transcriptional
level6. Interestingly, recent in silico predictions identified EBOV-encoded microRNAs (miRNAs)1-3. However,
the functional relevance of these viral miRNAs remains elusive.
Recent preliminary data from our labs validated the expression of two published EBOV miRNAs, EBOV-
pre-miR-13 and EBOV-pre-miR-T21. However, the small RNA read support and the secondary structures of
these loci are incompatible with canonical miRNA processing. Moreover, the 5’-ends of these mature
miRNAs coincide with the transcription start site of the EBOV genes VP24 and VP40, respectively.
 The goal of this project is to uncover the processing pathways involved in the maturation of EBOV-pre-
miR-1 and EBOV-pre-miR-T2, and their function during infection. We hypothesize that these miRNAs are
processed by a non-canonical miRNA biogenesis pathway that bypasses Drosha cleavage and instead
relies on transcription initiation to define the 5’-ends of the miRNAs. We will further explore if the EBOV
miRNAs are the product of abortive transcription by the EBOV RNA-dependent RNA polymerase.
 To gain mechanistic insight into the function of these EBOV-encoded small RNAs, we propose to examine
whether EBOV-pre-miR-1 and EBOV-pre-miR-T2!repress host gene expression via the canonical miRNA-
effector pathway, or alternatively, if they interfere with EBOV mRNA expression by steric blocking of the
transcription start sites on the EBOV genome.
 Two highly integrated aims will address these hypotheses using a combination of state-of-the-art miRNA
analysis and virological approaches. Specifically, we will use the zebrafish embryo and EBOV infection
platforms to determine the biogenesis of EBOV-pre-miR-1 and -T2 (Aim 1). In Aim 2, we will perform reporter
assays to determine their cellular and viral targets. Finally, we will use modified antisense oligos to interfere
with EBOV miRNA function and examine their impact on host and viral gene expression during infection.
 With the synergy of an interdisciplinary team that combines expertise in microRNAs, zebrafish,
bioinformatics and BSL-4 level virology work, we will mechanistically probe the origin and function of EBOV
miRNAs. The results from this project will transform our understanding of how small RNAs regulate EBOV
infection and inform antiviral drug development to improve the standard of care for EBOV-infected patients.
!

## Key facts

- **NIH application ID:** 9963122
- **Project number:** 5R21AI147285-02
- **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:** $206,974
- **Award type:** 5
- **Project period:** 2019-07-01 → 2022-06-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/9963122

## Citation

> US National Institutes of Health, RePORTER application 9963122, Deep characterization of the biogenesis and function of Ebola virus microRNAs (5R21AI147285-02). Retrieved via AI Analytics 2026-05-28 from https://api.ai-analytics.org/grant/nih/9963122. Licensed CC0.

---

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