# Functional Characterization of Herpesvirus-Activated Noncoding Retrotransposon RNAs

> **NIH NIH R21** · UNIVERSITY OF CALIFORNIA BERKELEY · 2020 · $188,969

## Abstract

The advancement of sequencing technologies has resulted in the discovery of numerous types of non-coding
RNAs (ncRNA) that play important role in both tissue homeostasis and disease pathology. Additionally, several
studies have identified host and pathogen-encoded ncRNA whose expression patterns are associated with
viral pathogenesis, host defense and activation from latency. One specific class of ncRNA that has been
shown to modulate viral replication and inflammatory responses in mouse and human cells, respectively, are
the short interspersed nuclear elements (SINEs), termed B1-B4 in mice and Alu in humans. These repetitive
elements are epigenetically silenced in healthy somatic cells but can be induced and transcribed by RNA
polymerase III (Pol3) upon exposure to various cellular stresses
, including infection with a variety of DNA
viruses. Recent studies suggest that SINE ncRNA expression can influence viral and host gene expression
and NFκB signaling during infection with the murine gammaherpesvirus MHV68, a close relative of Kaposi's
sarcoma-associated herpesvirus. Additional studies have linked SINE expression to increased transcription of
interferon-stimulated genes (ISG) . Given that SINE ncRNAs accumulate in the nucleus and the
cytoplasm, how their gene regulatory and signaling activities are coordinated in each compartment is a
fundamental question in the field. We will address this by first constructing a SINE locus activation map in
cells infected with alpha or gammaherpesviruses, which will be used to identify direct SINE ncRNA-driven gene
expression signatures in the nucleus and their consequences for viral replication. We will then identify which
components of the innate immune pathway in the cytoplasm are involved in sensing natively transcribed SINE
ncRNAs. Collectively, these results will provide new mechanistic insights into how these “self” ncRNAs function
to influence the gene expression landscape during DNA virus infection.

## Key facts

- **NIH application ID:** 9975697
- **Project number:** 5R21AI147183-02
- **Recipient organization:** UNIVERSITY OF CALIFORNIA BERKELEY
- **Principal Investigator:** Britt A Glaunsinger
- **Activity code:** R21 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $188,969
- **Award type:** 5
- **Project period:** 2019-07-10 → 2021-06-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/9975697

## Citation

> US National Institutes of Health, RePORTER application 9975697, Functional Characterization of Herpesvirus-Activated Noncoding Retrotransposon RNAs (5R21AI147183-02). Retrieved via AI Analytics 2026-05-22 from https://api.ai-analytics.org/grant/nih/9975697. Licensed CC0.

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