# SINE-mediated Regulation of mRNA Epitranscriptome for Pluripotency Maintenance and Differentiation

> **NIH NIH R21** · COLUMBIA UNIVERSITY HEALTH SCIENCES · 2022 · $246,750

## Abstract

PROJECT SUMMARY
The transcriptional control of mRNA expression has been extensively investigated; however, less attention has
been paid to their internal modifications, the mRNA “epitranscriptome”. Recently, evidence is accumulating that
modifications on mRNAs are functionally significant in a variety of molecular processes including pre-mRNA
splicing, nuclear export, and stability, and play important biological roles in stem cells differentiation and human
development. Transposable elements (TEs), including SINEs, LINEs, and LTRs are the most abundant DNA
elements in the mammalian genomes. Unlike the other TEs such as LINEs and ERVs, SINEs are frequently
embedded in the non-coding regions inside a gene, such as the introns and UTRs, with functional implications
on their host mRNA expression. SINEs have more than a million genomic copies and occupy 8.22% of DNA
sequences of the mouse genome and 13.64% of the human genome. TEs, including SINEs, were historically
considered as “junk” DNA but now it is widely accepted that this portion of the genome plays a significant role in
diverse cellular processes. Our preliminary analysis of RNA-bisulfite sequencing (BS-seq) in embryonic stem
cells (ESCs) identified that the 5-methylcytosine (m5C)-enriched regions on mRNA transcripts are significantly
associated with the embedded SINE elements at introns or UTRs of the host genes. Despite the well-established
metabolism of DNA methylation and demethylation by Dnmt1/3a/3b and Tet1/2/3 for epigenetic regulations, our
knowledge on RNA m5C for posttranscriptional gene regulation is quite limited. We hypothesize that self-renewal
and differentiation of ESCs may be controlled by m5C-mediated active nuclear export and nuclear retention/
destabilization, respectively, of pluripotency mRNAs bearing SINE elements. We propose two aims to test this
hypothesis. Aim 1. We will determine the regulation of pluripotency mRNA with embedded SINE region and m5C
for nuclear export in ESC self-renewal. We determined that Alyref is indispensable for ESC self-renewal. We will
examine if active nuclear export of pluripotency mRNAs (e.g. Nanog) are mediated by the m5C reader Alyref.
Next, we will test if Alyref represses the affinity of m5C-modified mRNAs to the Pspc1/Nono heterodimer. Aim 2.
We will dissect the mechanism of SINE non-coding (nc) RNA-mediated pluripotency mRNA degradation in ESC
differentiation. Our preliminary work revealed that m5C-modified pluripotency gene transcripts (e.g., Nanog) have
impaired degradation in Pspc1KO ESCs upon retinoic acid (RA)-induced differentiation. RA treatment activates
SINE ncRNAs, which form double-stranded (ds) RNAs in trans with the host mRNAs and recruit the Nono/Pspc1/
Tet2 complex for mRNA nuclear retention and destabilization. We will explore the Pspc1 RNA targets by eCLIP-
seq in ESCs and with RA treatment to examine the interactions between SINE ncRNAs and host mRNAs. Next,
we will examine if Tet2 is recruited by Pspc1 for mRNA dem...

## Key facts

- **NIH application ID:** 10417866
- **Project number:** 1R21HD106263-01A1
- **Recipient organization:** COLUMBIA UNIVERSITY HEALTH SCIENCES
- **Principal Investigator:** Xin Huang
- **Activity code:** R21 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2022
- **Award amount:** $246,750
- **Award type:** 1
- **Project period:** 2022-07-05 → 2024-06-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10417866

## Citation

> US National Institutes of Health, RePORTER application 10417866, SINE-mediated Regulation of mRNA Epitranscriptome for Pluripotency Maintenance and Differentiation (1R21HD106263-01A1). Retrieved via AI Analytics 2026-05-25 from https://api.ai-analytics.org/grant/nih/10417866. Licensed CC0.

---

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