# Long Non-Coding RNA-mediated Differential Regulation of Notch Pathway Targets in Early T-cell Development

> **NIH NIH F30** · CALIFORNIA INSTITUTE OF TECHNOLOGY · 2021 · $42,080

## Abstract

PROJECT SUMMARY
Notch signaling is critical for early T-cell development. At its core, Notch signaling relies on the interaction
between Notch-family receptors with their cognate, transmembrane-bound Delta-like family ligands. Upon
ligand recognition and binding, Notch receptors undergo a series of proteolytic cleavage events, allowing the
release and translocation of Notch intracellular domain (NotchICD) into the cell nucleus. Within the nucleus,
NotchICD can interact with its DNA-binding partner, Recombination Signal Binding Protein-Jk (RBPJk) to activate
expression of target genes. Despite the essential role for Notch-mediated gene regulation in this
developmental context, it remains a mystery how NotchICD can localize to DNA and differentially regulate gene
expression, given its near-uniform expression pattern. One important negative regulator of Notch signaling is
Spen. Spen has been shown to compete with NotchICD for RBPJk binding and can recruit co-repressive
complexes to remodel chromatin and repress genomic loci. Recently, Spen was shown to directly interact with
a group of nucleic acid molecules called long non-coding RNA (lncRNA). Given their preferential localization
within the cell nucleus, ability to coordinate nuclear organization through protein-scaffolding, and documented
tissue and temporal specificity greater than mRNA or protein, lncRNAs are an attractive and as of yet-
uncharacterized class of regulatory molecules that could mediate differential expression of Notch-target genes.
We hypothesize that lncRNAs recruit Spen to distinct RBPJk bound sites on DNA. This in turn, biases NotchICD
towards sites of `un-occupied' RBPJk, leading to activation of target genes. Changes in lncRNA expression
would modulate Spen localization and alter NotchICD's accessible genomic repertoire in a stage- and
temporally-specific manner. We will this hypothesis by characterizing the dynamics of NotchICD and Spen
genomic localization using Chromatin-ImmunoPrecipitation, determining if Spen's interactions with RNA are
critical for regulation of Notch signaling using Spen truncation analysis, and characterizing the roles of specific
lncRNA-Spen interactions on differential expression of Notch target genes using genetic perturbation, in ex
vivo differentiated pro-T cell subsets. The results of this study have the potential to incorporate lncRNAs into
our understanding of dynamic gene regulation during development and differentiation, generalizable to
signaling pathways in other biologic contexts. Moreover, dysregulation of the Notch signaling pathway has
been linked to a variety of hematologic and solid malignancies, including T-Acute Lymphoblastic Leukemia and
Pancreatic cancer. By identifying and characterizing novel lncRNA-Spen interactions in this study, we hope to
identify new, increasingly specific targets for pharmacologic manipulation of the Notch signaling pathway
towards the treatment of human disease.

## Key facts

- **NIH application ID:** 10080749
- **Project number:** 5F30HL136080-05
- **Recipient organization:** CALIFORNIA INSTITUTE OF TECHNOLOGY
- **Principal Investigator:** Abhik Banerjee
- **Activity code:** F30 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2021
- **Award amount:** $42,080
- **Award type:** 5
- **Project period:** 2017-02-01 → 2021-09-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10080749

## Citation

> US National Institutes of Health, RePORTER application 10080749, Long Non-Coding RNA-mediated Differential Regulation of Notch Pathway Targets in Early T-cell Development (5F30HL136080-05). Retrieved via AI Analytics 2026-05-23 from https://api.ai-analytics.org/grant/nih/10080749. Licensed CC0.

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