# Functional long noncoding RNAs in neural development

> **NIH NIH R01** · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · 2022 · $630,472

## Abstract

ABSTRACT
Long noncoding RNAs (lncRNAs) have been implicated in a wide range of human neurological disorders
including cancer, developmental delay, psychiatric and neurodegenerative disease. While it is known that the
brain is enriched in specific lncRNAs, relatively few have been characterized in terms of function and molecular
mechanism. Our long-term goal is to understand the function and molecular mechanisms of lncRNAs in
neurodevelopment. Such fundamental knowledge is critical to understanding how this large aspect of the
noncoding genome regulates brain development and disease. We have taken two approaches for the study of
lncRNA function. The first approach is a “traditional” molecular-genetic study of a brain-specific, evolutionarily
conserved lncRNA that is a potent regulator of neural stem cells (NSCs). In previous studies, we identified a
novel lncRNA transcript that we named Pnky (Pou3f2 intergenic non-koding). In cultured NSCs, either Pnky
transcript knockdown or Pnky conditional knockout (Pnky-cKO) increases neuronal production by ~4-fold.
Pnky is required for proper cortical neurogenesis in vivo, and the expression of Pnky from a BAC transgene
(BAC-Pnky) fully rescues Pnky-deletion – including at the level of the transcriptome – indicating that this
lncRNA functions in trans. Pnky interacts with the splicing regulator PTBP1 (Polypyrimidine tract binding
protein 1) – a critical regulator of neurogenesis from NSCs – and Pnky appears to function in the same
molecular pathway as PTBP1. Preliminary Studies demonstrate that Pnky folds into a compact, monodisperse
state that contains intricate structures including a pseudoknot, which is a structural module known to have
important function in noncoding RNAs. Given these data, we hypothesize that Pnky contains functional
structural modules and regulates the function of PTBP1. Our second approach is to use systematic functional
screens to discover key principles of lncRNA genome function. In Preliminary Studies, we used CRISPRi to
screen in parallel 10,671 lncRNA and 18,905 mRNA genes for roles in the neural induction of NSCs from
human induced pluripotent stem cells (iPSCs). We also performed CRISPRi perturbation coupled with droplet-
based single-cell RNA-Seq (Perturb-Seq) for hundreds of screen hits. Based on results from these systematic
studies, our working hypothesis is that functional lncRNAs – in comparison to coding genes – are enriched for
roles in “focusing” differentiation to specific neural cell types. To further test this hypothesis, we will study
lncRNA function in human brain organoids and extend our screens to analyze neurogenesis. Determining the
unique functional roles of lncRNAs and coding genes at genome-scale will have important, broad impact on the
interpretation of transcriptomic and epigenomic studies of neurodevelopment. Together, by studying lncRNA
function at the level of individual transcripts and also at genome scale, we expect to gain fundamental insights
into t...

## Key facts

- **NIH application ID:** 10530928
- **Project number:** 1R01NS124881-01A1
- **Recipient organization:** UNIVERSITY OF CALIFORNIA, SAN FRANCISCO
- **Principal Investigator:** DANIEL A LIM
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2022
- **Award amount:** $630,472
- **Award type:** 1
- **Project period:** 2022-07-01 → 2027-06-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10530928

## Citation

> US National Institutes of Health, RePORTER application 10530928, Functional long noncoding RNAs in neural development (1R01NS124881-01A1). Retrieved via AI Analytics 2026-05-23 from https://api.ai-analytics.org/grant/nih/10530928. Licensed CC0.

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