# Functional Elucidation of the Sequence-Encoded Regulatory Activity of Enhancers in Vivo in the Brain

> **NIH NIH R35** · UNIVERSITY OF CALIFORNIA AT DAVIS · 2020 · $351,313

## Abstract

Title - Functional elucidation of the sequence-encoded regulatory activity of enhancers in vivo in the brain
P.I. – Alex Nord, PhD
Research Summary:
Once considered junk, non-coding regions of the genome have emerged as central components of evolution,
development, and disease. The most common non-coding regulatory elements in the human genome are
enhancers, which ensure expression of target genes at the right time in the right cells by controlling their
activation. While recent efforts have made headway annotating enhancers in the genome, characterization of
their sequence-encoded function remains a major challenge. This represents a significant barrier in
understanding the important role of enhancers in complex biological processes, as well as in interpreting the
effect of enhancer sequence variation on human evolution and disease. Rapid adoption of whole genome
sequencing promises to amplify this issue, since considerably more potential causal mutations will be identified
than can be functionally classified using current approaches. As such, there is a critical need for effective
mechanisms to functionally characterize regulatory DNA at the sequence level to reveal the role of non-coding
elements in human development. Massively parallel reporter assays provide a potential solution toward
dissecting sequence-encoded enhancer activity, enabling quantitative measurement of hundreds to thousands
of individual candidate enhancer sequences in a single experiment. Applying this approach in vivo could
illuminate the normal versus pathogenic functions of enhancers in the assemblage of cells comprising
mammalian tissues. It also could reveal their role mediating gene-by-environment interactions in complex
conditions, such as learning and stress. In preliminary experiments, we adapted a high-throughput reporter
assay to characterize enhancer function in mouse frontal cortex, and we applied single cell transcriptomics to
define enhancer function in vivo in the developing mouse brain. These novel approaches open exciting long-
term research avenues, enabling testing of enhancer sequence variation and cell-specific function in vivo at a
scale and resolution not previously possible. We will couple our powerful functional assay with single cell
genomics to address significant questions regarding gene regulatory wiring in the brain. We propose to: 1)
Extend our function-based methods for the study of enhancer activity in vivo in mouse brain, and 2) Apply
these methods to characterize the function of enhancers we previously mapped that control stage-specific
gene expression associated with neuroplasticity, and to test the consequences on in vivo enhancer function of
non-coding variation linked to brain evolution and pathology. These scientific questions build on our previous
work on enhancers in the brain, using our new methods to transform the scope at which we can address key
gaps in the understanding of enhancer function and fundamental questions of gene reg...

## Key facts

- **NIH application ID:** 9939616
- **Project number:** 5R35GM119831-05
- **Recipient organization:** UNIVERSITY OF CALIFORNIA AT DAVIS
- **Principal Investigator:** Alexander Nord
- **Activity code:** R35 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $351,313
- **Award type:** 5
- **Project period:** 2016-09-01 → 2021-12-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/9939616

## Citation

> US National Institutes of Health, RePORTER application 9939616, Functional Elucidation of the Sequence-Encoded Regulatory Activity of Enhancers in Vivo in the Brain (5R35GM119831-05). Retrieved via AI Analytics 2026-05-23 from https://api.ai-analytics.org/grant/nih/9939616. Licensed CC0.

---

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