# Functionally Assessing Transcriptional Enhancers In Vivo

> **NIH NIH R01** · UNIVERSITY OF CALIF-LAWRENC BERKELEY LAB · 2023 · $1,436,554

## Abstract

PROJECT SUMMARY
Hundreds of thousands of distant-acting enhancers control the function of the human genome by orchestrating
the transcription of genes during pre- and postnatal development and in normal and disease states of cells and
tissues. They display remarkable cell type specificity and dynamic spatial and temporal activity patterns. While
there is now abundant indirect evidence that sequence changes in enhancers are likely to impact substantially
on human phenotypic variation and many disease processes, our understanding of how biological function is
encoded within enhancer sequences remains incomplete. This represents a major challenge for the
interpretation of variation in enhancer sequences observed by whole-genome sequencing (WGS) in patients and
for linking sequence variants within enhancers to diseases and other phenotypes. Over the past 16 years, the
research program supported by this R01 has provided major insights into enhancer biology and groundbreaking
tools for enhancer discovery and characterization. This included the first demonstration of ChIP-seq from
mammalian tissues for enhancer discovery, and a constantly evolving suite of mouse engineering methods for
studying enhancers in vivo. This program has also produced the largest cohesive collection of human and mouse
in vivo-characterized enhancers available to date and provides the VISTA Enhancer Browser as a major
community resource. In the next phase of this research program, we propose to leverage the unique capabilities
previously developed under this program to further advance our understanding of general enhancer biology, to
complement the work of the recently established NHGRI Impact of Genomic Variation on Function (IGVF)
consortium with critically needed in vivo assessments of enhancer variants, and to provide enhancer resources
for the extended community. Our specific aims include: (1) We will explore the inner anatomy of enhancer
sequences through large-scale mutagenesis coupled to in vivo mouse assays. We will also delete large non-
coding genome intervals (gene deserts) from the mouse genome to determine the broad functional significance
of non-coding DNA beyond individual enhancer elements. (2) Working as Affiliates with the IGVF Consortium,
we will perform large-scale in vivo exploration of human variants with predicted impact on enhancer function to
assess human variation/mutation through our unique mouse engineering capabilities. This will include careful
validation and calibration of massively parallel reporter assays (MPRAs) and CRISPR screens through
comparison with in vivo mouse reporter assays. (3) We will continue to provide access to in vivo mouse assays
for the community and make our results available through the VISTA Enhancer Browser. In combination, in the
next phase of this program we expect to deliver impactful insights into the biology of enhancers as a major
category of non-coding genome function, apply innovative tools to demonstrate the in vi...

## Key facts

- **NIH application ID:** 10682174
- **Project number:** 2R01HG003988-18
- **Recipient organization:** UNIVERSITY OF CALIF-LAWRENC BERKELEY LAB
- **Principal Investigator:** Len Alexander Pennacchio
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2023
- **Award amount:** $1,436,554
- **Award type:** 2
- **Project period:** 2006-09-26 → 2028-05-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10682174

## Citation

> US National Institutes of Health, RePORTER application 10682174, Functionally Assessing Transcriptional Enhancers In Vivo (2R01HG003988-18). Retrieved via AI Analytics 2026-05-23 from https://api.ai-analytics.org/grant/nih/10682174. Licensed CC0.

---

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