# Analysis of combinatorial cis-regulation in synthetic and genomic promoters

> **NIH NIH R01** · WASHINGTON UNIVERSITY · 2024 · $470,232

## Abstract

Project Summary/Abstract
 A majority of heritable disease-causing variation resides in the non-coding portions of the human
genome. A leading hypothesis is that most of this variation exerts its effects on cell-type-specific cis-
regulatory sequences (CRSs). Interpreting such variation will therefore require quantitative models of the
‘regulatory grammar’ that controls the cell-type-specific activities of CRSs. We define the regulatory
grammar of a cell type to be the independent and interacting contributions of transcription factor binding
sites (TFBSs) to cis-regulatory activity. Models of regulatory grammar must also include the dependencies
of those contributions on the number, orientation, spacing, and affinity of TFBSs. Detailed models of
regulatory grammars are still in their infancy, partly because we lack systematic training data for how CRSs
behave across diverse cell types in vivo. We propose to address this gap by systematically measuring the
activities of CRSs across cell types within intact mammalian tissues. To collect this data, we will introduce
a single-cell massively parallel reporter gene assay (scMPRA) that measures the cell-type-specific
activities of CRSs in vivo. We will model the resulting data using a formal thermodynamic model in which
each TF-DNA or TF-TF interaction is represented by its free energy (ΔG) of interaction. By comparing the
magnitudes of the resulting ΔG values, we will quantify the independent and interacting contributions of
specific TFBSs, thus deriving quantitative regulatory grammars that capture the differences between cell
types within the mammalian retina (Aim 1) and the mammalian brain (Aim 2). By validating our models on
sequence variants of endogenous CRSs, we hope to make progress towards a framework for accurately
predicting the effects of non-coding genetic variation on the function of CRSs.

## Key facts

- **NIH application ID:** 10896307
- **Project number:** 5R01GM092910-14
- **Recipient organization:** WASHINGTON UNIVERSITY
- **Principal Investigator:** Barak A Cohen
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2024
- **Award amount:** $470,232
- **Award type:** 5
- **Project period:** 2011-01-01 → 2027-08-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10896307

## Citation

> US National Institutes of Health, RePORTER application 10896307, Analysis of combinatorial cis-regulation in synthetic and genomic promoters (5R01GM092910-14). Retrieved via AI Analytics 2026-05-23 from https://api.ai-analytics.org/grant/nih/10896307. Licensed CC0.

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