# How does a gene integrate multiple signals?

> **NIH NIH F30** · UNIVERSITY OF PENNSYLVANIA · 2020 · $32,947

## Abstract

Project Summary
 How does transcription of a gene change when the gene receives multiple input signals? A wide variety
of outcomes are possible, ranging from sub-additive to super-multiplicative integration of each signal’s effects.
A common belief is that it is not possible to predict how a gene will integrate two or more signals because
cellular signal responses depend on “context”. Nevertheless, gene regulation studies select either an additive
or multiplicative null model when determining cooperativity or antagonism in transcriptional responses to pairs
of signals. However, it remains unknown what the “default” mode of integration is for multiple cell signals.
Moreover, newer epigenetic profiling methods have yet to reveal the context that determines how a gene
integrates two signals. We propose transcriptome-wide profiling of signal integration outcomes in human cells
to map the degree to which genes use additive, multiplicative, or other modes of integration. In parallel, we will
analyze changes in chromatin accessibility near these genes to reveal the nature of cis-regulatory element
activities that corresponds to a gene’s signal integration mode. We will use a simple model system where we
co-expose human breast carcinoma (MCF-7) cells to two potent cell signals: retinoic acid and TGF-beta. After
exposing these cells to either or both signals, we will perform paired RNA-seq and ATAC-seq measurements.
Our preliminary data suggest that TGF-beta and retinoic acid change the expression of 693 shared target
genes. Comparing individual versus combined signal effects at these genes, we observe a variety of signal
integration functions that range from sub-additive to super-multiplicative. Our preliminary findings also suggest
that a gene’s signal integration function remains consistent across multiple dosages. This implies that the
structure of nearby regulatory elements may determine a gene’s mode of integration. Do two signals add their
effects when they act on distinct enhancers, but multiply their effects when they act on the same enhancers?
Or do specific transcription factor combinations dictate a gene’s mode of integration? We will analyze our
paired ATAC-seq data to distinguish between possible “epigenetic arrangements” that enable different signal
integration functions, using differential peak analysis to measure activated regulatory elements and
transcription factor motif analysis to test for associations between genes and specific transcription factor pairs.
We will test our predictions by silencing specific enhancers near endogenous genes with CRISPR-based
approaches. Our studies in MCF-7 cells will provide a rich starting point for our question, but we will also
expand the scope of our work to test the effects of cell type, relative timing of signal onset, and higher order
signal combinations (up to four simultaneous signals). This work could revise leading quantitative models of
how genes respond to interacting input signals, which c...

## Key facts

- **NIH application ID:** 10067663
- **Project number:** 1F30HG010986-01A1
- **Recipient organization:** UNIVERSITY OF PENNSYLVANIA
- **Principal Investigator:** Eric Sanford
- **Activity code:** F30 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $32,947
- **Award type:** 1
- **Project period:** 2020-07-01 → 2021-06-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10067663

## Citation

> US National Institutes of Health, RePORTER application 10067663, How does a gene integrate multiple signals? (1F30HG010986-01A1). Retrieved via AI Analytics 2026-05-22 from https://api.ai-analytics.org/grant/nih/10067663. Licensed CC0.

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