The best of both worlds: Blending assays to understand human genome regulation

By Caroline Cencer

Assistant Professor of Biochemistry Emily Hodges and graduate student Tyler Hansen used a blended approach to create a new, multi-omic method to identify and characterize gene regulatory elements—non-coding DNA sequences that control gene expression—in the human genome. The new technique, ATAC-STARR-seq, was published in Genome Research.

During DNA transcription, regions of the genome called enhancers and silencers can increase or decrease gene activity, respectively, when bound by transcription factors. DNA and proteins are packaged into a tightly coiled complex called chromatin that must be uncoiled so that transcription factors can access the enhancer regions and drive transcription of their target genes. As dysfunctions in gene regulation can lead to debilitating diseases, including cancer, characterizing the specific regions where transcription factors can act on the human genome is essential for understanding the pathogenesis of some disorders.

In the past, scientists studying gene regulatory elements have used STARR-seq to identify “active” enhancers—meaning they are actively driving gene expression to produce a given cellular identity (e.g., heart cell, neuron, epithelial cell, etc.). However, STARR-seq lacks the resolution and precision required to identify most of the active enhancer repertoire controlling the identity of a given cell type. By combining STARR-seq with ATAC-seq, a method used to identify open chromatin regions, Hodges and Hansen improved the sensitivity of STARR-seq by only testing accessible regions for enhancer activity. Because chromatin accessibility is required for cellular processes such as transcription and because only about two percent of the genome is accessible at any given time, ATAC-STARR-seq dramatically improves the resolution and precision of STARR-seq and narrows the focus of the assay to the biologically relevant active DNA regulatory elements.

In addition to improving STARR-seq, Hodges and Hansen demonstrated that ATAC-STARR-seq can be co-opted to measure chromatin accessibility and transcription factor occupancy (which identifies where on the genome different transcription factors bind). “We were able to explore three different facets of gene regulation in the human genome from one assay, which is novel for this type of approach,” Hansen said. “This method could be used to explore a variety of questions, from investigating gene regulatory dysfunction in cancer to understanding how gene regulatory elements evolved to make us human.”

The Hodges lab is currently using their new method to examine the regulatory differences between human and macaque immune cells to understand how enhancers and silencers evolved to drive genes encoding human-specific phenotypes. In the long term, the researchers hope that their new assay will facilitate gene regulation studies and lead to critical discoveries that ultimately improve human health.

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The paper “ATAC-STARR-seq reveals transcription factor-bound activators and silencers across the chromatin accessible human genome” was published online in July 2022 in Genome Research in advance of print.