The Genome in 3D – How Chromatin Conformation Impacts Gene Regulation

By mapping the structure of the genome in a three-dimensional (3D) format, it becomes possible to reveal long-range promoter–enhancer interactions that may have an impact on disease. Understanding how these interactions occur could help identify new diagnostic biomarkers and avenues for designing therapeutics.

Dovetail Genomics produce assay kits that enable researchers to view the chromatin structure of human genomes in 3D. Technology Networks spoke with Dovetail Genomics CEO, Todd Dickinson, to learn more about how Hi-C chromatin immunoprecipitation works and how it has been applied in prostate cancer research.

Katie Brighton (KB): Could you outline the importance of genomics approaches in cancer research? What role does Dovetail Genomics play within this space?

Todd Dickinson (TD): Cancer dysregulates gene transcriptional programs, leading to cell proliferation, immune surveillance evasion and ultimately metastasis. Gene promoter interactions with regulatory elements, such as enhancers and silencers, are critical to understanding the mechanisms that drive cancer initiation and progression. Chromatin loops tether enhancers, which can be many kilobases to megabases away, to their cognate gene promoters. If incorrectly tethered to oncogenic promoters, this erroneously drives their expression. This mechanism of “enhancer hijacking” has been tied to multiple cancers.

3D mapping of these enhancer–promoter interactions can not only help elucidate the mechanism of disease, but also identify new biomarkers, enabling earlier diagnoses and ushering in novel therapies. Traditionally, such studies have viewed enhancer–promoter interactions through a linear lens that reveals only part of the story. Proximity ligation adds the extra dimension currently missing from today’s oncology studies and therapeutic research. Ultimately, with proximity ligation, researchers can better understand the role that these distal DNA regulatory mechanisms play in oncogenic progression.

Proximity ligation kits, such as those offered by Dovetail Genomics, enable researchers to see critical 3D features of human disease, revealing currently unprobed dimensions contributing to oncogenic mechanisms and leading to a broader understanding of how regulatory elements modulate promoter activity. Only with the addition of this 3D interplay between genes and regulatory elements can one fully power translational research studies.

KB: Can you explain a little more about how Hi-C chromatin immunoprecipitation (HiChIP) technology works and the advantages it brings over other methods used to analyze the genome?

TD: HiChIP technology enables researchers to see ChIP-seq data in a whole new dimension. With ChIP-seq, scientists only see where a protein of interest is bound in the genome. In the context of transcription factors and other chromatin modulators, this only partially captures their role and protein-mediated interactions with distal factors are missed. In other words, ChIP-seq only offers a linear view and does not capture all the necessary details to fully understand how enhancer–promoter interactions and protein-directed chromatin architecture regulates gene expression. While HiChIP captures the same protein-binding information as ChIP-seq, it uses proximity ligation to capture contact information representative of the spatial relationships conferred by the protein-directed interactions. In the context of a transcription factor, these are representative of interactions involving regulatory elements and gene promoters that can influence gene expression and drive disease progression.

KB: A recent study revealed inhibiting a chromatin remodeling complex prevented oncogene expression and cancer spread in prostate cancer models. Could you highlight the role of HiChIP in this study?

TD: This study, led by University of Michigan researchers, investigated a proprietary proteolysis targeting chimera (PROTAC) drug targeting the SWI/SNF chromatin remodeling complex as a potential prostate cancer therapeutic. The publication demonstrated, for the first time, that inhibiting the SWI/SNF complex suppresses oncogene expression, thereby slowing prostate cancer growth in cell and animal models. Understanding the underlying mechanisms of this observation was made possible largely by Dovetail’s proximity-ligation technology. Dovetail’s HiChIP MNase kit provided essential information about 3D chromatin architecture, demonstrating the involvement of promoter hijacking by oncogenes that drive prostate cancer progression in disease samples and reversal of this mechanism in PROTAC treated samples.

KB: Are there any other areas of research that would benefit from HiChIP technology, or are perhaps already benefiting?

TD: Due to the richness of the data generated, there are numerous research areas that can benefit from HiChIP technology, including epigenetics, developmental biology, neurobiology and oncology to name a few. To truly understand the mechanics of gene regulation, the protein factors must be studied in their native 3D environment. The HiChIP proximity ligation method captures long-range interactions using standard Illumina paired-end sequencing and helps researchers explore how primary protein binding and protein-mediated chromatin interactions influence gene expression.

Using the Dovetail HiChIP MNase assay gives researchers new capabilities to uncover enhancer–promoter interactions that control gene expression. These assays reveal where proteins bind and the long-range interactions they mediate. The assay also provides ultra-high nucleosome-level resolution of chromatin contacts, boosting the signal-to-noise ratio. While it is not a complete replacement to ChIP-seq (ChIP-seq data is helpful in interpreting the more complex nature of HiChIP data), it adds a currently ignored dimension to ChIP-seq data by uncovering the interactomes associated with proteins of interest.

Todd Dickinson was speaking to Katie Brighton, Scientific Copywriter for Technology Networks.