Enrich Your Understanding of Gene Expression with Promoter Capture Hi-C
If you haven’t heard the news yet, the Dovetail Genomics® team recently launched a new product line for Target Enrichment of Dovetail® proximity ligation libraries. Our first two products are Pan Promoter Enrichment Panels specific to human and mouse samples. These products enable researchers to study epigenetic modulated gene regulation in a variety of research areas, including developmental biology and complex trait mapping, a simple and effective means to probe both known and unknown regulatory elements and their interaction with gene promoters at a significantly reduced cost.
In a collaboration with Twist Bioscience, Dovetail’s promoter panels incorporate Twist’s proprietary target enrichment technology into Dovetail’s tried-and-true proximity ligation workflow, streamlining chromatin topology studies by enriching for promoter regions. The result is a reduction in the sequencing costs typically required to achieve optimal depth for statistically significant analyses. When paired with Dovetail’s® Omni-C® or Micro-C Assays – which utilize sequence-independent nucleases to diminish coverage bias – the final proximity ligation libraries are enriched for promoters and their engaged regulatory elements, greatly reducing genomic background noise (and the cost associated with sequencing that noise) as well as time spent on the downstream analyses.
So how does this all work?
The panels have been engineered to integrate seamlessly into the Dovetail Omni-C and Micro-C workflows. With over 100,000 oligos designed against promoter regions, incubation of the panel with the sequencing ready library enables the capture and enrichment of promoters containing proximally ligated sequences, prior to sequencing the library. The panels are designed to target over 98% of known promoter regions (covering more than 84,000 and 47,000 regions and over 27,000 and 24,000 coding and non-coding genes in human and mouse samples, respectively; Table 1). An enriched library contains comprehensive coverage of the promoter landscape, enabling researchers a focused view of interactions between promoter regions and their cognate distal regulatory elements (promoter-enhancer and promoter-promoter interactions).
Table 1. Targets of Dovetail’s Pan Promoter Enrichment Panels
Why is this significant?
Chromatin topology is intimately involved in the process of gene regulation, as promoter regions are more often than not influenced by distal regulatory elements that are found kilobases or even megabases away. Complex looping and folding patterns bring the regulatory elements into close proximity of promoters enabling cross-talk. Mapping these distally interacting regions is essential to gaining a full understanding of transcriptional control. While this has been a well-defined problem for some time, the barrier to implementing a successful workflow using Hi-C approaches has been high. Specifically, the coverage depth required for statistical significance previously resulted in a very large sequencing burden when considering whole-genome Hi-C approaches. The Dovetail® Pan Promoter Enrichment Panels greatly reduce this barrier by lowering the sequencing burden by 10-fold (Table 2).
Table 2. Sequence requirements to statistically identify looping events
“The ability of regulatory elements to act across large genomic distances has long been known and, through chromatin conformation capture techniques, the looping events that bring promoters and their regulatory elements, such as transcriptional enhancers, into close proximity are just starting to be probed. Our new panels now enable these experiments to be completed at a fraction of the cost of genome-wide Hi-C approaches. This opens up avenues for translational research that rely on larger sample cohorts. In working with Twist, we are confident that these new best-in-class tools will help to accelerate understanding of human disease mechanisms, aid in drug discovery programs and offer a novel and valuable class of biomarker benefiting human disease diagnosis and management.”
Todd Dickinson, CEO, Dovetail Genomics
This all sounds great! But how do I make sense of the data?
While not the only analysis solution, Dovetail has identified a statistical tool, developed at the Babraham Institute, called CHiCAGO®. The advantage of this analytical approach is that it uses a convolution background model to statistically prioritize contacts, generating a highly actionable ranked list of detected interactions. To better support our panel users, we will be releasing comprehensive documentation soon; in the meantime, you can check out Babraham’s guide.