Advanced Genomics: 3D Genomic Services

Unlock a deeper understanding of chromatin interactions with 3D genomics

Map the 3D organisation of the genome to understand how 3D genome architecture links genes to regulatory elements to influence expression and other key aspects of genome function. 3D genomics is a key component of any multi-omics approach, and can be combined with ATAC-seq, ChIP-seq, and RNA-seq to quantitively link chromatin features to the genes they are regulating for a more comprehensive view of gene regulation. Whether it be single promoter-enhancer loops, tangled polycomb chromatin, or complex super enhancer networks - 3D genomics maps and describes these features in exquisite detail.

3D Genomics for Genome Assembly

A high-quality reference genome is the foundation of any genomic research program. Through our genome assembly services, powered by Dovetail Genomics, we deliver assemblies of the highest quality. Whether your focus is on species conservation, evolutionary biology or enhancing agricultural efficiencies, assembling a reference genome is often the first step in building a genetic understanding of your species of interest.

Our services support a wide range of applications including breeding programs, population studies, cultivar verification, pest research and disease screening. Whatever your industry needs, we’re here to provide the genomic tools and expertise to help you.

• Assembly link: Powered by Dovetail Genomics’ Assembly Link, get rapid genome assembly from sample to sequencing ready libraries in a single day.

• Omni-C: Complimenting your long-read contigs, we utilise Hi-C technology to generate chromosome-scale, haplotype-resolved genome assemblies for both diploid and polyploid species. While advances in long-read sequencing have been significant, these platforms alone are often insufficient for assembling full chromosomes, except in the smallest genomes. Hi-C bridges this gap, transforming draft assemblies into chromosome-level resolutions, providing the most complete and biologically relevant assemblies possible.

3D Genomics for Epigenetics

The organisation of chromatin can have a significant impact on gene expression and regulation and can be influenced by epigenetic modifications such as DNA methylation, histone modifications and non-coding RNA.[1]

Genome-wide approach
Gain a comprehensive genome-wide view of 3D chromatin architecture through the detection of topological features, including A/B compartments, TADs, and chromatin loops, across the genome.

• MicroC: Whole genome ultra-high-resolution topology

• Topolink: Whole genome rapid high-resolution topology, sample to a sequencing-ready library in a single day

Targeted approach
Focus your 3D genomics on the regions that interest you most and save on sequencing costs. Targeted 3D genomics can be achieved through HiChIP for a protein-centric view of 3D topology, or through target-enrichment to focus in on specific genomic regions.

• HiChIP: Give your ChIP-seq experiment a 3D boost - capture ChIP-seq and Hi-C data together in a single library to explore protein-directed chromatin architecture.

• Pan Promoter target enrichment panel: Focus 3D genomic data on promoter regions with the pan promoter panel for humans or mouse. This targeted approach allows you to focus in on promoter regions to identify specific promoter-enhancer looping events at a fraction of the sequencing cost compared to whole genome approaches.

Multi-omics Integration - 3D complimentary Assays

Integrating 3D genomics into multi-omic studies unleashes a powerful synergy with other omics datasets, elevating our understanding of genome function. Integrating the 3D genome uncovers relationships missed by linear sequencing assays. Layering 3D organisation across two-dimensional datasets can reveal measurable connections between genes and their regulatory elements (typically described with linear-omics), providing a more accurate, in situ, representation of gene regulation. Integrate 3D genomics data with:

• ATAC-seq: A streamlined approach to studying chromatin accessibility across the genome, focusing on providing broad insights rather than delving into specific mechanisms. ATAC-seq serves as a preliminary screening method. Its major advantages include its ability to work with smaller cell quantities, and the simplicity of its efficient two-step protocol, setting it apart form other techniques that explore similar chromatin features.

• CUTANA CUT&RUN/CUT&Tag: Achieve high-resolution mapping of histone post-translational modifications (PTMs) and chromatin-interacting proteins with a cost-effective approach that outperforms standard ChIP-seq. This method requires fewer cells, fewer sequencing reads per sample, and significantly lowers overall costs from sample preparation to sequencing.

• WGS to connect variants with impacted genes

• DNA methylation to understand the extent that silenced DNA has beyond the primary sequence

• RNA-seq to decipher how genomic features impact gene expression

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References:
1. 3D Genomics, The Next Frontier, The What the Why and the How. (2023) Dovetail 3D genomics e-book, Cantata Bio, accessed 25 Oct 2024. https://go.dovetailgenomics.com/3dgenomicsebook#form

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