As genetics research evolves, scientists are recognizing that it’s not just the DNA sequence that matters, it’s how that DNA is packaged.
The study of epigenetics, how chromatin structure and chemical modifications influence gene activity, reveals the mechanisms that link genome organization to development, disease, and human health.
Now, with the launch of the CUTANA Fiber-seq kit, EpiCypher is giving researchers extraordinary access to the chromatin’s architecture. Designed to work seamlessly with PacBio HiFi sequencing, this kit enables a truly multiomic view of chromatin structure and gene regulation that connects genetic variation to gene expression with remarkable clarity.
This launch brings Fiber-seq to more scientists than ever before, unlocking a powerful new way to study genetic variants, DNA methylation, chromatin accessibility, and protein interactions all at once.
In this post, we’ll look at how Fiber-seq, when paired with PacBio HiFi sequencing, delivers a single-assay, multiomic view of the genome that captures the intricate relationship between DNA sequence, structure, and function in detail.
Understanding epigenetics and chromatin structure
The genome is like a songbook: every song holds the same notes, but how it’s performed makes all the difference. Think I Will Always Love You sung by Dolly Parton versus Whitney Houston. Same lyrics, completely different delivery. That’s how chromatin works: the same genetic code, but arranged and expressed in ways that can change the entire outcome.
Chromatin is made of DNA wrapped around histone proteins, together making a structure called a nucleosome. The main function of chromatin is to regulate gene expression, so when it’s open, genes can be expressed; when it’s closed, they’re quiet. These structural and chemical changes influence development, differentiation, and disease. Understanding how that structure shifts is key to decoding how the genome performs its song.
To study these patterns, scientists have long relied on a variety of chromatin profiling assays like ATAC-seq, ChIP-seq, CUT&RUN, Hi-C, and bisulfite sequencing to piece together the full score. Each method provides a piece of it, but none reveal how all the components work together from a single-molecule perspective. Fiber-seq changes that.
One assay, multiple insights
Fiber-seq “stencils” chromatin features onto the underlying DNA strand by using a non-sequence-specific adenine methyltransferase to mark accessible regions of the chromatin. Because modified bases can be detected alongside the canonical bases during HiFi sequencing, Fiber-seq merges the DNA sequence, methylation state, chromatin accessibility, and nucleosome and transcription factor positioning into a single assay and workflow.
This means an all-in-one long-read sequencing assay that profiles individual DNA molecules without PCR or antibodies, replacing separate assays like ATAC-Seq, WGS, WGBS, and MNase, while overlapping and complementing assays like ChIP-seq or CUT&RUN that target specific histone modifications or proteins. EpiCypher’s protocol accommodates diverse sample types and can be completed in just under 2 hours allowing further simplification of lab workflows. With this quick and easy workflow users can get a more unified view of chromatin architecture for a deeper understanding of the mechanisms controlling gene regulation and chromatin organization.
How Fiber-seq compares to traditional epigenetic assays
Each of the traditional epigenetic assays can be informative in their own right, but have shortcomings associated with short-read sequencing like fragmented views, loss of long-range cis context, and poor mapping in repetitive parts of the genome. These assays also aggregate signal across cells and mask haplotypic variation.
Fiber-seq with HiFi resolves these limitations while still integrating their individual benefits. The result is a panoramic view of chromatin structure revealing regulatory logic between elements within the same DNA molecule. Fiber-seq provides a simple and intuitive way to quantify accessibility at regulatory elements because each read represents a single chromatin fiber from a single cell.
Fiber-seq also provides the ability for high resolution TF footprinting as shown here in the region surrounding the ABCA3 gene. Where ATAC-seq data only shows a broad region of accessibility, Fiber-seq shows three distinct protein footprints containing binding motifs of the transcription factor CTCF within this accessible region. Separate CUT&RUN peak data confirms the presence of CTCF at this locus (data and figures provided by EpiCypher).
Powered by HiFi long-read sequencing
Combining the power of Fiber-seq with the precision of HiFi sequencing, allows detailed chromatin information to be found in even the most repetitive and structurally complex regions of the genome. With long, highly accurate reads, it spans regions in their entirety, captures both CpG methylation and adenine accessibility marks, and connects them with genetic variants, including SNVs, indels, and structural variants.
Fiber-seq runs smoothly on both the Revio and Vega systems, offering flexibility across scales of research. Revio provides high coverage and throughput for large projects, while Vega delivers the same HiFi accuracy for smaller or model organism studies. Both systems support native detection of 6mA and 5mC, ensuring every experiment produces integrated, high-resolution multiomic data.
High-resolution long-read chromatin insights
This unified view enables discoveries like:
- A haplotype-resolved view of human gene regulation – This research links noncoding variants to disease risk, identifying haplotype-specific somatic epimutations, and illuminating gene regulation in highly variable genomic regions.
- The regulatory impact of structural variants – This Nature Genetics paper integrates genome, methylome, and chromatin information to pinpoint pathogenic mechanisms in a Mendelian condition.
- The regulatory role of transposable elements – This Nature Plants study used Fiber-seq to explore the potential regulatory role of TEs in maize.
These studies represent just the tip of the iceberg for how Fiber-seq can transform epigenetic research in biology and human health. Importantly, Fiber-seq holds strong promise for revealing the chromatin and epimutation landscape in diseases like cancer, which are essentially diseases of chromatin dysregulation.
Fiber-seq with PacBio HiFi sequencing is changing how researchers study epigenetics, advancing discoveries in development, disease, and beyond.
To see Fiber-seq in action, explore the PacBio HG002 Fiber-seq dataset, read the PacBio application note, or visit EpiCypher’s CUTANA Fiber-seq webpage to learn more.