Epigenetics offers critical insight into how the genome is regulated beyond DNA sequence alone, shaping cellular identity, function, and disease. Along with our co-sponsor EpiCypher, we are excited to introduce the recipients of the 2025 Epigenetics SMRT Grant, whose research focuses on understanding chromatin structure and gene regulation at a level of resolution that has traditionally been difficult to achieve.
These projects will use Fiber-seq, a long-read, whole genome assay that maps genetic and epigenetic features along individual chromatin fibers in a single experiment. By applying this approach, these researchers aim to uncover regulatory mechanisms and chromatin dynamics that are difficult to study with other methods.
Join us in congratulating these visionary researchers and read below to learn how they plan to use Fiber-seq to move their research forward.
Winner: Wen Shen, PhD
Associate Professor, Weill Cornell Medicine Weill Cornell Medicine Graduate School of Medical Sciences
Mapping PTEN-driven chromatin states in breast cancer
We will apply Fiber-seq to a panel of isogenic murine breast cancer cell lines differing in PTEN status and a chromatin-regulatory pathway recently implicated in genome maintenance. Single-molecule maps of chromatin accessibility and DNA methylation will define how PTEN and cooperating chromatin regulators shape local and global chromatin organization. These analyses will benchmark the performance of Fiber-seq in engineered cancer models and generate foundational datasets for studying tumor suppressor–driven chromatin reprogramming. The results will provide an integrated framework to understand PTEN-linked epigenetic regulation relevant to cancer development and therapeutic response.
Winner: Gemma Carvill, PhD
Associate Professor, Northwestern University Feinberg School of Medicine
Co-director, Adult Epilepsy Genetics Program
Fiber-seq for dissecting the allele-specific regulation of CHD2 via the long non-coding RNA, CHASERR
CHASERR, a long noncoding RNA adjacent to CHD2, regulates CHD2 dosage, with deletions in CHASERR causing a novel neurodevelopmental disorder. CHASERR loss increases CHD2 transcript and protein abundance, revealing bidirectional CHD2 dosage sensitivity in human disease. CHASERR acts exclusively in cis, making allele-specific resolution essential to uncover its regulatory mechanism. Fiber-seq, which uniquely enables single-molecule, allele-resolved chromatin mapping, offers an unprecedented opportunity to dissect this cis-regulation. We plan to highlight how Fiber-seq can illuminate allele-specific lncRNA function and establish a paradigm for studying regulatory variants underlying Mendelian disorders.
Runner-up: Elfride Da Baere, PhD
Senior Full Professor, Ghent University
Head of Lab at the Center for Medical Genetics Ghent (CMGG) of the Ghent University Hospital
SMRT-SV: Single Molecule Real-Time sequencing to understand structural variation in developmental disorders
Structural variations (SVs) can drastically alter gene regulation, often causing developmental disorders (DDs). Multiple DD cases with complex SVs are known in our genetics department, often not well understood. We recently identified an 8.5 Mb complex SV – combining four events including a translocation between the PAX6 and PITX2 regions – in a family with a rare developmental eye disease. Through the Epigenetics SMRT Grant, we will dissect its pathogenic mechanisms using Fiber-seq, MAS-seq, and CiFi on patient-derived iPSCs, providing genomic, epigenomic, and transcriptomic insights. This integrated approach will serve as a model for future SV studies in patient cohorts.
Runner-up: Senyene Hunter, MD, PhD
Assistant Professor of Neurology, University of North Carolina at Chapel Hill
Co-founder and Research Core Leader of the UNC Epilepsy Neurogenetics Initiative
Genetic determinants of neurological and developmental disorders
Developmental and epileptic encephalopathies (DEEs) are severe neurodevelopmental disorders in which more than half of affected children remain without a genetic diagnosis despite short-read sequencing. My research uses Oxford Nanopore long-read sequencing (LRS) to identify variants underlying DEEs and to understand how they influence gene regulation. Integrating Fiber-seq with PacBio HiFi sequencing will allow us to examine methylation and chromatin accessibility in DEE-associated genes, including those in noncoding or structurally complex regions missed by standard approaches. These insights will help reveal pathogenic mechanisms, refine variant interpretation, and move us closer to targeted therapies for children with severe genetic epilepsies.
How to apply for PacBio grants
The PacBio Grant Program invites researchers across the world to apply for complimentary PacBio sequencing services for a diverse array of genomics research projects. To participate, choose an active grant program that aligns with your research area and complete the application by explaining how your important work would benefit from PacBio sequencing. Applications are thoroughly reviewed by experts in each application. Selected winners are notified by PacBio to arrange for free sequencing, which can include free consumables, library preparation, and preliminary bioinformatic analyses, all provided by an authorized sequencing service provider (terms and conditions apply).These opportunities include research across all areas of life sciences. For researchers decoding complex microbial communities, investigating cancer, conserving biodiversity, or exploring the most challenging regions of the human genome, there’s a PacBio grant designed to support your vision.
A huge thank-you to all the applicants for sharing your inspiring ideas, and to our co-sponsor EpiCypher for making the 2025 Epigenetics SMRT Grant possible.
Interested in applying Fiber-seq in your own research? Reach out to EpiCypher at services@epicypher.com. EpiCypher was founded in response to the growing demand for high-quality reagents to study chromatin regulation and enable epigenetics-focused drug discovery. The company is at the forefront of chromatin mapping technologies with the CUTANA® platform for ultra-sensitive genomic profiling assays, including CUT&RUN and CUT&Tag, and now, the groundbreaking Fiber-seq platform. EpiCypher also offers the largest collection of defined designer nucleosomes (dNucs) on the market along with complementary high-throughput assays and services.
EpiCypher is dedicated to bringing these transformative technologies to market and offers superior products and assay services to researchers worldwide.
