High-throughput and accessible single-cell multiomic technologies for dnamethylation analysis

The National Institutes of Health National Human Genome Research Institute awarded Oregon Health & Science University $2.737 million on September 1, 2026, under the Human Genome Research program (CFDA 93.172) to develop high-throughput and cost-effective single-cell multiomic technologies for DNA methylation analysis.

The project will develop new strategies to measure DNA methylation alongside other cellular properties at high throughput, leveraging cell encapsulation technology to achieve high cell capture efficiency and new techniques for capturing mRNA-derived cDNA through the methylation assay. The work will enable simultaneous detection of RNA transcription and methylation with a nearly two order-of-magnitude throughput improvement over existing workflows. The project will also employ transposase-based library construction and cell indexing to produce single-cell libraries compatible with Nanopore sequencing for direct detection of methylation patterns. These technologies address DNA methylation's role in cell development and its dysregulation in genomic imprinting disorders, cancer, autoimmune disorders, and neurodevelopmental and neurodegenerative diseases.

The award runs through August 31, 2030, with place of performance in Portland, Oregon. This is a Project Grant assistance type under the NHGRI's mandate to develop genomic resources, technologies, and methods applicable to biomedical research and advance genomics applications to medical science and clinical care.

Abstract

DNA methylation forms one of the key layers the epigenome - shaping the gene regulatory landscape to produce a specified cell phenotype. As a covalent modification to the DNA itself, DNA methylation is one of the more stable modifications, conveying long-term repression of genomic loci, often in the form of "CPG islands" spanning promoter regions of genes as well as its ability to impede transcription factor binding at enhancer loci. Despite the relative stability, DNA methylation is highly dynamic during development to establish and enforce cell lineage specification. Furthermore, DNA methylation is often dysregulated in a number of diseases, including those associated with genomic imprinting, cancer, autoimmune disorders, as well as neurodevelopmental disorders and neurodegenerative diseases among many others. Due to its dynamic nature, DNA methylation, like other cell-type and state specific properties, necessitates the use of single-cell technologies for which we have developed the first high-throughput and cost-effective platform. Here, we will develop new strategies to probe DNA methylation alongside other properties efficiently at high -throughput. We will first leverage a cutting-edge cell encapsulation technology to enable high cell capture efficiency, a property currently lacking for platforms that rely on multi-tier cell barcoding. We will also leverage new techniques for capture and retention of mrna-derived cdna through our high-throughput methylation assay, enabling the capture of RNA transcription alongside methylation with the ability to produce a nearly two order-of-magnitude throughput improvement over existing workflows. Finally, we will leverage our extensive expertise in efficient transposase-based library construction and cell indexing to produce single-cell libraries compatible with nanopore sequencing for the direct detection of standard DNA methylation using long reads that do not undergo conversion. This technology will enable the assessment of previously elusive regions of the genome, including repetitive regions where DNA methylations serves as a primary regulatory control mechanism, as well as assess allele-specific methylation patterns within cell types. We will demonstrate these technologies on a diverse set of index samples that exhibit distinct or dynamic cell type and state methylation patterns including human pbmcs, cerebral cortex and induced pluripotent stem cells (ipscs) in addition to human and mouse control cell lines. These index samples will demonstrate sample type versatility, ensuring broad utility of the developed technologies.