ArticleNature methods2022
DiMeLo-seq: a long-read, single-molecule method for mapping protein-DNA interactions genome wide.
Article in Nature methods, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 104 papers.
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Who cites it
104 citing papers in PubMed.
- Epigenetic regulation of humoral immunity: molecular mechanisms, diseases and therapeutic targets.Signal transduction and targeted therapy · 2026Review
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- Decoding chromosome organization using proximity labeling and long-read sequencing.Journal of genetics and genomics = Yi chuan xue bao · 2026Article
- Structure and function of the centromere and inner kinetochore.Nature reviews. Molecular cell biology · 2026Review
- A practical guide to studying genome function using single-molecule genomics.Nature reviews. Molecular cell biology · 2026Review
- Telomere variant sequences encode the genetic blueprint for allele-specific telomere length.Nature communications · 2026Article
- Genome-wide profiling of histone modifications and transcription factor binding at single-cell resolution by DeChIC-seq.Cell research · 2026Article
- Haplotype-resolved DiMeLo-seq maps centromeric chromatin in a complete diploid human genome.Cell genomics · 2026Article
- Neocentromeres fail to maintain DNA methylation boundaries, driving CENP-A drift, instability, and chromosome missegregation.Cell reports · 2026Article
- Dual Roads of CENP-A for Centromere Identification.BioEssays : news and reviews in molecular, cellular and developmental biology · 2026Review
- Article
- Article
- Direct detection of alternative DNA conformations with long-read sequencing and machine learning approaches.bioRxiv : the preprint server for biology · 2026Article
- kmerRRR: A k-mer based tool for functional genomics in Repeat Rich Regions.bioRxiv : the preprint server for biology · 2026Article
- Influence ofGenome research · 2026Article
- Review
- Two melanic pigment patterns are associated with a sex chromosome-linked oncogene in the mountain swordtailbioRxiv : the preprint server for biology · 2026Article
- Single-molecule nucleosome spacing coordinates chromatin fiber interactions.bioRxiv : the preprint server for biology · 2026Article
- Next generation technologies for CRISPR-based epigenome and transcriptional modulation.Current opinion in biomedical engineering · 2026Article
- SVScope improves somatic structural variations detection via graph-genome optimization.Genome biology · 2026Article
44 more citing papers are in PubMed but not listed here.
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Authors and funding
11 authors.
Funding
Abstract
Studies of genome regulation routinely use high-throughput DNA sequencing approaches to determine where specific proteins interact with DNA, and they rely on DNA amplification and short-read sequencing, limiting their quantitative application in complex genomic regions. To address these limitations, we developed directed methylation with long-read sequencing (DiMeLo-seq), which uses antibody-tethered enzymes to methylate DNA near a target protein's binding sites in situ. These exogenous methylation marks are then detected simultaneously with endogenous CpG methylation on unamplified DNA using long-read, single-molecule sequencing technologies. We optimized and benchmarked DiMeLo-seq by mapping chromatin-binding proteins and histone modifications across the human genome. Furthermore, we identified where centromere protein A localizes within highly repetitive regions that were unmappable with short sequencing reads, and we estimated the density of centromere protein A molecules along single chromatin fibers. DiMeLo-seq is a versatile method that provides multimodal, genome-wide information for investigating protein-DNA interactions.
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