ArticleGenome research2019
Single-molecule long-read sequencing reveals the chromatin basis of gene expression.
Article in Genome research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 50 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
50 citing papers in PubMed, 74 citations in OpenAlex.
- Nuclear mechanotransduction: tools for mechanical perturbation and chromatin characterization.Nucleus (Austin, Tex.) · 2026Review
- Review
- Fiber-TEnCATS reveals haplotype-specific chromatin accessibility and DNA methylation at human L1HS loci.bioRxiv : the preprint server for biology · 2026Article
- Mapping Protein Occupancy on DNA with an Unnatural Cytosine Modification.ACS chemical biology · 2026Article
- From Spatial Epigenomes to Clinical Diagnostics: Integrative Methylomics Across Scales and Modalities.International journal of molecular sciences · 2026Review
- Coupling CRISPR scanning with targeted chromatin accessibility profiling using a double-stranded DNA deaminase.Nature methods · 2025Article
- SMAdd-seq: probing chromatin accessibility with small molecule DNA intercalation and nanopore sequencing.Nucleic acids research · 2025Article
- Revealing long-range heterogeneous organization of nucleoproteins with 6mA footprinting by ipdTrimming.Genome biology · 2025Article
- ReQuant: improved base modification calling by k-mer value imputation.Nucleic acids research · 2025Article
- Zygotic activation of transposable elements during zebrafish early embryogenesis.Nature communications · 2025Article
- SMAdd-seq: Probing chromatin accessibility with small molecule DNA intercalation and nanopore sequencing.bioRxiv : the preprint server for biology · 2025Article
- Integrating Single-Molecule Sequencing and Deep Learning to Predict Haplotype-Specific 3D Chromatin Organization in a Mendelian Condition.bioRxiv : the preprint server for biology · 2025Article
- Profiling the epigenome using long-read sequencing.Nature genetics · 2025Review
- Single chromatin fiber profiling and nucleosome position mapping in the human brain.Cell reports methods · 2024Article
- Mapping protein-DNA interactions with DiMeLo-seq.Nature protocols · 2024Article
- Opportunities and challenges of single-cell and spatially resolved genomics methods for neuroscience discovery.Nature neuroscience · 2024Review
- guidedNOMe-seq quantifies chromatin states at single allele resolution for hundreds of custom regions in parallel.BMC genomics · 2024Article
- ReadCurrent: a VDCNN-based tool for fast and accurate nanopore selective sequencing.Briefings in bioinformatics · 2024Article
- Simultaneous profiling of chromatin accessibility and DNA methylation in complete plant genomes using long-read sequencing.Nucleic acids research · 2024Article
- Direct transposition of native DNA for sensitive multimodal single-molecule sequencing.Nature genetics · 2024Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
11 authors at 1 institution in 1 country.
Funding
Abstract
Genome-wide chromatin accessibility and nucleosome occupancy profiles have been widely investigated, while the long-range dynamics remain poorly studied at the single-cell level. Here, we present a new experimental approach, methyltransferase treatment followed by single-molecule long-read sequencing (MeSMLR-seq), for long-range mapping of nucleosomes and chromatin accessibility at single DNA molecules and thus achieve comprehensive-coverage characterization of the corresponding heterogeneity. MeSMLR-seq offers direct measurements of both nucleosome-occupied and nucleosome-evicted regions on a single DNA molecule, which is challenging for many existing methods. We applied MeSMLR-seq to haploid yeast, where single DNA molecules represent single cells, and thus we could investigate the combinatorics of many (up to 356) nucleosomes at long range in single cells. We illustrated the differential organization principles of nucleosomes surrounding the transcription start site for silent and actively transcribed genes, at the single-cell level and in the long-range scale. The heterogeneous patterns of chromatin status spanning multiple genes were phased. Together with single-cell RNA-seq data, we quantitatively revealed how chromatin accessibility correlated with gene transcription positively in a highly heterogeneous scenario. Moreover, we quantified the openness of promoters and investigated the coupled chromatin changes of adjacent genes at single DNA molecules during transcription reprogramming. In addition, we revealed the coupled changes of chromatin accessibility for two neighboring glucose transporter genes in response to changes in glucose concentration.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.