ArticleGenome biology2016
Simultaneous profiling of transcriptome and DNA methylome from a single cell.
Article in Genome biology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 157 papers, 1 of them a synthesis that pooled it.
What it found
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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
157 citing papers in PubMed, 1 synthesis or guideline pooled it, 304 citations in OpenAlex.
- DNA methylation aging and transcriptomic studies in horses.Nature communications · 2022Pooled it
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- Single-Cell Triomics Analysis of Tumor Cells Infiltrating Patient-Derived Breast Cancer Scaffolds.The American journal of pathology · 2026Article
- Single-Cell and Spatial Omics: Methods and Applications.MedComm · 2026Review
- A Region-Aware Structured Framework Improves Prediction of Gene Expression from DNA Methylation.Computational and structural biotechnology journal · 2026Article
- Review
- Research progress of single cell RNA sequencing in nervous system.Molecular biology reports · 2025Review
- Epigenetic links between paternal age, reproduction, and offspring health: a focus on sncRNAs.Reproduction & fertility · 2025Review
- Single-cell epigenomics and proteomics methods integrated in multiomics.Fundamental research · 2025Review
- Single-cell multi-omics in cancer immunotherapy: from tumor heterogeneity to personalized precision treatment.Molecular cancer · 2025Review
- scMultiNODE: Integrative and Scalable Framework for Multi-Modal Temporal Single-Cell Data.bioRxiv : the preprint server for biology · 2025Article
- RNA polymerase I is essential for driving the formation of 3D genome in early embryonic development in mouse, but not in human.Genome medicine · 2025Article
- Advances and applications in single-cell and spatial genomics.Science China. Life sciences · 2025Review
- DNA methylation in melanoma immunotherapy: mechanisms and therapeutic opportunities.Clinical epigenetics · 2025Review
- DNA methylation memory of pancreatic acinar-ductal metaplasia transition state altering Kras-downstream PI3K and Rho GTPase signaling in the absence of Kras mutation.Genome medicine · 2025Article
- Exploring genome-transcriptome correlations in cancer.Biochemical Society transactions · 2025Review
- Unveiling Long Non-coding RNA Networks from Single-Cell Omics Data Through Artificial Intelligence.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Single-cell omics: experimental workflow, data analyses and applications.Science China. Life sciences · 2025Review
- Multi-omics PGT: re-evaluation of euploid blastocysts for implantation potential based on RNA sequencing.Human reproduction (Oxford, England) · 2024Article
- Epigenetic Explorations of Neurological Disorders, the Identification Methods, and Therapeutic Avenues.International journal of molecular sciences · 2024Review
97 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
10 authors at 2 institutions in 2 countries.
Funding
Abstract
backgroundSingle-cell transcriptome and single-cell methylome technologies have become powerful tools to study RNA and DNA methylation profiles of single cells at a genome-wide scale. A major challenge has been to understand the direct correlation of DNA methylation and gene expression within single-cells. Due to large cell-to-cell variability and the lack of direct measurements of transcriptome and methylome of the same cell, the association is still unclear.
resultsHere, we describe a novel method (scMT-seq) that simultaneously profiles both DNA methylome and transcriptome from the same cell. In sensory neurons, we consistently identify transcriptome and methylome heterogeneity among single cells but the majority of the expression variance is not explained by proximal promoter methylation, with the exception of genes that do not contain CpG islands. By contrast, gene body methylation is positively associated with gene expression for only those genes that contain a CpG island promoter. Furthermore, using single nucleotide polymorphism patterns from our hybrid mouse model, we also find positive correlation of allelic gene body methylation with allelic expression.
conclusionsOur method can be used to detect transcriptome, methylome, and single nucleotide polymorphism information within single cells to dissect the mechanisms of epigenetic gene regulation.
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What Socratic 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 Socratic graph.