ArticleMolecular cell2022
Single-cell profiling of transcriptome and histone modifications with EpiDamID.
Article in Molecular cell, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 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
36 citing papers in PubMed, 58 citations in OpenAlex.
- Genome-wide chromatin recording resolves dynamic cell state changes.Cell systems · 2026Article
- Genome-wide profiling of histone modifications and transcription factor binding at single-cell resolution by DeChIC-seq.Cell research · 2026Article
- mmVelo: a deep generative model for estimating cell state-dependent dynamics across multiple modalities.Bioinformatics (Oxford, England) · 2026Article
- Genome-wide chromatin recording resolves dynamic cell state changes.bioRxiv : the preprint server for biology · 2026Article
- RNA modification-mediated multidimensional crosstalk: a novel perspective on gene expression regulation.Genome biology · 2026Review
- Predictive modeling of molecular activity underlying physical cell-cell interactions.Cell reports methods · 2026Article
- A hitchhiker's guide to single-cell epigenomics: Methods and applications for cancer research.International journal of cancer · 2026Review
- A computational framework to dissect imputation strategies for single-cell histone modification data.NAR genomics and bioinformatics · 2025Article
- Dynamic genome-wide mapping reveals how chromatin context shapes OGG1-mediated repair and related mutagenesis in human cells.Nucleic acids research · 2025Article
- Review
- Mapping SET1B chromatin interactions with DamID using DamMapper, a comprehensive Snakemake workflow.BMC genomics · 2025Article
- Single-cell sequencing technology in renal cancer: insights into tumor biology and clinical application.Biomarker research · 2025Review
- Replication stress-induced nuclear hypertrophy alters chromatin topology and impacts cancer cell fitness.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Retrospective and multifactorial single-cell profiling reveals sequential chromatin reorganization during X inactivation.Nature cell biology · 2025Article
- Empowering integrative and collaborative exploration of single-cell and spatial multimodal data with SGS genome browser.Cell genomics · 2025Article
- Advances and applications in single-cell and spatial genomics.Science China. Life sciences · 2025Review
- Targeted DamID detects cell-type-specific histone modifications in intact tissues or organisms.PLoS biology · 2025Article
- scTrends: A living review of commercial single-cell and spatial 'omic technologies.Cell genomics · 2024Review
- Antagonism between H3K27me3 and genome-lamina association drives atypical spatial genome organization in the totipotent embryo.Nature genetics · 2024Article
- Quantification of escape from X chromosome inactivation with single-cell omics data reveals heterogeneity across cell types and tissues.Cell genomics · 2024Article
Corrections and comments
- Commented on by
Authors and funding
11 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Recent advances in single-cell sequencing technologies have enabled simultaneous measurement of multiple cellular modalities, but the combined detection of histone post-translational modifications and transcription at single-cell resolution has remained limited. Here, we introduce EpiDamID, an experimental approach to target a diverse set of chromatin types by leveraging the binding specificities of single-chain variable fragment antibodies, engineered chromatin reader domains, and endogenous chromatin-binding proteins. Using these, we render the DamID technology compatible with the genome-wide identification of histone post-translational modifications. Importantly, this includes the possibility to jointly measure chromatin marks and transcription at the single-cell level. We use EpiDamID to profile single-cell Polycomb occupancy in mouse embryoid bodies and provide evidence for hierarchical gene regulatory networks. In addition, we map H3K9me3 in early zebrafish embryogenesis, and detect striking heterochromatic regions specific to notochord. Overall, EpiDamID is a new addition to a vast toolbox to study chromatin states during dynamic cellular processes.
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.