ArticleNature protocols2020
Simultaneous quantification of protein-DNA interactions and transcriptomes in single cells with scDam&T-seq.
Article in Nature protocols, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Graph-based deep learning approach for high-throughput protein-DNA interaction scoring.Acta pharmacologica Sinica · 2026Article
- Retrospective and multifactorial single-cell profiling reveals sequential chromatin reorganization during X inactivation.Nature cell biology · 2025Article
- Advances and applications in single-cell and spatial genomics.Science China. Life sciences · 2025Review
- Genome-wide profiling of DNA repair proteins in single cells.Nature communications · 2024Article
- Antagonism between H3K27me3 and genome-lamina association drives atypical spatial genome organization in the totipotent embryo.Nature genetics · 2024Article
- Combinatorial single-cell profiling of major chromatin types with MAbID.Nature methods · 2024Article
- Single-cell technologies in multiple myeloma: new insights into disease pathogenesis and translational implications.Biomarker research · 2023Review
- Single-cell RNA sequencing to identify cellular heterogeneity and targets in cardiovascular diseases: from bench to bedside.Basic research in cardiology · 2023Review
- Simultaneous Single-Cell Profiling of the Transcriptome and Accessible Chromatin Using SHARE-seq.Methods in molecular biology (Clifton, N.J.) · 2023Article
- A pendulum of induction between the epiblast and extra-embryonic endoderm supports post-implantation progression.Development (Cambridge, England) · 2022Article
- scPCOR-seq enables co-profiling of chromatin occupancy and RNAs in single cells.Communications biology · 2022Article
- Single-cell profiling of transcriptome and histone modifications with EpiDamID.Molecular cell · 2022Article
- Integrated single-cell sequencing of 5-hydroxymethylcytosine and genomic DNA using scH&G-seq.STAR protocols · 2021Article
- Applications of single-cell sequencing in cancer research: progress and perspectives.Journal of hematology & oncology · 2021Review
- Single-cell genomics to understand disease pathogenesis.Journal of human genetics · 2021Review
- Tissue-specific DamID protocol using nanopore sequencing.Journal of biological methods · 2021Article
Corrections and comments
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Authors and funding
10 authors.
Funding
Abstract
Protein-DNA interactions are essential for establishing cell type-specific chromatin architecture and gene expression. We recently developed scDam&T-seq, a multi-omics method that can simultaneously quantify protein-DNA interactions and the transcriptome in single cells. The method effectively combines two existing methods: DNA adenine methyltransferase identification (DamID) and CEL-Seq2. DamID works through the tethering of a protein of interest (POI) to the Escherichia coli DNA adenine methyltransferase (Dam). Upon expression of this fusion protein, DNA in proximity to the POI is methylated by Dam and can be selectively digested and amplified. CEL-Seq2, in contrast, makes use of poly-dT primers to reverse transcribe mRNA, followed by linear amplification through in vitro transcription. scDam&T-seq is the first technique capable of providing a combined readout of protein-DNA contact and transcription from single-cell samples. Once suitable cell lines have been established, the protocol can be completed in 5 d, with a throughput of hundreds to thousands of cells. The processing of raw sequencing data takes an additional 1-2 d. Our method can be used to understand the transcriptional changes a cell undergoes upon the DNA binding of a POI. It can be performed in any laboratory with access to FACS, robotic and high-throughput-sequencing facilities.
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