ArticleNature biotechnology2023
Retrospective analysis of enhancer activity and transcriptome history.
Article in Nature biotechnology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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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.
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Who cites it
17 citing papers in PubMed, 23 citations in OpenAlex.
- Genome-wide chromatin recording resolves dynamic cell state changes.Cell systems · 2026Article
- Genome-wide chromatin recording resolves dynamic cell state changes.bioRxiv : the preprint server for biology · 2026Article
- Conference report: current advances in embryo model research at the International Dutch Embryo Model Meeting 2025.Biology open · 2026Article
- Multiplexed enrichment and tracking of lineages with CloneSweeper.bioRxiv : the preprint server for biology · 2026Article
- Intestinal stem cells as innate immune sentinels: coupling environmental sensing to epithelial adaptation.Frontiers in immunology · 2026Review
- Improved circulating tumor DNA profiling by simultaneous extraction of DNA methylation and copy number information from methylated DNA sequencing data.NPJ precision oncology · 2025Article
- Building a human pluripotent stem cell-based gonadal niche: improving in vitro systems with in vivo insights.Human reproduction update · 2025Review
- CUT&TIME captures the history of open chromatin in developing neurons.bioRxiv : the preprint server for biology · 2025Article
- Retrospective and multifactorial single-cell profiling reveals sequential chromatin reorganization during X inactivation.Nature cell biology · 2025Article
- Profiling (placental) DNA methylation in cell-free DNA across gestation: the Rotterdam Periconception Cohort.Molecular human reproduction · 2025Article
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- Spatial multi-omics in whole skeletal muscle reveals complex tissue architecture.Communications biology · 2024Article
- Toward DNA-Based Recording of Biological Processes.International journal of molecular sciences · 2024Review
- Emerging methylation-based approaches in microbiome engineering.Biotechnology for biofuels and bioproducts · 2024Review
- The epigenetic landscape in intestinal stem cells and its deregulation in colorectal cancer.Stem cells (Dayton, Ohio) · 2024Review
- From Genotype to Phenotype: How Enhancers Control Gene Expression and Cell Identity in Hematopoiesis.HemaSphere · 2023Review
Corrections and comments
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Authors and funding
14 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Cell state changes in development and disease are controlled by gene regulatory networks, the dynamics of which are difficult to track in real time. In this study, we used an inducible DCM-RNA polymerase subunit b fusion protein which labels active genes and enhancers with a bacterial methylation mark that does not affect gene transcription and is propagated in S-phase. This DCM-RNA polymerase fusion protein enables transcribed genes and active enhancers to be tagged and then examined at later stages of development or differentiation. We apply this DCM-time machine (DCM-TM) technology to study intestinal homeostasis, revealing rapid and coordinated activation of enhancers and nearby genes during enterocyte differentiation. We provide new insights in absorptive-secretory lineage decision-making in intestinal stem cell (ISC) differentiation and show that ISCs retain a unique chromatin landscape required to maintain ISC identity and delineate future expression of differentiation-associated genes. DCM-TM has wide applicability in tracking cell states, providing new insights in the regulatory networks underlying cell state changes.
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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.