ArticleeLife2022
Identification of putative enhancer-like elements predicts regulatory networks active in planarian adult stem cells.
Article in eLife, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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.
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Who cites it
19 citing papers in PubMed, 25 citations in OpenAlex.
- SoxB1-mediated chromatin remodeling promotes sensory neuron differentiation in planarians.Genetics · 2026Article
- SoxB1-Mediated Chromatin Remodeling Promotes Sensory Neuron Differentiation in Planarians.bioRxiv : the preprint server for biology · 2025Article
- Multimodal single cell analyses reveal gene networks of planarian stem cell differentiation.Nature communications · 2025Article
- Article
- A dynamic histone-based chromatin regulatory toolkit underpins genome and developmental evolution in an invertebrate clade.Genome biology · 2025Article
- Cardiac enhancers: Gateway to the regulatory mechanisms of heart regeneration.Seminars in cell & developmental biology · 2025Review
- Systemic identification and characterization of the conserved core NuRD complex in planarian.Frontiers in aging · 2025Article
- The DNA methyltransferase DMAP1 is required for tissue maintenance and planarian regeneration.Developmental biology · 2024Article
- A comparative analysis of planarian genomes reveals regulatory conservation in the face of rapid structural divergence.Nature communications · 2024Article
- RNaseH-based ribodepletion of total planarian RNA improves detection of longer and non-polyadenylated transcripts.bioRxiv : the preprint server for biology · 2024Article
- The DNA Methyltransferase DMAP1 is Required for Tissue Maintenance and Planarian Regeneration.bioRxiv : the preprint server for biology · 2024Article
- A transcription factor atlas of stem cell fate in planarians.Cell reports · 2024Article
- Functional genomics in Spiralia.Briefings in functional genomics · 2023Article
- Isolation of planarian viable cells using fluorescence-activated cell sorting for advancing single-cell transcriptome analysis.Genes to cells : devoted to molecular & cellular mechanisms · 2023Article
- The BAF chromatin remodeling complex licenses planarian stem cells access to ectodermal and mesodermal cell fates.BMC biology · 2023Article
- Chromatin analysis of adult pluripotent stem cells reveals a unique stemness maintenance strategy.Science advances · 2023Article
- The known, unknown, and unknown unknowns of cell-cell communication in planarian regeneration.Zoological research · 2023Review
- Wnt/β-catenin signalling is required for pole-specific chromatin remodeling during planarian regeneration.Nature communications · 2023Article
- Article
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 2 countries.
Funding
Abstract
Planarians have become an established model system to study regeneration and stem cells, but the regulatory elements in the genome remain almost entirely undescribed. Here, by integrating epigenetic and expression data we use multiple sources of evidence to predict enhancer elements active in the adult stem cell populations that drive regeneration. We have used ChIP-seq data to identify genomic regions with histone modifications consistent with enhancer activity, and ATAC-seq data to identify accessible chromatin. Overlapping these signals allowed for the identification of a set of high-confidence candidate enhancers predicted to be active in planarian adult stem cells. These enhancers are enriched for predicted transcription factor (TF) binding sites for TFs and TF families expressed in planarian adult stem cells. Footprinting analyses provided further evidence that these potential TF binding sites are likely to be occupied in adult stem cells. We integrated these analyses to build testable hypotheses for the regulatory function of TFs in stem cells, both with respect to how pluripotency might be regulated, and to how lineage differentiation programs are controlled. We found that our predicted GRNs were independently supported by existing TF RNAi/RNA-seq datasets, providing further evidence that our work predicts active enhancers that regulate adult stem cells and regenerative mechanisms.
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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.