ArticleNature communications2021
An all-to-all approach to the identification of sequence-specific readers for epigenetic DNA modifications on cytosine.
Article in Nature communications, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 23 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.
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Who cites it
23 citing papers in PubMed, 33 citations in OpenAlex.
- Clinical translational research on stem cell products: prospects and challenges.Signal transduction and targeted therapy · 2026Review
- MeDReaders 2.0: an updated database for modified DNA readers.BMC genomics · 2026Article
- Mammalian Proteome Profiling Reveals Readers and Antireaders of Strand-Symmetric and -Asymmetric 5-Hydroxymethylcytosine-Modifications in DNA.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- The role of cytosine modification symmetry in mammalian epigenome regulation.Chemical science · 2026Review
- TET knockout cells transit between pluripotent states and exhibit precocious germline entry.The EMBO journal · 2025Article
- DNA Methylation Recognition Using Hybrid Deep Learning with Dual Nucleotide Visualization Fusion Feature Encoding.Interdisciplinary sciences, computational life sciences · 2025Article
- Assessment and applications of joint profiling of single-cell chromatin accessibility and transcriptome.Briefings in bioinformatics · 2025Review
- Active DNA demethylation upstream of rod-photoreceptor fate determination is required for retinal development.PLoS biology · 2025Article
- Advancing TET Inhibitor Development: From Structural Insights to Biological Evaluation.ACS medicinal chemistry letters · 2025Article
- Identifying the "stripe" transcription factors and cooperative binding related to DNA methylation.Communications biology · 2024Article
- Modeling methyl-sensitive transcription factor motifs with an expanded epigenetic alphabet.Genome biology · 2024Article
- StableDNAm: towards a stable and efficient model for predicting DNA methylation based on adaptive feature correction learning.BMC genomics · 2023Article
- Role of TET1-mediated epigenetic modulation in Alzheimer's disease.Neurobiology of disease · 2023Article
- Chemical Biology Approaches to Identify and Profile Interactors of Chromatin Modifications.ACS chemical biology · 2023Review
- Autism Spectrum Disorder: Neurodevelopmental Risk Factors, Biological Mechanism, and Precision Therapy.International journal of molecular sciences · 2023Review
- The mechanisms and factors that induce trained immunity in arthropods and mollusks.Frontiers in immunology · 2023Review
- A high-throughput effector screen identifies a novel small molecule scaffold for inhibition of ten-eleven translocation dioxygenase 2.RSC medicinal chemistry · 2022Article
- Evolved DNA Duplex Readers for Strand-Asymmetrically Modified 5-Hydroxymethylcytosine/5-Methylcytosine CpG Dyads.Journal of the American Chemical Society · 2022Article
- Epigenetic regulation in the neurogenic niche of the adult dentate gyrus.Neuroscience letters · 2022Review
- Mechanisms and Biological Roles of DNA Methyltransferases and DNA Methylation: From Past Achievements to Future Challenges.Advances in experimental medicine and biology · 2022Review
Corrections and comments
- Erratum issued
Authors and funding
11 authors at 4 institutions in 2 countries.
Funding
Abstract
Epigenetic modifications of DNA play important roles in many biological processes. Identifying readers of these epigenetic marks is a critical step towards understanding the underlying mechanisms. Here, we present an all-to-all approach, dubbed digital affinity profiling via proximity ligation (DAPPL), to simultaneously profile human TF-DNA interactions using mixtures of random DNA libraries carrying different epigenetic modifications (i.e., 5-methylcytosine, 5-hydroxymethylcytosine, 5-formylcytosine, and 5-carboxylcytosine) on CpG dinucleotides. Many proteins that recognize consensus sequences carrying these modifications in symmetric and/or hemi-modified forms are identified. We further demonstrate that the modifications in different sequence contexts could either enhance or suppress TF binding activity. Moreover, many modifications can affect TF binding specificity. Furthermore, symmetric modifications show a stronger effect in either enhancing or suppressing TF-DNA interactions than hemi-modifications. Finally, in vivo evidence suggests that USF1 and USF2 might regulate transcription via hydroxymethylcytosine-binding activity in weak enhancers in human embryonic stem cells.
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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.