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An all-to-all approach to the identification of sequence-specific readers for epigenetic DNA modifications on cytosine

https://doi.org/10.1101/638700
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1002/bies.201600126openalex-snapshot
Are there specific readers of oxidized 5‐methylcytosine bases?
inferredcites →https://doi.org/10.1016/j.cell.2008.05.024openalex-snapshot
Variation in Homeodomain DNA Binding Revealed by High-Resolution Analysis of Sequence Preferences
inferredcites →https://doi.org/10.1016/j.cell.2009.08.037openalex-snapshot
Profiling the Human Protein-DNA Interactome Reveals ERK2 as a Transcriptional Repressor of Interferon Signaling
inferredcites →https://doi.org/10.1016/j.cell.2010.10.012openalex-snapshot
Nucleosome-Interacting Proteins Regulated by DNA and Histone Methylation
inferredcites →https://doi.org/10.1016/j.cell.2012.12.009openalex-snapshot
DNA-Binding Specificities of Human Transcription Factors
inferredcites →https://doi.org/10.1016/j.cell.2013.02.004openalex-snapshot
Dynamic Readers for 5-(Hydroxy)Methylcytosine and Its Oxidized Derivatives
inferredcites →https://doi.org/10.1016/j.cell.2013.04.001openalex-snapshot
Genome-wide Profiling of 5-Formylcytosine Reveals Its Roles in Epigenetic Priming
inferredcites →https://doi.org/10.1016/j.cell.2013.04.002openalex-snapshot
Genome-wide Analysis Reveals TET- and TDG-Dependent 5-Methylcytosine Oxidation Dynamics
inferredcites →https://doi.org/10.1016/j.cell.2014.08.009openalex-snapshot
Determination and Inference of Eukaryotic Transcription Factor Sequence Specificity
inferredcites →https://doi.org/10.1016/j.celrep.2013.01.001openalex-snapshot
High-Resolution Enzymatic Mapping of Genomic 5-Hydroxymethylcytosine in Mouse Embryonic Stem Cells
inferredcites →https://doi.org/10.1016/j.celrep.2014.05.003openalex-snapshot
Transient Accumulation of 5-Carboxylcytosine Indicates Involvement of Active Demethylation in Lineage Specification of Neural Stem Cells
inferredcites →https://doi.org/10.1016/j.celrep.2015.12.044openalex-snapshot
Tet3 Reads 5-Carboxylcytosine through Its CXXC Domain and Is a Potential Guardian against Neurodegeneration
inferredcites →https://doi.org/10.1016/j.isci.2019.07.041openalex-snapshot
TET-Catalyzed 5-Carboxylcytosine Promotes CTCF Binding to Suboptimal Sequences Genome-Wide
inferredcites →https://doi.org/10.1016/j.molcel.2010.05.004openalex-snapshot
Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities
inferredcites →https://doi.org/10.1016/j.molonc.2007.01.004openalex-snapshot
Genetic and epigenetic alterations as biomarkers for cancer detection, diagnosis and prognosis
inferredcites →https://doi.org/10.1016/j.stem.2016.03.013openalex-snapshot
Activation of Endogenous Retroviruses in Dnmt1 −/− ESCs Involves Disruption of SETDB1-Mediated Repression by NP95 Binding to Hemimethylated DNA
inferredcites →https://doi.org/10.1016/j.ygeno.2014.08.019openalex-snapshot
Environmental enrichment modulates 5-hydroxymethylcytosine dynamics in hippocampus
inferredcites →https://doi.org/10.1021/acssynbio.8b00333openalex-snapshot
Comprehensive Profiling of Four Base Overhang Ligation Fidelity by T4 DNA Ligase and Application to DNA Assembly
inferredcites →https://doi.org/10.1038/cr.2011.113openalex-snapshot
Lineage-specific distribution of high levels of genomic
inferredcites →https://doi.org/10.1038/nature10008openalex-snapshot
Dynamic regulation of 5-hydroxymethylcytosine in mouse ES cells and during differentiation
inferredcites →https://doi.org/10.1038/nature10102openalex-snapshot
Genome-wide mapping of 5-hydroxymethylcytosine in embryonic stem cells
inferredcites →https://doi.org/10.1038/nature11247openalex-snapshot
An integrated encyclopedia of DNA elements in the human genome
inferredcites →https://doi.org/10.1038/nature14319openalex-snapshot
Disruption of DNA-methylation-dependent long gene repression in Rett syndrome
inferredcites →https://doi.org/10.1038/nchem.2064openalex-snapshot
5-Hydroxymethylcytosine is a predominantly stable DNA modification
inferredcites →https://doi.org/10.1038/ncomms2562openalex-snapshot
UHRF1 targets DNMT1 for DNA methylation through cooperative binding of hemi-methylated DNA and methylated H3K9
inferredcites →https://doi.org/10.1038/nmeth.4143openalex-snapshot
SMiLE-seq identifies binding motifs of single and dimeric transcription factors
inferredcites →https://doi.org/10.1038/nn.2959openalex-snapshot
5-hmC–mediated epigenetic dynamics during postnatal neurodevelopment and aging
inferredcites →https://doi.org/10.1038/nn.3607openalex-snapshot
Distribution, recognition and regulation of non-CpG methylation in the adult mammalian brain
inferredcites →https://doi.org/10.1038/nrg.2017.33openalex-snapshot
TET-mediated active DNA demethylation: mechanism, function and beyond
inferredcites →https://doi.org/10.1038/tp.2013.111openalex-snapshot
Genome-wide DNA methylation analysis of human brain tissue from schizophrenia patients
inferredcites →https://doi.org/10.1038/tp.2014.70openalex-snapshot
DNA methylation analysis of the autistic brain reveals multiple dysregulated biological pathways
inferredcites →https://doi.org/10.1073/pnas.1618737114openalex-snapshot
DNA methylation in the gene body influences MeCP2-mediated gene repression
inferredcites →https://doi.org/10.1073/pnas.93.19.10315openalex-snapshot
Reverse two-hybrid and one-hybrid systems to detect dissociation of protein-protein and DNA-protein interactions.
inferredcites →https://doi.org/10.1093/hmg/ddy193openalex-snapshot
5-Hydroxymethylcytosine alterations in the human postmortem brains of autism spectrum disorder
inferredcites →https://doi.org/10.1093/nar/gks155openalex-snapshot
Recognition and potential mechanisms for replication and erasure of cytosine hydroxymethylation
inferredcites →https://doi.org/10.1093/nar/gkw1184openalex-snapshot
MAX is an epigenetic sensor of 5-carboxylcytosine and is altered in multiple myeloma
inferredcites →https://doi.org/10.1093/nar/gky104openalex-snapshot
Structural and mechanistic insights into UHRF1-mediated DNMT1 activation in the maintenance DNA methylation
inferredcites →https://doi.org/10.1101/gad.179184.111openalex-snapshot
Mechanisms and functions of Tet protein-mediated 5-methylcytosine oxidation
inferredcites →https://doi.org/10.1101/gad.947102openalex-snapshot
DNA methylation patterns and epigenetic memory
inferredcites →https://doi.org/10.1101/gr.112680.110openalex-snapshot
DNA methylation profiles of human active and inactive X chromosomes
inferredcites →https://doi.org/10.1101/gr.163147.113openalex-snapshot
The dynamics of DNA methylation fidelity during mouse embryonic stem cell self-renewal and differentiation
inferredcites →https://doi.org/10.1126/science.1162327openalex-snapshot
Diversity and Complexity in DNA Recognition by Transcription Factors
inferredcites →https://doi.org/10.1126/science.1170116openalex-snapshot
Conversion of 5-Methylcytosine to 5-Hydroxymethylcytosine in Mammalian DNA by MLL Partner TET1
inferredcites →https://doi.org/10.1126/science.1210597openalex-snapshot
Tet Proteins Can Convert 5-Methylcytosine to 5-Formylcytosine and 5-Carboxylcytosine
inferredcites →https://doi.org/10.1126/science.1210944openalex-snapshot
Tet-Mediated Formation of 5-Carboxylcytosine and Its Excision by TDG in Mammalian DNA
inferredcites →https://doi.org/10.1126/science.aaj2239openalex-snapshot
Impact of cytosine methylation on DNA binding specificities of human transcription factors
inferredcites →https://doi.org/10.1126/science.aan5480openalex-snapshot
Nascent DNA methylome mapping reveals inheritance of hemimethylation at CTCF/cohesin sites
inferredcites →https://doi.org/10.1126/science.aat0789openalex-snapshot
Hemimethylation: DNA's lasting odd couple
inferredcites →https://doi.org/10.1186/1471-2105-5-194openalex-snapshot
Optimized LOWESS normalization parameter selection for DNA microarray data
inferredcites →https://doi.org/10.1186/gb-2007-8-2-r24openalex-snapshot
Quantifying similarity between motifs
inferredcites →https://doi.org/10.1186/gb-2011-12-6-r54openalex-snapshot
5-Hydroxymethylcytosine is associated with enhancers and gene bodies in human embryonic stem cells
inferredcites →https://doi.org/10.1186/gb-2013-14-10-r119openalex-snapshot
A screen for hydroxymethylcytosine and formylcytosine binding proteins suggests functions in transcription and chromatin regulation
inferredcites →https://doi.org/10.1242/dev.070771openalex-snapshot
Tet family proteins and 5-hydroxymethylcytosine in development and disease
inferredcites →https://doi.org/10.2210/pdb5ydr/pdbopenalex-snapshot
Structure of DNMT1 RFTS domain in complex with ubiquitin
inferredcites →https://doi.org/10.7554/elife.00726openalex-snapshot
DNA methylation presents distinct binding sites for human transcription factors

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Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1186/s12864-023-09802-7openalex-snapshot
StableDNAm: towards a stable and efficient model for predicting DNA methylation based on adaptive feature correction learning
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