ArticleGenome research2013
CG methylated microarrays identify a novel methylated sequence bound by the CEBPB|ATF4 heterodimer that is active in vivo.
Article in Genome research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 91 papers.
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Who cites it
91 citing papers in PubMed, 137 citations in OpenAlex.
- The Drosophila CEBPG homolog Irbp18 partners with crc (ATF4) to mediate the integrated stress response in degenerative disease models.Cell reports · 2026Article
- BPabZIP, a new bZIP protein motif that promotes binding near, and displacement of, nucleosomes.bioRxiv : the preprint server for biology · 2026Article
- MeDReaders 2.0: an updated database for modified DNA readers.BMC genomics · 2026Article
- DNA methylation shapes transcription factor binding beyond canonical CpG contexts.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Quantifying transcription factor specificity with advanced DNA universal microarrays featuring long and modified binding sites.Nucleic acids research · 2025Article
- TFProtBert: Detection of Transcription Factors Binding to Methylated DNA Using ProtBert Latent Space Representation.International journal of molecular sciences · 2025Article
- Epigenetic gene regulation in plants and its potential applications in crop improvement.Nature reviews. Molecular cell biology · 2025Review
- Article
- Identifying the "stripe" transcription factors and cooperative binding related to DNA methylation.Communications biology · 2024Article
- Epigenetic Reprogramming and Inheritance of the Cellular Differentiation Status Following Transient Expression of a Nonfunctional Dominant-Negative Retinoblastoma Mutant in Murine Mesenchymal Stem Cells.International journal of molecular sciences · 2024Article
- The markers of the predictive DNA test for canine hip dysplasia may have a stronger relationship with elbow dysplasia.Heliyon · 2024Article
- Molecular Signatures of CB-6644 Inhibition of the RUVBL1/2 Complex in Multiple Myeloma.International journal of molecular sciences · 2024Article
- The regulation of methylation on the Z chromosome and the identification of multiple novel Male Hyper-Methylated regions in the chicken.PLoS genetics · 2024Article
- Kidney-specific methylation patterns correlate with kidney function and are lost upon kidney disease progression.Clinical epigenetics · 2024Article
- Widespread effects of DNA methylation and intra-motif dependencies revealed by novel transcription factor binding models.Nucleic acids research · 2023Article
- TET2 lesions enhance the aggressiveness of CEBPA-mutant acute myeloid leukemia by rebalancing GATA2 expression.Nature communications · 2023Article
- Shared gene targets of the ATF4 and p53 transcriptional networks.bioRxiv : the preprint server for biology · 2023Article
- Review
- Transcriptome and methylome of the supraoptic nucleus provides insights into the age-dependent loss of neuronal plasticity.Frontiers in aging neuroscience · 2023Article
- Shared Gene Targets of the ATF4 and p53 Transcriptional Networks.Molecular and cellular biology · 2023Article
31 more citing papers are in PubMed but not listed here.
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Authors and funding
7 authors at 2 institutions in 2 countries.
Funding
Abstract
To evaluate the effect of CG methylation on DNA binding of sequence-specific B-ZIP transcription factors (TFs) in a high-throughput manner, we enzymatically methylated the cytosine in the CG dinucleotide on protein binding microarrays. Two Agilent DNA array designs were used. One contained 40,000 features using de Bruijn sequences where each 8-mer occurs 32 times in various positions in the DNA sequence. The second contained 180,000 features with each CG containing 8-mer occurring three times. The first design was better for identification of binding motifs, while the second was better for quantification. Using this novel technology, we show that CG methylation enhanced binding for CEBPA and CEBPB and inhibited binding for CREB, ATF4, JUN, JUND, CEBPD, and CEBPG. The CEBPB|ATF4 heterodimer bound a novel motif CGAT|GCAA 10-fold better when methylated. The electrophoretic mobility shift assay (EMSA) confirmed these results. CEBPB ChIP-seq data using primary female mouse dermal fibroblasts with 50× methylome coverage for each strand indicate that the methylated sequences well-bound on the arrays are also bound in vivo. CEBPB bound 39% of the methylated canonical 10-mers ATTGC|GCAAT in the mouse genome. After ATF4 protein induction by thapsigargin which results in ER stress, CEBPB binds methylated CGAT|GCAA in vivo, recapitulating what was observed on the arrays. This methodology can be used to identify new methylated DNA sequences preferentially bound by TFs, which may be functional in vivo.
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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.