ArticleIntegrative biology : quantitative biosciences from nano to macro2016
5-Hydroxymethylcytosine in E-box motifs ACAT|GTG and ACAC|GTG increases DNA-binding of the B-HLH transcription factor TCF4.
Article in Integrative biology : quantitative biosciences from nano to macro, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 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
19 citing papers in PubMed, 27 citations in OpenAlex.
- The role of cytosine modification symmetry in mammalian epigenome regulation.Chemical science · 2026Review
- 5mC and 5hmC methylation sequencing: the power of 6-base sequencing in a multiomic era.Epigenomics · 2026Review
- Quantifying transcription factor specificity with advanced DNA universal microarrays featuring long and modified binding sites.Nucleic acids research · 2025Article
- Cell identity and 5-hydroxymethylcytosine.Epigenetics & chromatin · 2025Review
- Modeling methyl-sensitive transcription factor motifs with an expanded epigenetic alphabet.Genome biology · 2024Article
- Identifying unique exposure-specific transgenerational differentially DNA methylated region epimutations in the genome using hybrid deep learning prediction models.Environmental epigenetics · 2023Article
- Altering the Double-Stranded DNA Specificity of the bZIP Domain of Zta with Site-Directed Mutagenesis at N182.ACS omega · 2022Article
- REL Domain of NFATc2 Binding to Five Types of DNA Using Protein Binding Microarrays.ACS omega · 2021Article
- bZIP Dimers CREB1, ATF2, Zta, ATF3|cJun, and cFos|cJun Prefer to Bind to Some Double-Stranded DNA Sequences Containing 5-Formylcytosine and 5-Carboxylcytosine.Biochemistry · 2020Article
- Custom DNA Microarrays Reveal Diverse Binding Preferences of Proteins and Small Molecules to Thousands of G-Quadruplexes.ACS chemical biology · 2020Article
- Structural basis for preferential binding of human TCF4 to DNA containing 5-carboxylcytosine.Nucleic acids research · 2019Article
- The bZIP mutant CEBPB (V285A) has sequence specific DNA binding propensities similar to CREB1.Biochimica et biophysica acta. Gene regulatory mechanisms · 2019Article
- Replacing C189 in the bZIP domain of Zta with S, T, V, or A changes DNA binding specificity to four types of double-stranded DNA.Biochemical and biophysical research communications · 2018Article
- Comprehensive, high-resolution binding energy landscapes reveal context dependencies of transcription factor binding.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- Reading cytosine modifications within chromatin.Transcription · 2018Review
- The Epstein-Barr Virus B-ZIP Protein Zta Recognizes Specific DNA Sequences Containing 5-Methylcytosine and 5-Hydroxymethylcytosine.Biochemistry · 2017Article
- TET proteins in natural and induced differentiation.Current opinion in genetics & development · 2017Review
- Impact of cytosine methylation on DNA binding specificities of human transcription factors.Science (New York, N.Y.) · 2017Article
- 5-Methylcytosine (5mC) and 5-Hydroxymethylcytosine (5hmC) Enhance the DNA Binding of CREB1 to the C/EBP Half-Site Tetranucleotide GCAA.Biochemistry · 2016Article
Corrections and comments
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Authors and funding
11 authors at 6 institutions in 2 countries.
Funding
Abstract
We evaluated DNA binding of the B-HLH family members TCF4 and USF1 using protein binding microarrays (PBMs) containing double-stranded DNA probes with cytosine on both strands or 5-methylcytosine (5mC) or 5-hydroxymethylcytosine (5hmC) on one DNA strand and cytosine on the second strand. TCF4 preferentially bound the E-box motif (CAN|NTG) with strongest binding to the 8-mer CAG|GTGGT. 5mC uniformly decreases DNA binding of both TCF4 and USF1. The bulkier 5hmC also inhibited USF1 binding to DNA. In contrast, 5hmC dramatically enhanced TCF4 binding to E-box motifs ACAT|GTG and ACAC|GTG, being better bound than any 8-mer containing cytosine. Examination of X-ray structures of the closely related TCF3 and USF1 bound to DNA suggests TCF3 can undergo a conformational shift to preferentially bind to 5hmC while the USF1 basic region is bulkier and rigid precluding a conformation shift to bind 5hmC. These results greatly expand the regulatory DNA sequence landscape bound by TCF4.
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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.