ArticleNucleic acids research2020
Landscape of DNA binding signatures of myocyte enhancer factor-2B reveals a unique interplay of base and shape readout.
Article in Nucleic acids research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers, 1 of them a synthesis that pooled it.
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Who cites it
16 citing papers in PubMed, 1 synthesis or guideline pooled it, 27 citations in OpenAlex.
- Trans-ethnic genome-wide association study of severe COVID-19.Communications biology · 2021Pooled it
- The Diverse Roles of the MEF2 Transcription Factor Family in Tumor Progression and Emerging Therapeutic Opportunities.Biomedicines · 2026Review
- Review
- So close yet so far apart: distinct flanking sequence recognition by DNMT3A and DNMT3B.Communications biology · 2025Article
- Article
- A Rare Noncoding Enhancer Variant inCirculation · 2025Article
- Predicting DNA structure using a deep learning method.Nature communications · 2024Article
- Probing the role of the protonation state of a minor groove-linker histidine in Exd-Hox-DNA binding.Biophysical journal · 2024Article
- Noncanonical binding of transcription factors: time to revisitMolecular biology of the cell · 2023Review
- Cracking the Floral Quartet Code: How Do Multimers of MIKCInternational journal of molecular sciences · 2023Review
- Structural predictions of protein-DNA binding: MELD-DNA.Nucleic acids research · 2023Article
- Physicochemical models of protein-DNA binding with standard and modified base pairs.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Top-Down Crawl: a method for the ultra-rapid and motif-free alignment of sequences with associated binding metrics.Bioinformatics (Oxford, England) · 2022Article
- Insights into protein-DNA interactions from hydrogen bond energy-based comparative protein-ligand analyses.Proteins · 2022Article
- SAMPDI-3D: predicting the effects of protein and DNA mutations on protein-DNA interactions.Bioinformatics (Oxford, England) · 2021Article
- MEF2C shapes the microtranscriptome during differentiation of skeletal muscles.Scientific reports · 2021Article
Corrections and comments
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Authors and funding
6 authors at 1 institution in 1 country.
Funding
Abstract
Myocyte enhancer factor-2B (MEF2B) has the unique capability of binding to its DNA target sites with a degenerate motif, while still functioning as a gene-specific transcriptional regulator. Identifying its DNA targets is crucial given regulatory roles exerted by members of the MEF2 family and MEF2B's involvement in B-cell lymphoma. Analyzing structural data and SELEX-seq experimental results, we deduced the DNA sequence and shape determinants of MEF2B target sites on a high-throughput basis in vitro for wild-type and mutant proteins. Quantitative modeling of MEF2B binding affinities and computational simulations exposed the DNA readout mechanisms of MEF2B. The resulting binding signature of MEF2B revealed distinct intricacies of DNA recognition compared to other transcription factors. MEF2B uses base readout at its half-sites combined with shape readout at the center of its degenerate motif, where A-tract polarity dictates nuances of binding. The predominant role of shape readout at the center of the core motif, with most contacts formed in the minor groove, differs from previously observed protein-DNA readout modes. MEF2B, therefore, represents a unique protein for studies of the role of DNA shape in achieving binding specificity. MEF2B-DNA recognition mechanisms are likely representative for other members of the MEF2 family.
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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.