ArticleGenome research2018
Intrinsic DNA binding properties demonstrated for lineage-specifying basic helix-loop-helix transcription factors.
Article in Genome research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed, 47 citations in OpenAlex.
- Article
- The cistrome response to hypoxia in human umbilical vein endothelial cells.bioRxiv : the preprint server for biology · 2026Article
- MYOD represses gene expression from non-E-box motifs.Genes & development · 2025Article
- Chromatin-dependent motif syntax defines differentiation trajectories.Molecular cell · 2025Article
- Cell fate acquisition and reprogramming by the proneural transcription factor ASCL1.Open biology · 2025Review
- Asymmetry of Motif Conservation Within Their Homotypic Pairs Distinguishes DNA-Binding Domains of Target Transcription Factors in ChIP-Seq Data.International journal of molecular sciences · 2025Article
- Phospho-regulation of ASCL1-mediated chromatin opening during cellular reprogramming.Development (Cambridge, England) · 2024Article
- Recruitment of homodimeric proneural factors by conserved CAT-CAT E-boxes drives major epigenetic reconfiguration in cortical neurogenesis.Nucleic acids research · 2024Article
- NEUROD1: transcriptional and epigenetic regulator of human and mouse neuronal and endocrine cell lineage programs.Frontiers in cell and developmental biology · 2024Review
- Insights and applications of direct neuronal reprogramming.Current opinion in genetics & development · 2023Review
- Ascl1 and Ngn2 convert mouse embryonic stem cells to neurons via functionally distinct paths.Nature communications · 2023Article
- Global chromatin landscapes identify candidate noncoding modifiers of cardiac rhythm.The Journal of clinical investigation · 2023Article
- Review
- Probing cell identity hierarchies by fate titration and collision during direct reprogramming.Molecular systems biology · 2022Article
- Measuring transcription factor binding and gene expression using barcoded self-reporting transposon calling cards and transcriptomes.NAR genomics and bioinformatics · 2022Article
- Elevated ASCL1 activity creates de novo regulatory elements associated with neuronal differentiation.BMC genomics · 2022Article
- Genetic and epigenetic basis of hepatoblastoma diversity.Nature communications · 2021Article
- Mechanisms of Binding Specificity among bHLH Transcription Factors.International journal of molecular sciences · 2021Review
- Amino Acid Composition in Various Types of Nucleic Acid-Binding Proteins.International journal of molecular sciences · 2021Review
- An interpretable bimodal neural network characterizes the sequence and preexisting chromatin predictors of induced transcription factor binding.Genome biology · 2021Article
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Authors and funding
4 authors at 1 institution in 1 country.
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Abstract
During development, transcription factors select distinct gene programs, providing the necessary regulatory complexity for temporal and tissue-specific gene expression. How related factors retain specificity, especially when they recognize the same DNA motifs, is not understood. We address this paradox using basic helix-loop-helix (bHLH) transcription factors ASCL1, ASCL2, and MYOD1, crucial mediators of lineage specification. In vivo, these factors recognize the same DNA motifs, yet bind largely different genomic sites and regulate distinct transcriptional programs. This suggests that their ability to identify regulatory targets is defined either by the cellular environment of the partially defined lineages in which they are endogenously expressed, or by intrinsic properties of the factors themselves. To distinguish between these mechanisms, we directly compared the chromatin binding properties of this subset of bHLH factors when ectopically expressed in embryonic stem cells, presenting them with a common chromatin landscape and cellular components. We find that these factors retain distinct binding sites; thus, specificity of binding is an intrinsic property not requiring a restricted landscape or lineage-specific cofactors. Although the ASCL factors and MYOD1 have some distinct DNA motif preference, it is not sufficient to explain the extent of the differential binding. All three factors can bind inaccessible chromatin and induce changes in chromatin accessibility and H3K27ac. A reiterated pattern of DNA binding motifs is uniquely enriched in inaccessible chromatin at sites bound by these bHLH factors. These combined properties define a subclass of lineage-specific bHLH factors and provide context for their central roles in development and disease.
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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.