ArticleeLife2021
Analysis of long and short enhancers in melanoma cell states.
Article in eLife, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- CREsted: modeling genomic and synthetic cell-type-specific enhancers across tissues and species.Nature methods · 2026Article
- Multi-scale dissection, compaction and derivatization of mammalian developmental enhancers.bioRxiv : the preprint server for biology · 2026Article
- Interaction of lncRNA LENT with DHX36 regulates translation and suppresses autophagy in melanoma.Cell death & disease · 2025Article
- SOX10 Regulates Melanoma Metastasis Through the IRF1-ITGA3/EphA2-FAK Pathway.Cancer science · 2025Article
- Article
- Discovery of oligodendrocyte enhancers that regulate Sox10 expression.PLoS genetics · 2025Article
- Large-scale discovery of potent, compact and erythroid specific enhancers for gene therapy vectors.Nature communications · 2025Article
- SpecificbioRxiv : the preprint server for biology · 2024Article
- ZEB1 controls a lineage-specific transcriptional program essential for melanoma cell state transitions.Oncogene · 2024Article
- Cell-type-directed design of synthetic enhancers.Nature · 2024Article
- Cell state dependent effects of Bmal1 on melanoma immunity and tumorigenicity.Nature communications · 2024Article
- Functional analysis of recurrent CDC20 promoter variants in human melanoma.Communications biology · 2023Article
- Landscape of enhancer disruption and functional screen in melanoma cells.Genome biology · 2023Article
- SCENIC+: single-cell multiomic inference of enhancers and gene regulatory networks.Nature methods · 2023Article
- Evaluating deep learning for predicting epigenomic profiles.Nature machine intelligence · 2022Article
- DeepSTARR predicts enhancer activity from DNA sequence and enables the de novo design of synthetic enhancers.Nature genetics · 2022Article
- Cancer Cell Phenotype Plasticity as a Driver of Immune Escape in Melanoma.Frontiers in immunology · 2022Review
- Article
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Authors and funding
9 authors.
Funding
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Abstract
Understanding how enhancers drive cell-type specificity and efficiently identifying them is essential for the development of innovative therapeutic strategies. In melanoma, the melanocytic (MEL) and the mesenchymal-like (MES) states present themselves with different responses to therapy, making the identification of specific enhancers highly relevant. Using massively parallel reporter assays (MPRAs) in a panel of patient-derived melanoma lines (MM lines), we set to identify and decipher melanoma enhancers by first focusing on regions with state-specific H3K27 acetylation close to differentially expressed genes. An in-depth evaluation of those regions was then pursued by investigating the activity of overlapping ATAC-seq peaks along with a full tiling of the acetylated regions with 190 bp sequences. Activity was observed in more than 60% of the selected regions, and we were able to precisely locate the active enhancers within ATAC-seq peaks. Comparison of sequence content with activity, using the deep learning model DeepMEL2, revealed that AP-1 alone is responsible for the MES enhancer activity. In contrast, SOX10 and MITF both influence MEL enhancer function with SOX10 being required to achieve high levels of activity. Overall, our MPRAs shed light on the relationship between long and short sequences in terms of their sequence content, enhancer activity, and specificity across melanoma cell states.
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