ArticleCell systems2018
Comparative Analysis of Immune Cells Reveals a Conserved Regulatory Lexicon.
Article in Cell systems, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- PervasivebioRxiv : the preprint server for biology · 2025Article
- Transposable elements as instructors of the immune system.Nature reviews. Immunology · 2025Review
- An evolutionarily conserved constellation of functional cis-elements programs the virus-responsive fate of the human (epi)genome.Nucleic acids research · 2025Article
- ChIP-DIP maps binding of hundreds of proteins to DNA simultaneously and identifies diverse gene regulatory elements.Nature genetics · 2024Article
- Omics-based construction of regulatory variants can be applied to help decipher pig liver-related traits.Communications biology · 2024Article
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- Systems-level identification of key transcription factors in immune cell specification.PLoS computational biology · 2022Article
- Extended intergenic DNA contributes to neuron-specific expression of neighboring genes in the mammalian nervous system.Nature communications · 2022Article
- Article
- LINE retrotransposons characterize mammalian tissue-specific and evolutionarily dynamic regulatory regions.Genome biology · 2021Article
- Meeting Report: 68The Journal of investigative dermatology · 2020Article
- High-Resolution Mapping of Multiway Enhancer-Promoter Interactions Regulating Pathogen Detection.Molecular cell · 2020Article
- DolphinNext: a distributed data processing platform for high throughput genomics.BMC genomics · 2020Article
- Specific subfamilies of transposable elements contribute to different domains of T lymphocyte enhancers.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Identification and Massively Parallel Characterization of Regulatory Elements Driving Neural Induction.Cell stem cell · 2019Article
- DEBrowser: interactive differential expression analysis and visualization tool for count data.BMC genomics · 2019Article
Corrections and comments
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Authors and funding
13 authors.
Funding
Abstract
Most well-characterized enhancers are deeply conserved. In contrast, genome-wide comparative studies of steady-state systems showed that only a small fraction of active enhancers are conserved. To better understand conservation of enhancer activity, we used a comparative genomics approach that integrates temporal expression and epigenetic profiles in an innate immune system. We found that gene expression programs diverge among mildly induced genes, while being highly conserved for strongly induced genes. The fraction of conserved enhancers varies greatly across gene expression programs, with induced genes and early-response genes, in particular, being regulated by a higher fraction of conserved enhancers. Clustering of conserved accessible DNA sequences within enhancers resulted in over 60 sequence motifs including motifs for known factors, as well as many with unknown function. We further show that the number of instances of these motifs is a strong predictor of the responsiveness of a gene to pathogen detection.
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