ArticleNature immunology2020
Charting the cis-regulome of activated B cells by coupling structural and functional genomics.
Article in Nature immunology, 2020. 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, 50 citations in OpenAlex.
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- Decoding biology with massively parallel reporter assays and machine learning.Genes & development · 2024Review
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- DNA methylation-environment interactions in the human genome.bioRxiv : the preprint server for biology · 2023Article
- A variegated model of transcription factor function in the immune system.Trends in immunology · 2023Review
- Cis-regulatory atlas of primary human CD4+ T cells.BMC genomics · 2023Article
- Challenges and considerations for reproducibility of STARR-seq assays.Genome research · 2023Article
- Three-dimensional genome organization in immune cell fate and function.Nature reviews. Immunology · 2023Review
- Gene Regulatory Circuits in Innate and Adaptive Immune Cells.Annual review of immunology · 2022Review
- FoxP3 associates with enhancer-promoter loops to regulate TScience immunology · 2022Article
- Assessing genome-wide dynamic changes in enhancer activity during early mESC differentiation by FAIRE-STARR-seq.Nucleic acids research · 2021Article
- Deficiencies in the DNA Binding Protein ARID3a Alter Chromatin Structures Important for Early Human Erythropoiesis.ImmunoHorizons · 2021Article
- An IRF4-MYC-mTORC1 Integrated Pathway Controls Cell Growth and the Proliferative Capacity of Activated B Cells during B Cell Differentiation In Vivo.Journal of immunology (Baltimore, Md. : 1950) · 2021Article
- Epigenetic gene regulation in plasma cells.Immunological reviews · 2021Review
- CISH attenuates homeostatic cytokine signaling to promote lung-specific macrophage programming and function.Science signaling · 2021Article
- Article
- A flexible repertoire of transcription factor binding sites and a diversity threshold determines enhancer activity in embryonic stem cells.Genome research · 2021Article
- Roadmap to a plasma cell: Epigenetic and transcriptional cues that guide B cell differentiation.Immunological reviews · 2021Review
- Signaling-to-chromatin pathways in the immune system.Immunological reviews · 2021Review
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Cis-regulomes underlying immune-cell-specific genomic states have been extensively analyzed by structure-based chromatin profiling. By coupling such approaches with a high-throughput enhancer screen (self-transcribing active regulatory region sequencing (STARR-seq)), we assembled a functional cis-regulome for lipopolysaccharide-activated B cells. Functional enhancers, in contrast with accessible chromatin regions that lack enhancer activity, were enriched for enhancer RNAs (eRNAs) and preferentially interacted in vivo with B cell lineage-determining transcription factors. Interestingly, preferential combinatorial binding by these transcription factors was not associated with differential enrichment of their sites. Instead, active enhancers were resolved by principal component analysis (PCA) from all accessible regions by co-varying transcription factor motif scores involving a distinct set of signaling-induced transcription factors. High-resolution chromosome conformation capture (Hi-C) analysis revealed multiplex, activated enhancer-promoter configurations encompassing numerous multi-enhancer genes and multi-genic enhancers engaged in the control of divergent molecular pathways. Motif analysis of pathway-specific enhancers provides a catalog of diverse transcription factor codes for biological processes encompassing B cell activation, cycling and differentiation.
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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.