ArticleProceedings of the National Academy of Sciences of the United States of America2011
Genome-wide analysis reveals conserved and divergent features of Notch1/RBPJ binding in human and murine T-lymphoblastic leukemia cells.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 166 papers.
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166 citing papers in PubMed, 239 citations in OpenAlex.
- FOXP3 expression depends on cell-type-specific cis-regulatory elements and transcription factor circuitry.Immunity · 2026Article
- NOTCH1 dimeric signaling is essential for T-cell leukemogenesis and leukemia maintenance.Blood · 2025Article
- Early Notch signals from fibroblastic reticular cells program effector CD8+ T cell differentiation.The Journal of experimental medicine · 2025Article
- Cis-Regulatory Element and Transcription Factor Circuitry Required for Cell-Type Specific Expression of FOXP3.bioRxiv : the preprint server for biology · 2025Article
- ZNF143 is a transcriptional regulator of nuclear-encoded mitochondrial genes that acts independently of looping and CTCF.Molecular cell · 2025Article
- Notch induces transcription by stimulating release of paused RNA polymerase II.Genes & development · 2024Article
- Notch1 Phase Separation Coupled Percolation facilitates target gene expression and enhancer looping.Scientific reports · 2024Article
- The cellular Notch1 protein promotes KSHV reactivation in an Rta-dependent manner.Journal of virology · 2024Article
- Notch1 Phase Separation Coupled Percolation facilitates target gene expression and enhancer looping.bioRxiv : the preprint server for biology · 2024Article
- Reciprocal suppression between TGFβ signaling and TNF stimulation finetunes the macrophage inflammatory response.FASEB journal : official publication of the Federation of American Societies for Experimental Biology · 2024Article
- Notch induces transcription by stimulating release of paused RNA Polymerase II.bioRxiv : the preprint server for biology · 2024Article
- Comprehensive genomic features indicative for Notch responsiveness.Nucleic acids research · 2024Article
- Regulatory mechanisms and context-dependent roles of TAL1 in T-cell acute lymphoblastic leukemia.Haematologica · 2024Article
- The Notch1 signaling pathway directly modulates the human RANKL-induced osteoclastogenesis.Scientific reports · 2023Article
- Isoforms of the TAL1 transcription factor have different roles in hematopoiesis and cell growth.PLoS biology · 2023Article
- Review
- A DNA tumor virus globally reprograms host 3D genome architecture to achieve immortal growth.Nature communications · 2023Article
- Notch Partners in the Long Journey of T-ALL Pathogenesis.International journal of molecular sciences · 2023Review
- A Therapeutically Targetable NOTCH1-SIRT1-KAT7 Axis in T-cell Leukemia.Blood cancer discovery · 2023Article
- Selective ferroptosis vulnerability due to familial Alzheimer's disease presenilin mutations.Cell death and differentiation · 2022Article
106 more citing papers are in PubMed but not listed here.
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13 authors at 5 institutions in 1 country.
Funding
Abstract
Notch1 regulates gene expression by associating with the DNA-binding factor RBPJ and is oncogenic in murine and human T-cell progenitors. Using ChIP-Seq, we find that in human and murine T-lymphoblastic leukemia (TLL) genomes Notch1 binds preferentially to promoters, to RBPJ binding sites, and near imputed ZNF143, ETS, and RUNX sites. ChIP-Seq confirmed that ZNF143 binds to ∼40% of Notch1 sites. Notch1/ZNF143 sites are characterized by high Notch1 and ZNF143 signals, frequent cobinding of RBPJ (generally through sites embedded within ZNF143 motifs), strong promoter bias, and relatively low mean levels of activating chromatin marks. RBPJ and ZNF143 binding to DNA is mutually exclusive in vitro, suggesting RBPJ/Notch1 and ZNF143 complexes exchange on these sites in cells. K-means clustering of Notch1 binding sites and associated motifs identified conserved Notch1-RUNX, Notch1-ETS, Notch1-RBPJ, Notch1-ZNF143, and Notch1-ZNF143-ETS clusters with different genomic distributions and levels of chromatin marks. Although Notch1 binds mainly to gene promoters, ∼75% of direct target genes lack promoter binding and are presumably regulated by enhancers, which were identified near MYC, DTX1, IGF1R, IL7R, and the GIMAP cluster. Human and murine TLL genomes also have many sites that bind only RBPJ. Murine RBPJ-only sites are highly enriched for imputed REST (a DNA-binding transcriptional repressor) sites, whereas human RPBJ-only sites lack REST motifs and are more highly enriched for imputed CREB sites. Thus, there is a conserved network of cis-regulatory factors that interacts with Notch1 to regulate gene expression in TLL cells, as well as unique classes of divergent RBPJ-only sites that also likely regulate transcription.
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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 Socratic graph.