NOTCH1-RBPJ complexes drive target gene expression through dynamic interactions with superenhancers.

Abstract

The main oncogenic driver in T-lymphoblastic leukemia is NOTCH1, which activates genes by forming chromatin-associated Notch transcription complexes. Gamma-secretase-inhibitor treatment prevents NOTCH1 nuclear localization, but most genes with NOTCH1-binding sites are insensitive to gamma-secretase inhibitors. Here, we demonstrate that fewer than 10% of NOTCH1-binding sites show dynamic changes in NOTCH1 occupancy when T-lymphoblastic leukemia cells are toggled between the Notch-on and -off states with gamma-secretase inhibiters. Dynamic NOTCH1 sites are functional, being highly associated with Notch target genes, are located mainly in distal enhancers, and frequently overlap with RUNX1 binding. In line with the latter association, we show that expression of IL7R, a gene with key roles in normal T-cell development and in T-lymphoblastic leukemia, is coordinately regulated by Runx factors and dynamic NOTCH1 binding to distal enhancers. Like IL7R, most Notch target genes and associated dynamic NOTCH1-binding sites cooccupy chromatin domains defined by constitutive binding of CCCTC binding factor, which appears to restrict the regulatory potential of dynamic NOTCH1 sites. More remarkably, the majority of dynamic NOTCH1 sites lie in superenhancers, distal elements with exceptionally broad and high levels of H3K27ac. Changes in Notch occupancy produces dynamic alterations in H3K27ac levels across the entire breadth of superenhancers and in the promoters of Notch target genes. These findings link regulation of superenhancer function to NOTCH1, a master regulatory factor and potent oncoprotein in the context of immature T cells, and delineate a generally applicable roadmap for identifying functional Notch sites in cellular genomes.

• Authors: Hongfang Wang, Chongzhi Zang, Len Taing, Kelly L Arnett, Yinling Joey Wong, Warren S Pear, Stephen C Blacklow, X Shirley Liu, Jon C Aster
• Journal: Proceedings of the National Academy of Sciences of the United States of America (Proc Natl Acad Sci U S A) Vol. 111 Issue 2 Pg. 705-10 (Jan 14 2014) ISSN: 1091-6490 [Electronic] United States
• PMID: 24374627 (Publication Type: Journal Article, Research Support, N.I.H., Extramural, Research Support, Non-U.S. Gov't)

Chemical References

• DNA Primers
• Immunoglobulin J Recombination Signal Sequence-Binding Protein
• Multiprotein Complexes
• NOTCH1 protein, human
• RBPJ protein, human
• Receptor, Notch1
• Receptors, Interleukin-7
• Luciferases

Topics

• Binding Sites (genetics)
• Cell Line, Tumor
• Chromatin Immunoprecipitation
• DNA Primers (genetics)
• Enhancer Elements, Genetic (genetics)
• Gene Expression Regulation (genetics, physiology)
• Humans
• Immunoglobulin J Recombination Signal Sequence-Binding Protein (metabolism)
• Luciferases
• Multiprotein Complexes (metabolism)
• Plasmids (genetics)
• Promoter Regions, Genetic (genetics)
• Real-Time Polymerase Chain Reaction
• Receptor, Notch1 (metabolism)
• Receptors, Interleukin-7 (metabolism)
• Signal Transduction (genetics, physiology)