Genome-wide analysis reveals conserved and divergent features of Notch1/RBPJ binding in human and murine T-lymphoblastic leukemia cells

Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115, USA.
Proceedings of the National Academy of Sciences (Impact Factor: 9.81). 07/2011; 108(36):14908-13. DOI: 10.1073/pnas.1109023108
Source: PubMed

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.

Download full-text


Available from: Eric Johannsen, Aug 14, 2015
  • Source
    • "It has been observed that some sites in the genome are occupied only when Notch signaling is active (''dynamic sites'') (Bray and Bernard, 2010; Castel et al., 2013; Housden et al., 2013; Krejcí et al., 2009; Wang et al., 2014, 2011). These dynamic sites show increased recoverability by RBP ChIP when NICD is present, leading to the proposal that the NICD/RBP complex acts as a pioneer factor to modify chromatin at these sites (Castel et al., 2013). "
    [Show abstract] [Hide abstract]
    ABSTRACT: We developed Split DamID (SpDamID), a protein complementation version of DamID, to mark genomic DNA bound in vivo by interacting or juxtapositioned transcription factors. Inactive halves of DAM (DNA adenine methyltransferase) were fused to protein pairs to be queried. Either direct interaction between proteins or proximity enabled DAM reconstitution and methylation of adenine in GATC. Inducible SpDamID was used to analyze Notch-mediated transcriptional activation. We demonstrate that Notch complexes label RBP sites broadly across the genome and show that a subset of these complexes that recruit MAML and p300 undergo changes in chromatin accessibility in response to Notch signaling. SpDamID differentiates between monomeric and dimeric binding, thereby allowing for identification of half-site motifs used by Notch dimers. Motif enrichment of Notch enhancers coupled with SpDamID reveals co-targeting of regulatory sequences by Notch and Runx1. SpDamID represents a sensitive and powerful tool that enables dynamic analysis of combinatorial protein-DNA transactions at a genome-wide level. Copyright © 2015 Elsevier Inc. All rights reserved.
    Molecular cell 08/2015; DOI:10.1016/j.molcel.2015.07.008 · 14.46 Impact Factor
  • Source
    • "In support of our hypothesis that NOTCH1 controls the lncRNA transcriptional program in T-ALL, we observed that lncRNAs associated with the top 1,000 most enriched NOTCH1-binding sites were significantly downregulated upon administration of g-SI according to gene set enrichment analysis (GSEA) (Figure 2E). Upon closer examination of many of these lncRNA loci, we observed strong NOTCH1/RBPJk-binding sites (Wang et al., 2011a) at both promoters and intragenic enhancer elements (Figure S2B, highlighted yellow), suggesting direct transcriptional control by Notch signaling. Together these data suggest the presence of a Notch-dependent T-ALL lncRNA expression program, members of which, we believe, may carry important biological functions. "
    [Show abstract] [Hide abstract]
    ABSTRACT: Notch signaling is a key developmental pathway that is subject to frequent genetic and epigenetic perturbations in many different human tumors. Here we investigate whether long noncoding RNA (lncRNA) genes, in addition to mRNAs, are key downstream targets of oncogenic Notch1 in human T cell acute lymphoblastic leukemia (T-ALL). By integrating transcriptome profiles with chromatin state maps, we have uncovered many previously unreported T-ALL-specific lncRNA genes, a fraction of which are directly controlled by the Notch1/Rpbjκ activator complex. Finally we have shown that one specific Notch-regulated lncRNA, LUNAR1, is required for efficient T-ALL growth in vitro and in vivo due to its ability to enhance IGF1R mRNA expression and sustain IGF1 signaling. These results confirm that lncRNAs are important downstream targets of the Notch signaling pathway, and additionally they are key regulators of the oncogenic state in T-ALL.
    Cell 07/2014; 158(3):593-606. DOI:10.1016/j.cell.2014.05.049 · 33.12 Impact Factor
  • Source
    • "ZNF143 is essential for the normal embryonic development of zebra fish [11] and is important for the maintenance and the self-renewal of embryonic stem cells [12e14]. Transcription factor ZNF143 is widely involved in cooperative/competitive regulation with other transcription factors such as THAP11 and Notch1 [9] [15] [16], and is broadly associated to GABPA, CTCF, Cohesin, SIX5, NFY, USF and YY1 occupied loci [16] [17]. "
    [Show abstract] [Hide abstract]
    ABSTRACT: ZNF143 is a ubiquitously expressed transcription factor conserved in all vertebrates, regulating genes involved in primary metabolism and cell growth. It is therefore crucial to tightly maintain the adequate level of this factor in the cell. Although ZNF143 expression is auto-regulated at the transcriptional level, nothing is known about the post-transcriptional events influencing its expression. In this work, performed in mammalian cells, we show that ZNF143 expresses different 3'-untranslated regions (3'-UTR) as a result of alternative polyadenylation. These 3'UTR isoforms have a diverse impact on the ZNF143 transcript fate. Indeed, we show that the longest isoform, unlike the short one, contains a destabilizing AU-Rich element and is targeted by the miRNA 590-3p. Additionally we observed a correlation between ZNF143 downregulation and miR-590-3p up-regulation in retinoic acid treated teratocarcinoma cells. This strongly suggests that ZNF143 post-transcriptional regulation depends on the long 3'UTR isoform during teratocarcinoma cells differentiation. Finally we evidenced that the alternative polyadenylation site usage is independent of the previously identified ZNF143 transcriptional auto-regulation.
    Biochimie 06/2014; 104C. DOI:10.1016/j.biochi.2014.06.008 · 3.12 Impact Factor
Show more