Ikaros DNA-Binding Proteins as Integral Components of B Cell Developmental-Stage-Specific Regulatory Circuits

Article (PDF Available)inImmunity 26(3):335-44 · April 2007with38 Reads
DOI: 10.1016/j.immuni.2007.02.010 · Source: PubMed
Abstract
Ikaros DNA-binding proteins are critical for the development of lymphocytes and other hematopoietic lineages, but it remains unclear how they cooperate with other regulators of signaling and transcription to achieve ordered gene expression during development. Here, we show that Ikaros proteins regulate the pre-BCR component lambda5 in a stage-specific manner. In pre-BI cells, Ikaros modulated lambda5 expression in competition with the transcriptional activator EBF. This required Ikaros binding to the Igll1 (lambda5) promoter and was abolished either by mutation of the Ikaros DNA-binding domain or by deletion of a single Ikaros site from the Igll1 promoter. At the transition from the pre-BI to pre-BII stage, the expression of the Ikaros family member Aiolos was upregulated and required for the efficient silencing of Igll1. Aiolos expression was controlled by pre-BCR signals via the adaptor protein SLP-65. Thus, pre-BCR signaling regulates Aiolos and the silencing of Igll1 via a developmental-stage-specific feedback loop.
Immunity
Erratum
Ikaros DNA-Binding Proteins
as Integral Components of B Cell
Developmental-Stage-Specific Regulatory Circuits
Elizabeth C. Thompson, Bradley S. Cobb, Pierangela Sabbattini, Sonja Meixlsperger, Vania Parelho,
David Liberg, Benjamin Taylor, Niall Dillon, Katia Georgopoulos, Hassan Jumaa, Stephen T. Smale,
Amanda G. Fisher, and Matthias Merkenschlager
*
*Correspondence: matthias.merkenschlager@csc.mrc.ac.uk
DOI 10.1016/j.immuni.2007.03.007
(Immunity 26, 335–344; March 2007)
In the version of this paper published originally online, the publication date was incorrectly listed as March 8, 2007. The
correct date is March 15, 2007. This has now been corrected online and in print, and we regret the error.
Immunity 26, 533, April 2007 ª2007 Elsevier Inc. 533
    • "As seen in Fig. 9, the knockdown of Ikaros did not affect THAP11 mRNA levels significantly. In contrast, it substantially increased the mRNA amount of some well established Ikaros target genes (lacking M4 sequences), like the B cell-specific lambda5 [16] or T cell-specific Hes1-gene, for which Ikaros is known to function as a transcriptional repres- sor [25, 26] . In parallel, the Ikaros knockdown dramatically reduces the expression level of the Ikaros family gene Aiolos, for which Ikaros serves as an important transcriptional activator [27]. "
    [Show abstract] [Hide abstract] ABSTRACT: Background The motif ACTAYRNNNCCCR (Y being C or T, R being A or G, and N any nucleotide), called M4, was discovered as a putative cis-regulatory element, present 520 times in human promoter regions. Of these, 317 (61 %) are conserved within promoter sequences of four related organisms: human, mouse, rat, and dog. Recent genome-wide studies have described M4 as a transcription factor (TF) binding site for THAP11 that does often overlap with SBS (STAF Binding Site) a second core-promoter associated TF binding module, which associates with the TFs STAF/ZNF143 and RBP-J. Human M4-promoter genes show enhanced expression in cells of hematopoietic origin, especially in B lymphoblasts and peripheral blood B and T cells. Apart from RBP-J that is well known to recruit ICN1 (the intracellular transcriptional mediator of activated Notch1), the functional role of the hyperconserved M4 cis-element in the context of transcriptional regulation of M4-genes in lymphoid cells remains poorly defined. Results Here, we present a quantitative proteomic investigation of the M4 motif TF binding landscape in lymphoid cell lines that is further validated by ChIP experiments and functional assays. Our data strongly suggest that THAP11 and Ikaros interact directly, while NFKB1 (NF-kappa B p50) and HCF-1 are binding indirectly to M4-promoters in vitro and in living cells. Further analysis reveals that M4 is a bipartite composite cis-element, which is recognized by THAP11 via binding to the ACTAYR sequence module, thereby promoting ternary complex formation with HCF-1. Similarly, Ikaros binds to the CCCR module of the M4 motif and this interaction is crucial for recruiting NFKB1 to M4 harboring genes. Transient reporter assays in HEK293 and loss-of-function experiments in Molt4 T cells unequivocally demonstrate that binding of Ikaros and/or THAP11 to M4 bearing promoters is functionally important and therefore biologically relevant. Accordingly, this study validates our SILAC-based DNA protein interaction screening methodology as a valuable surrogate for a bona fide reverse ChIP technology. Conclusions The M4 motif (ACTAYRNNNCCCR) is a functional regulatory bipartite cis-element, which engages a THAP11/HCF-1 complex via binding to the ACTAYR module, while the CCCRRNRNRC subsequence part constitutes a binding platform for Ikaros and NFKB1.
    Full-text · Article · Aug 2016
    • "The closely related Ikaros and Aiolos TFs share highly conserved zinc finger domains that confer DNA-binding specificity (Cobb & Smale, 2005), and ChIP-seq experiments in T cells revealed numerous shared binding sites (Zhang et al., 2012). Both are upregulated at the pro-to-pre-B cell transition and in vitro experiments have suggested that Ikaros and Aiolos cooperate to silence pre-BCR genes and promote IgL gene rearrangement (Ma et al., 2010Ma et al., , 2008 Mandal et al., 2009; Thompson et al., 2007 ). Moreover, comparison of deregulated genes in Aiolos and Ikaros-deficient pre-B cells revealed a $50% overlap (Ferreiros-Vidal et al., 2013). "
    [Show abstract] [Hide abstract] ABSTRACT: The Igκ locus, which is spread over 3Mb of genomic DNA and contains >100 variable (V) genes, serves as an important model system to study long-range chromatin interactions. Here, we will discuss how in developing B cells in the bone marrow the accessibility of individual Vκ segments is controlled by many lineage-specific and ubiquitously expressed transcription factors that act on various cis-regulatory elements, including promoters, enhancers, and insulators. This dynamic control furthermore involves changes in subnuclear localization, histone modification, DNA demethylation, and three-dimensional locus compaction. In pro-B cells, the Igκ locus adopts a poised conformation as full contraction has been achieved and many key transcription factors already occupy the locus. Subsequently, the combined activation of pre-B cell antigen receptor signaling pathways and attenuation of IL-7R signaling in small resting pre-B cells dramatically modifies the transcription factor landscape, supporting the induction of monoallelic Igκ gene rearrangements. Hereby, the intronic and 3' Igκ enhancer elements coordinately focus their activities in the Vκ region toward frequently used Vκ genes. Recent work has drawn attention to the intriguing role of the CTCF-associated regulatory elements Cer and Sis, which are located in the Vκ-Jκ intervening region and control Igκ locus contraction and Vκ repertoire diversity. This involves CTCF-mediated locus insulation, restricting enhancer activity to the Vκ region and suppressing the preferential recombination to proximal Vκ genes. A picture emerges in which the dynamic control of long-range genomic interactions ensures correct timing of Igκ locus recombination and provides appropriate opportunities for individual Vκ gene segments to engage in Vκ-Jκ rearrangement.
    Full-text · Chapter · Dec 2015
    • "It is interesting that some outcomes of pre–BCR-induced differentiation seemed to occur normally amid failed cell cycle exit, yet others did not. For example, several studies have shown that pre–BCR signaling initiates a negative feedback loop, through which transcriptional up-regulation of Irf4 and Ikzf3 (Aiolos) leads to transcriptional silencing of the pre–BCR surrogate light chain components Vpre–B and 5 (Parker et al., 2005; Thompson et al., 2007; Johnson et al., 2008). In Dyrk1a-deficient small pre–B cells, Vpre–B1 and Igll1 (5) transcript levels remained high, despite normal up-regulation of the indicated genotypes were treated with vehicle or 150 mg/kg Palbociclib (oral gavage) for 1 wk after completion of pI:pC treatment. "
    [Show abstract] [Hide abstract] ABSTRACT: Pre-B and pre-T lymphocytes must orchestrate a transition from a highly proliferative state to a quiescent one during development. Cyclin D3 is essential for these cells' proliferation, but little is known about its posttranslational regulation at this stage. Here, we show that the dual specificity tyrosine-regulated kinase 1A (DYRK1A) restrains Cyclin D3 protein levels by phosphorylating T283 to induce its degradation. Loss of DYRK1A activity, via genetic inactivation or pharmacologic inhibition in mice, caused accumulation of Cyclin D3 protein, incomplete repression of E2F-mediated gene transcription, and failure to properly couple cell cycle exit with differentiation. Expression of a nonphosphorylatable Cyclin D3 T283A mutant recapitulated these defects, whereas inhibition of Cyclin D:CDK4/6 mitigated the effects of DYRK1A inhibition or loss. These data uncover a previously unknown role for DYRK1A in lymphopoiesis, and demonstrate how Cyclin D3 protein stability is negatively regulated during exit from the proliferative phases of B and T cell development. © 2015 Thompson et al.
    Full-text · Article · May 2015
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