The Tumor Suppressor Ikaros Shapes the Repertoire of Notch Target Genes in T Cells

Abstract

The Notch signaling pathway is activated in many cell types, but its effects are cell type- and stage-specific. In the immune system, Notch activity is required for the differentiation of T cell progenitors, but it is reduced in more mature thymocytes, in which Notch is oncogenic. Studies based on single-gene models have suggested that the tumor suppressor protein Ikaros plays an important role in repressing the transcription of Notch target genes. We used genome-wide analyses, including chromatin immunoprecipitation sequencing, to identify genes controlled by Notch and Ikaros in gain- and loss-of-function experiments. We found that Ikaros bound to and directly repressed the expression of most genes that are activated by Notch. Specific deletion of Ikaros in thymocytes led to the persistent expression of Notch target genes that are essential for T cell maturation, as well as the rapid development of T cell leukemias in mice. Expression of Notch target genes that are normally silent in T cells, but are activated by Notch in other cell types, occurred in T cells of mice genetically deficient in Ikaros. We propose that Ikaros shapes the timing and repertoire of the Notch transcriptional response in T cells through widespread targeting of elements adjacent to Notch regulatory sequences. These results provide a molecular framework for understanding the regulation of tissue-specific and tumor-related Notch responses.

Site-specific methylation of Notch1 controls the amplitude and duration of the Notch1 response

“…In cells expressing a Bio-NICD, we detected NICD at several enhancer sites of known Notch target genes, including Ptcra, Gm266, Nrarp, CD25, and Hes1 ( fig. S3B), which agrees with previously reported ChIP-sequencing data (28,29). In cells expressing CARM1, we detected CARM1 at NICD-bound enhancer sites of several Notch target genes, of which the expression was impaired by CARM1 knockdown ( NICD protein stability is regulated by CARM1-dependent methylation Phosphorylation (4-6), ubiquitination (8)(9)(10)(11), and acetylation (7) influence the stability of NICD; therefore, we investigated whether methylation also affected its stability.…”

The Notch Signaling Pathway Controls Short-Lived Effector CD8+ T Cell Differentiation but Is Dispensable for Memory Generation

“…Indeed, in absence of Notch signaling, Ag-specific CD8 + effectors show a severe reduction in Further studies are required to determine whether Cd25 is a direct Notch target gene in CD8 + T cells, a likely possibility because it has been reported that the NICD can be recruited to the Cd25 promoter in double-negative thymocytes (44) and to the Cd25 enhancer in leukemic T cells (10). The maintenance of CD25 expression on a subset of effector CD8 + T cells is required for the generation of SLECs, and it was proposed, by us and others, that this was necessary to allow for the proper upregulation of Blimp-1 (3, 4), a key transcriptional repressor controlling SLEC differentiation (5,6).…”

“…HES family members are common targets of Notch signaling in many tissues, whereas other target genes are tissue specific. Furthermore, a broad number of genes can be regulated by Notch, as shown using genome-wide methodologies (8)(9)(10)(11).…”

Cytokines, Transcription Factors, and the Initiation of T-Cell Development

“…Signaling through the newly expressed pre-TCR not only disrupts the quiescence of DN3a cells, but also rapidly shuts off the expression of Notch target genes in an IKAROS-dependent manner, and cells proceed to phase 3 (Chari and Winandy 2008; Kleinmann et al 2008; Geimer Le Lay et al 2014). The burst of proliferation that takes place upon β-selection amplifies clones of cells with productive TCRβ rearrangements to maximize the chance for productive TCR diversity.…”