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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Regulation of Gene Expression Dynamics during Developmental Transitions by the Ikaros Transcription Factor

ABSTRACT: The DNA-binding protein, Ikaros, functions as a potent tumor suppressor and hematopoietic regulator. However, the mechanisms by which Ikaros functions in the nucleus remain largely undefined, due in part to its atypical DNA-binding properties and partnership with the poorly understood Mi-2/NuRD complex. In this study, we extended our analysis of thymocyte development and lymphomagenesis in a mouse strain containing a specific deletion of Ikaros zinc finger 4, which exhibits a select subset of abnormalities observed in Ikaros null mice. By examining thymopoiesis in vivo and in vitro, numerous abnormalities were observed. RNA-sequencing revealed that each developmental stage is characterized by mis-regulation of a limited number of genes, with a strong preference for genes modulated in a stage-specific manner. Strikingly, individual genes and pathways rarely exhibited Ikaros-dependence at all developmental stages. Instead, the most consistent feature of aberrantly expressed genes was a reduced magnitude of expression level change during a developmental transition. These results and others suggest that Ikaros may not be a dedicated and consistent activator or repressor of a defined set of genes. Instead, its primary function may be to support the dynamic range of gene expression changes during developmental transitions via atypical molecular mechanisms that remain undefined. RNA-Seq of T cells at varying developmental stages and T cells expressing activated Notch in WT and Ikzf1-dF4/dF4 mutant backgrounds

ORGANISM(S): Mus musculus

SUBMITTER: Teresita Arenzana

PROVIDER: E-GEOD-67572 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Regulation of Gene Expression Dynamics during Developmental Transitions by the Ikaros Transcription Factor

Project description:The DNA-binding protein, Ikaros, functions as a potent tumor suppressor and hematopoietic regulator. However, the mechanisms by which Ikaros functions in the nucleus remain largely undefined, due in part to its atypical DNA-binding properties and partnership with the poorly understood Mi-2/NuRD complex. In this study, we extended our analysis of thymocyte development and lymphomagenesis in a mouse strain containing a specific deletion of Ikaros zinc finger 4, which exhibits a select subset of abnormalities observed in Ikaros null mice. By examining thymopoiesis in vivo and in vitro, numerous abnormalities were observed. RNA-sequencing revealed that each developmental stage is characterized by mis-regulation of a limited number of genes, with a strong preference for genes modulated in a stage-specific manner. Strikingly, individual genes and pathways rarely exhibited Ikaros-dependence at all developmental stages. Instead, the most consistent feature of aberrantly expressed genes was a reduced magnitude of expression level change during a developmental transition. These results and others suggest that Ikaros may not be a dedicated and consistent activator or repressor of a defined set of genes. Instead, its primary function may be to support the dynamic range of gene expression changes during developmental transitions via atypical molecular mechanisms that remain undefined.

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Selective Functions of Individual Zinc Fingers Within the DNA-Binding Domain of Ikaros (RNA-seq: sorted DP thymocytes)

Project description:The C2H2 zinc finger is the most prevalent DNA-binding motif in the mammalian proteome, with DNA-binding domains usually containing more tandem fingers than are needed for stable sequence-specific DNA recognition. To examine the reason for the frequent presence of multiple zinc fingers, we generated mice lacking finger 1 or finger 4 of the 4-finger DNA-binding domain of Ikaros, a critical regulator of lymphopoiesis and leukemogenesis. Each mutant strain exhibited a specific subset of the phenotypes observed with Ikaros null mice. Of particular relevance, fingers 1 and 4 contributed to distinct stages of B- and T-cell development and finger 4 was selectively required for tumor suppression in thymocytes and in a new model of BCR-ABL+ acute lymphoblastic leukemia. These results, combined with transcriptome profiling (this GEO submission: RNA-Seg of whole thymus from wt and the two ZnF mutants), reveal that different subsets of fingers within multi-finger transcription factors can regulate distinct target genes and biological functions, and they demonstrate that selective mutagenesis can facilitate efforts to elucidate the functions and mechanisms of action of this prevalent class of factors. Ikaros RNA-Seq from double positive thymocytes comparing wt (n=2), Ikaros-ZnF1-/- mutant (n=2) and Ikaros-ZnF4-/- mutant (n=2)

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2013-09-20 | E-GEOD-50156 | biostudies-arrayexpress

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Project description:Heterochromatic position effect variegation (PEV) is the epigenetic disruption of genes expression near the new-formed eu-heterochromatic border. We characterized the inversion In(2)A4, demonstrating cis-acting PEV as well as trans-inactivation of the reporter transgenes on the opposite normal chromosome in combination with the inversion. Euchromatic breakpoint of In(2)A4 inversion was localized at 105 bp region (chr2L:21182214-21182318) of the second exon of the Mcm10 gene, the heterochromatic breakpoint is located at the block of dodecasatellite in 2L pericentromeric heterochromatin. In order to check the effects of heterochromatin on neighbor euchromatic genes and estimate the distance of inactivation spreading, we performed RNA-seq analysis of genes expression in larvae and adults females of genotypes A12/A12 (control) and In(2)A4/In(2)A4. Cis-influence of heterochromatin in the inversion causes not only repression, but also activation of genes, and the effects of heterochromatin are different at different developmental stages. Cis-actions affect only a few genes located near the heterochromatin Comparison of genes expression in wild type and demonstrating PEV larvae and adults in two repeats each

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The SNF2 and RING domain proteins FRG1 and 2 are required for RNA-directed DNA methylation in Arabidopsis [mRNA-Seq]

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