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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Gene expression profiling of Nup98HoxA9 expressing ES cells

ABSTRACT: To know whether the Nup98-HoxA9 affects global gene expression, we performed DNA microarray analysis using the following four clones: two independent Nup98-HoxA9 ES clones (clone#1 and clone#9), parental ES cells, and HoxA9-Ct ES clone. Two independent Nup98-HoxA9 ES clones (clone#1 and clone#9), and HoxA9-Ct ES clone, was compared with parental ES cells (reference sample).

ORGANISM(S): Mus musculus

SUBMITTER: Masahiro Oka

PROVIDER: E-GEOD-67967 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Gene expression profiling of Nup98HoxA9 expressing ES cells

Project description:To know whether the Nup98-HoxA9 affects global gene expression, we performed DNA microarray analysis using the following four clones: two independent Nup98-HoxA9 ES clones (clone#1 and clone#9), parental ES cells, and HoxA9-Ct ES clone.

2016-01-04 | GSE67967 | GEO

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MLL is essential for NUP98-HOXA9-induced leukemia

Project description:Rearrangements involving the NUP98 gene resulting in fusions to several partner genes occur in acute myeloid leukemia and myelodysplastic syndromes. This study demonstrates that the second FG repeat domain of the NUP98 moiety of the NUP98-HOXA9 fusion protein is important for its cell immortalization and leukemogenesis activities. We demonstrate that NUP98-HOXA9 interacts with MLL via this FG repeat domain and that, in the absence of MLL, NUP98-HOXA9-induced cell immortalization and leukemogenesis are severely inhibited. Molecular analyses indicate that MLL is important for the recruitment of NUP98-HOXA9 to the HOXA locus and for NUP98-HOXA9-induced HOXA gene expression. Our data indicate that MLL is crucial for NUP98-HOXA9 leukemia initiation.

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Project description:By performing biotin-mediated chromatin immunoprecipitation followed by next generation sequencing (ChIP-seq) for two different NUP98 fusions, we defined the genome-wide direct binding sites of NUP98-HOXA9 or NUP98-HOXD13. To test whether NUP98 fusions and Mll1 were recruited to the same region of Hox genes promoters, Mll1 ChIP-seq analysis was carried out in murine NUP98-HOXA9 transformed cells using an anti-Mll1n antibody. In agreement with our results showing that NUP98-HOXA9 interacts with MLL1 in NSL/MLL1 complex, Mll1 binding targets significantly overlap with that of NUP98-HOXA9 at promoter region and gene body region. Given that MOF and MLL1 work in concert to modify H4K16ac and H3K4me3 at promoters, we further test whether H3K4me3 and H4K16ac marks are associated with NUP98-HOXA9-bound targets in murine NUP98-HOXA9 transformed cells by anti-H3K4me3 and anti-H4K16ac ChIP-seq. Our data show that both H3K4me3 and H4K16ac mark presents on NUP98-HOXA9 binding targets at promoters, and this is in line with the coordination role in the activities between MOF-mediated H4K16 acetylation and MLL/SET-mediated H3K4 methylation. In summary, our results confirmed that NUP98-HOXA9 and Mll1 are recruited to the same Hox loci, and this recruitment is associated with activating epigenetic marks, supporting the notion of the association between NUP98 fusions and NSL/Mll1 complex, suggesting that the recruitment of NUP98 fusions to the Hox gene loci maybe through MLL1.

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Gene expression changes upon Mll1 knockout in NUP98-HOXA9 transformed murine LSKs

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