Effect of Gfi1 36N variant on genome-wide H3K9 Acetylation patterns
ABSTRACT: ChIP-Seq Analysis of H3K9Ac in pairs of mouse and human samples carrying either the Gfi136S or the GFi136N variants. The objective of the study was to identify the changes in H3K9 acetylation at gene promoters that occur in samples expressing the 36N variant of the Gfi1 gene. 3 pairs of bone-marrow AML samples were obtained from mice where 1 mouse in each pair was homozygous for Gfi136S and 1 heterozygous for Gfi136N, or homozygous for 36N in one case. 2 pairs of AML samples were obtained from human patients were 1 patient was homozygous for Gfi1 36S and one was heterozygous for Gfi1 36N. H3 and H3K9Ac ChIP-Seq was carried out on each sample.
Project description:Genome-wide MeDIP-Sequencing of 23 monozygotic twin pairs (n=46) from Australia discordant for major depressive disorder (MDD). MeDIP-seq of 23 monozygotic twin pairs discordant for major depressive disorder. MZ twin pairs were compared to identify significantly differently methylated sites associated with MDD.
Project description:Growth factor independent-1 (Gfi1) is a zinc finger transcription factor with a SNAG amino-terminal repressor domain and is critically required for normal myelopoesis. Gfi1 is normally expressed in HSCs and induced during differentiation from CMPs to GMPs. Gfi1 loss-of-function mutation in mice and humans induces an arrest during myeloid differentiation and an absolute block to the formation mature neutrophils. This comparative microarray study was initiated to identify microRNAs which are potentially regulated by Gfi1 during granulopoiesis. The Gfi1 null allele from Orkin (deletion of exons 2 and 3) was backcrossed to B6 or Balb/c mice for at least 7 generations. RNA was isolated from low density bone marrow samples from Gfi1+/+ and Gfi1-/- B6 littermates, as well as Gfi1+/+ and Gfi1-/- Balb/c littermates.
Project description:We investigated the RNAPII and γH2AX occupancy genome wide by ChIP-Seq in MLL2 F/F and FC/FC80 MEF cells. We found that a week after MLL2 excision (FC/FC cells), a group of genes present higher levels of γH2AX and RNAPII near the TSS, as compared to the control (F/F cells). H3K4Me1, H3K4M2 and H3K4Me3 levels near the TSS were also studied. There is a total of 52 samples. 3 independent replicates for each experiment were performed. H3, H2AX and IgG ChIPs were used for normalisation or as controls.The experiments were performed using immortalised mouse embryonic fibroblasts (MEF) in which both MLL2 alleles were targeted by the loxp system (F/F cells). Tamoxifen treatment of the F/F cells for 24 hours results in the excision of both MLL2 alleles (FC/FC cells).
Project description:GFI1 is a transcriptional regulator expressed in lymphoid cells, and an "oncorequisite" factor required for development and maintenance of T-lymphoid leukemia. GFI1 deletion causes hypersensitivity to ionizing radiation, for which the molecular mechanism remains unknown. Here, we demonstrate that GFI1 is required in T cells for the regulation of key DNA damage signalling and repair proteins. Specifically, GFI1 interacts with the arginine methyltransferase PRMT1 and its substrates MRE11 and 53BP1. We demonstrate that GFI1 enables PRMT1 to bind and methylate MRE11 and 53BP1, which is necessary for their function in the DNA damage response. Thus, our results provide evidence that GFI1 can adopt non-transcriptional roles, mediating the post-translational modification of proteins involved in DNA repair. These findings have direct implications for treatment responses in tumours overexpressing GFI1 and suggest that GFI1's activity may be a therapeutic target in these malignancies.
Project description:Acute myeloid leukemia (AML) is characterized by accumulation of myeloid blast cells in the bone marrow. Despite all efforts, prognosis of AML patients remains poor, warranting new therapeutic approaches. A single nucleotide polymorphism of growth factor independence 1 (GFI1), a hematopoietic transcription factor, generates a protein with an asparagine (GFI136N) instead of a serine at position 36 (GFI136S), which we have previously reported to be associated with de novo AML in humans. Using knock-in mouse strains, in which the endogenous murine Gfi1 coding sequences are substituted by human GFI136N or GFI136S, we found that GFI136N shortened latency and increased incidence of AML in three different, well-established murine models of AML. On a molecular level, the presence of GFI136N was associated with increased acetylation of histone H3 at lysine 9 (H3K9) at Gfi1 target genes in both murine and human samples, contributing to AML development. Since in GFI136N containing leukemic cells Gfi1 target genes have hyperacetylated H3K9, the treatment strategy currently used with histone deacetylases inhibitors (HDACis) might not be beneficial. We show that treatment with an HDACi impeded growth of murine and human cells homozygous for GFI136S, but had a limited effect on cells expressing GFI136N. In contrast, treatment with a histone acetyltransferase inhibitor (HATi) specifically targeted GFI136N-expressing malignant cells while sparing non-malignant cells. These results establish, as a proof of principle, how epigenetic changes in GFI136N-induced AML can be exploited to treat AML and implicate HATi as a new, more effective potential therapeutic strategy for GFI136N AML patients. Overall design: one sample per genotype has been sequenced
Project description:Using bone marrow cells of GFP:Gfi1 knock in mice, we separated Gfi1-high and Gfi1-low expressing cells in the classical CD11b+, GR1-low monocytic cell fraction. We sorted CD11b+, GR1-low GFP:Gfi1-high and low cells as well as CD11b+, GR1-high granulocytes and CD11b-high, GR1-intermediate cells from Gfi1-knock-out mice for further analysis. We used Affymetrix Mouse Genome 430A 2.0 arrays (GPL8321) The study should determine how Gfi1 regulates the cell fate of monocytes/granulocytes in mice
Project description:Growth factor independent 1 (Gfi1) is a transcriptional repressor originally identified as a common integration site in Moloney-murine-leukemia-virus-induced T-cell leukemia. Gfi1-/- mice display increased apoptosis of developing thymocytes and T lymphopenia; however, there are contradictory reports of the absolute number of Gfi1-/- early T lineage progenitors. We used floxed alleles of Gfi1 crossed to various T-cell-specific Cre transgenes to map the requirements for Gfi1 during lymphoid priming and development. We show that Gfi1 is necessary for the proper formation and function of both lymphoid-primed multipotent progenitors and early T lineage progenitors. These defects correlate with a global inability of Gfi1-/- progenitors to enforce the activation of lymphoid genes including IL7R, Rag1, Flt3 and Notch1. Forced expression of intracellular Notch1 fails to rescue the Gfi1-/- defective lymphoid gene signature or Gfi1-/- T cell development. Instead, activation of Notch1 in Gfi1-/- cells results in a potent synthetic lethal phenotype that is most dramatic in immature thymocytes, but absent in mature peripheral T cells where developmental transcriptional programs are silent. Moreover, we find that the requirement for Gfi1-transcriptional integration of Notch-driven lymphoid transcriptional programs is cell autonomous. Our data indicate that Gfi1 is required at multiple independent stages of lymphoid development. In hematopoietic progenitors Gfi1 is necessary to integrate Notch1 signaling, mediate lymphoid priming, the formation of early T lineage progenitors and subsequent T lineage commitment. Lineage negative cells were purified by magnetic beads from RosaCreERT2 Gfi1 ex4-5 floxed mice and an activated Notch1 signal was introduced using a GFP+ retroviral vector. GFP+ progenitors were FACS-sorted and cultured in semi-solid media for one week to allow sufficient time to to instruct lymphoid differentiation, then replated in 1uM 4-OHT or EtOH control. After an additional 7 days, CFU were disrupted and RNA was isolated for global gene expression using microarrays.
Project description:The zinc finger transcription factor growth-factor-independent-1 (Gfi1) has been involved in various cellular differentiation processes. Gfi1 acts as a transcriptional repressor and splicing control factor upon binding to cognate binding sites in regulatory elements of its target genes. Here, we report that Gfi1-deficient mice develop autoimmunity. Gfi1-deficient peripheral B-cells show a hyperproliferative phenotype, leading to expansion of plasma cells, increased levels of nuclear autoantibodies, and immunoglobulin deposition in brain and kidneys. Dysregulation of multiple transcription factors and cell-cycle control elements may contribute to B-cell dependent autoimmunity. Gfi1 thus emerges as a novel master-regulator restricting autoimmunity. Experiment Overall Design: Splenic B220+CD19+ CD138- B cells of 4 week old Gfi1+/+ and Gfi1-/- mice were isolated and RNA was extracted from one sample per group and microarray analysis was performed.
Project description:The transcriptional repressor Gfi1 promotes Th2 cell development and inhibits Th17 and inducible regulatory T cell differentiation. However, the contribution of Gfi1 to Th1 cell differentiation and Th1-type immune responses has not been clarified yet. We herein demonstrate that Gfi1 inhibits the activation of Th1 program in CD4 T cells. The activated Gfi1-deficient naïve CD4 T cells spontaneously develop into Th1 cells in an IL-12- and IFN-g-independent manner. The increased in vivo Th1-type immune response in Gfi1-deficient mice is confirmed using murine model of nickel allergy and delayed-type hypersensitivity. The expressions of Th1-related transcription factors including Tbx21, Eomes, Atf3, Runx1, Runx2 and Runx3 are increased in Gfi1-deficient activated CD4 T cells. Tbx21, Eomes and Runx2 are identified as candidates for direct target of Gfi1. Gfi1 binds to the Tbx21, Eomes and Runx2 gene loci and represses histone H3K4 methylation levels. Together, these findings establish a novel role of Gfi1 in inhibiting Th1 cell differentiation and Th1-type immune response. Overall design: Examination of Gfi1 binding in WT and Gfi1-dficient CD4 T cells
Project description:Growth factor independent-1 (Gfi1) is a zinc finger transcription factor with a SNAG amino-terminal repressor domain and is critically required for normal myelopoesis. Gfi1 is normally expressed in HSCs and induced during differentiation from CMPs to GMPs. Gfi1 loss-of-function mutation in mice and humans induces an arrest during myeloid differentiation and an absolute block to the formation mature neutrophils. This comparative microarray study was initiated to identify microRNAs which are potentially regulated by Gfi1 during granulopoiesis. Overall design: The Gfi1 null allele from Orkin (deletion of exons 2 and 3) was backcrossed to B6 or Balb/c mice for at least 7 generations. RNA was isolated from low density bone marrow samples from Gfi1+/+ and Gfi1-/- B6 littermates, as well as Gfi1+/+ and Gfi1-/- Balb/c littermates.