Regulation of Erythro-Megakaryocytic Lineage Divergence By the Transcriptional Repressor Gfi1b and Its Rgs Targets

Blood ◽  
2015 ◽  
Vol 126 (23) ◽  
pp. 2385-2385
Author(s):  
Ananya Sengupta ◽  
Ghanshyam Upadhyay ◽  
Sayani Sen ◽  
Shireen Saleque
Keyword(s):  
Gene Expression ◽  
Transcription Factors ◽  
Target Genes ◽  
Transcriptional Repressor ◽  
Erythroid Differentiation ◽  
Mapk Signaling ◽  
Erythroid Cells ◽  
Hematopoietic Progenitors ◽  
Lineage Divergence

Abstract Introduction: Appropriate diversification of hematopoietic lineages from multi-potent progenitors is essential for normal development and health. The molecular programs that govern the divergence of erythroid and megakaryocytic lineages remain incompletely defined. Gene targeting experiments have shown the transcriptional repressor Gfi1b (Growth factor independence 1b) to be essential for erythro-megakaryocyte lineage development. Transcriptional repression of Gfi1b target genes is mediated by the cofactors LSD (lysine demethylase) 1 and Rcor (CoREST) 1. To understand the mechanism of Gfi1b action, its target genes were identified by chromatin immunoprecipitation (ChIP on Chip) screens. Three members of the Rgs (Regulator of G protein signaling) family were prominently represented in this target gene pool. In this study we present the role of Rgs18, a GTPase activating protein (GAP), in modulating erythro-megakaryocytic lineage divergence in hematopoietic progenitors. The results presented below demonstrate Rgs18 as a key arbitrator of this process in murine and human contexts. Approach: Following identification of Rgs18 as a potential Gfi1b and LSD1 target, its regulation by these factors was ascertained in erythro-megakaryocytic cells. Subsequently, to interrogate the role of Rgs18 in erythro-megakaryocyte differentiation, cDNA and shRNA mediated manipulations were performed in primary hematopoietic progenitors and cell lines, and the resulting phenotypes were analyzed. Finally, to trace the underlying mechanistic alterations responsible for these phenotypes the status of two branches of the MAPK (mitogen activated protein kinase) pathway and gene expression patterns of the mutually antagonistic transcription factors Fli1 (Friend leukemia integration [site] 1/Klf1 (Krupple like factor 1) were determined in Rgs18 manipulated cells. Result: Rgs18 expression was found to be low in immature megakaryoblasts in keeping with strong Gfi1b and LSD1 expression, but was reciprocally upregulated in mature megakaryocytes following declining Gfi1b and LSD1 levels in cells and on the rgs18 promoter. In contrast, expression of Gfi1b was strong in immature erythroid cells and increased further in mature cells, while Rgs18 expression which was modest in immature erythroid cells exhibited a reciprocal decline during maturation. Manipulation of Rgs18 expression in murine hematopoietic progenitors and a bipotential human cell line produced divergent outcomes, with expression augmenting megakaryocytic, and potently suppressing erythroid differentiation and vice versa. These phenotypes resulted from differential impact of Rgs18 expression on the P38 and ERK branches of MAPK signaling in the erythroid and megakaryocytic lineages. Repercussions of these signaling changes impacted relative expression of the mutually antagonistic transcription factors Fli1 and Klf1 and were compensated by ectopic Fli1 expression demonstrating activity of this transcription factor downstream of Rgs18. Conclusion: These results identify Rgs18 as a critical downstream effector of Gfi1b and an upstream regulator of MAPK signaling and Klf1/Fli1 gene expression. Sustained Gfi1b expression during erythroid differentiation represses Rgs18 and limits megakaryocytic gene expression. However during progression of megakaryocytic differentiation, declining Gfi1b levels results in robust expression of Rgs18 and lineage progression. Overall, this study provides new perspectives on lineage determination by highlighting multi-tier interactions between transcriptional and signaling networks in orchestrating hematopoietic lineage divergence. These insights could exemplify generic mechanisms exhibited by this large family of signal modulators in mediating lineage diversification in various contexts. Disclosures No relevant conflicts of interest to declare.

An Unexpected Role for Ribonuclease Inhibitor (RNH1) in Erythropoiesis

Blood ◽  
2014 ◽  
Vol 124 (21) ◽  
pp. 244-244
Author(s):  
Ramanjaneyulu Allam ◽  
Vijaykumar Chennupati ◽  
Diogo F.T. Veiga ◽  
Kendle M Maslowski ◽  
Aubry Tardivel ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcription Factors ◽  
Progenitor Cells ◽  
Biological Function ◽  
Erythroid Differentiation ◽  
Ribosomal Genes ◽  
Erythroid Cells ◽  
Ribonuclease Inhibitor ◽  
Erythroid Maturation ◽  
Ribosomal Complex

Abstract Ribonuclease Inhibitor (RNH1) is a ubiquitously expressed leucine-rich repeat protein. The human RNH1 gene evolved via gene duplication and is conserved among mammalian species. RNH1 binds to and inhibits pancreatic type ribonucleases. Further, RNH1 contains numerous cysteine residues whose sulfhydryl groups might play key structural roles and protect from oxidative damage (Dickson et al Prog. Nucleic Acid Res. Mol. Biol 2005). Despite of all these observations, the precise biological role of RNH1in vivo remains unexplored. Here, we describe an essential role for Rnh1 in the regulation of erythropoiesis by controlling erythroid differentiation. To understand the biological function of Rnh1, Rnh1-deficient (Rnh1-/-) mice were generated. Rnh1-/- embryos die between embryonic days E8.5 to E10 due to severe decrease in erythroid cells. Similar percentages of c-Kit+CD41+ cells (Hematopoietic stem/progenitor cells) were present in Rnh1-/- yolk sacs compared to control genotypes, however differentiation of mature erythroid cells was impaired. Rnh1 is expressed in erythroid cells and its expression coincides with the site of primitive erythropoiesis in the yolk sac. Gene expression studies revealed that levels of hematopoietic transcription factors (TF) in Rnh1-deficient yolk sacs were normal, but their target genes were down-regulated. These results indicate that a post-transcriptional mechanism that affects TF gene function. Supporting this, protein levels of the erythroid transcription factor GATA1 and PPARγ, previously shown to control the proliferation and differentiation of erythroid progenitors, were selectively impaired. Whereas myeloid transcription factors C/EBPa and C/EBPb were not affected in Rnh1-/- embryos, suggesting that Rnh1 deficiency specifically affects the translation of erythroid transcription factors. At the molecular level, using the human erythroid K562 cell line, we show that RNH1 is recruited to the ribosome complex and binds to the ribosomal proteins. RNH1-deficiency decreased polysome formation and conversely its overexpression increased polysome formation. Increased expression of RNH1 also increased globin gene expression in K562 cells. These results suggest that RNH1 associates with ribosomes and regulates the translation of erythroid-specific genes, which are necessary for erythroid differentiation. Furthermore, Rnh1 haploinsufficiency leads to decreased erythropoiesis in the spleen of adult mice. Ribosomal haploinsufficiency in several ribosomal genes is known to impair ribosome function and cause macrocytic anemia in Diamond–Blackfan anemia (DBA), a congenital bone marrow failure syndrome, and the 5q- syndrome, a subtype of myelodysplastic syndrome (Narla et al Int. J. Hematol 2011). Recently it has been shown that ribosomal haploinsufficiency can specifically cause a decrease in GATA1 mRNA translation (Ludwig et al Nature Med 2014). Similar to these ribosomal genes, we demonstrate that Rnh1 associates with ribosomes and its deficiency impairs the translation of Gata1 and other erythroid-specific transcription factors, which leads to arrest in erythroid maturation. Collectively our results unravel the important biological function of Rnh1 in the regulation of erythropoiesis, and point to novel therapeutic targets for disorders of erythropoiesis involving ribosomal defects. Summary Figure: RNH1 is recruited to ribosomal complex and is involved in translation of erythroid specific transcription factors (TF) e.g.GATA1. These TFs are necessary for differentiation of progenitor cells in to erythroid cells. RNH1 deficiency impairs the translation of GATA1 and other erythroid-specific transcription factors, which leads to arrest in erythroid maturation. Summary Figure:. RNH1 is recruited to ribosomal complex and is involved in translation of erythroid specific transcription factors (TF) e.g.GATA1. These TFs are necessary for differentiation of progenitor cells in to erythroid cells. RNH1 deficiency impairs the translation of GATA1 and other erythroid-specific transcription factors, which leads to arrest in erythroid maturation. Summary Figure: RNH1 is recruited to ribosomal complex and is involved in translation of erythroid specific transcription factors (TF) e.g.GATA1. These TFs are necessary for differentiation of progenitor cells in to erythroid cells. RNH1 deficiency impairs the translation of GATA1 and other erythroid-specific transcription factors, which leads to arrest in erythroid maturation. Disclosures No relevant conflicts of interest to declare.

scholarly journals ETO-2 Associates with SCL in Erythroid Cells and Megakaryocytes and Provides Repressor Functions in Erythropoiesis

2005 ◽  
Vol 25 (23) ◽  
pp. 10235-10250 ◽  
Author(s):  
Anna H. Schuh ◽  
Alex J. Tipping ◽  
Allison J. Clark ◽  
Isla Hamlett ◽  
Boris Guyot ◽  
...  
Keyword(s):  
Gene Expression ◽  
Target Genes ◽  
Protein Complexes ◽  
Fetal Liver ◽  
Regulation Of Gene Expression ◽  
Erythroid Differentiation ◽  
Cell Types ◽  
Erythroid Cells ◽  
Proteomic Approach ◽  
Endogenous Proteins

ABSTRACT Lineage specification and cellular maturation require coordinated regulation of gene expression programs. In large part, this is dependent on the activator and repressor functions of protein complexes associated with tissue-specific transcriptional regulators. In this study, we have used a proteomic approach to characterize multiprotein complexes containing the key hematopoietic regulator SCL in erythroid and megakaryocytic cell lines. One of the novel SCL-interacting proteins identified in both cell types is the transcriptional corepressor ETO-2. Interaction between endogenous proteins was confirmed in primary cells. We then showed that SCL complexes are shared but also significantly differ in the two cell types. Importantly, SCL/ETO-2 interacts with another corepressor, Gfi-1b, in red cells but not megakaryocytes. The SCL/ETO-2/Gfi-1b association is lost during erythroid differentiation of primary fetal liver cells. Genetic studies of erythroid cells show that ETO-2 exerts a repressor effect on SCL target genes. We suggest that, through its association with SCL, ETO-2 represses gene expression in the early stages of erythroid differentiation and that alleviation/modulation of the repressive state is then required for expression of genes necessary for terminal erythroid maturation to proceed.

Elucidation of the Role of LMO2 (LIM-only protein 2) in Erythroid Cells

Blood ◽  
2012 ◽  
Vol 120 (21) ◽  
pp. 3443-3443
Author(s):  
AI Inoue ◽  
Tohru Fujiwara ◽  
Yoko Okitsu ◽  
Noriko Fukuhara ◽  
Yasushi Onishi ◽  
...  
Keyword(s):  
Dna Binding ◽  
Cord Blood ◽  
Western Blotting ◽  
Target Genes ◽  
K562 Cells ◽  
Erythroid Differentiation ◽  
Dependent Manner ◽  
Erythroid Cells ◽  
In Erythroid Cells

Abstract Abstract 3443 Background: Developmental control mechanisms often utilize multimeric complexes containing transcription factors, coregulators, and additional non-DNA binding components. It is challenging to ascertain how such components contribute to complex function at endogenous loci. LMO2 (LIM-only protein 2) is a non-DNA binding transcriptional coregulator, and is an important regulator of hematopoietic stem cell development and erythropoiesis, as mice lacking this gene show defects in blood formation as well as fetal erythropoiesis (Warren et al. Cell. 1994). In the context of erythropoiesis, LMO2 has been demonstrated to be a part of multimetric complex, including master regulators of hematopoiesis (GATA-1 and SCL/TAL1), chromatin looping factor LDB1 and hematopoietic corepressor ETO2 (referred as GATA-SCL/TAL1 complex). As LMO2 controls hematopoiesis, its dysregulation is leukemogenic, and its influence on GATA factor function is still not evident, we investigated here the transcriptional regulatory mechanism via LMO2 in erythroid cells. Methods: For LMO2 knockdown, anti-LMO2 siRNA (Thermo Scientific Dharmacon) and pGIPZ lentiviral shRNAmir system (Open Biosystems) were used. Western blotting and Quantitative ChIP analysis were performed using antibodies for GATA-1, LMO2 (abcam), GATA-2, TAL1 and LDB1 (Santa Cruz). To obtain human primary erythroblasts, CD34-positive cells isolated from cord blood were induced in liquid suspension culture. For transcription profiling, human whole expression array was used (Agilent), and the data was analyzed with GeneSpring GX software. To induce erythroid differentiation of K562 cells, hemin was treated at a concentration of 30 uM for 24h. Results: siRNA-mediated LMO2 knockdown in hemin-treated K562 cells results in significantly decreased ratio of benzidine-staining positive cells, suggesting that LMO2 has an important role in the erythroid differentiation of K562 cells. Next, we conducted microarray analysis to characterize LMO2 target gene ensemble in K562 cells. In contrast to the predominantly repressive role of LMO2 in murine G1E-ER-GATA-1 cells (Fujiwara et al. PNAS. 2010), the analyses (n = 2) demonstrated that 177 and 78 genes were upregulated and downregulated (>1.5-fold), respectively, in the LMO2-knockdowned K562 cells. Downregulated gene ensemble contained prototypical erythroid genes such as HBB and SLC4A1 (encodes erythrocyte membrane protein band 3). To test what percentages of LMO2-regulated genes could be direct target genes of GATA-1 in K562 cells, we merged the microarray results with ChIP-seq profile (n= 5,749, Fujiwara et al. Mol Cell. 2009), and demonstrated that 26.4% and 23.1% of upregulated and downregulated genes, respectively, contained significant GATA-1 peaks in their loci. Furthermore, whereas LMO2 knockdown in K562 cells did not affect the expression of GATA-1, GATA-2 and SCL/TAL1 based on quantitative RT-PCR as well as Western blotting, the knockdown resulted in the significantly decreased chromatin occupancy of GATA-1, GATA-2, SCL/TAL1 and LDB1 at beta-globin locus control region and SLC4A1 locus. We subsequently analyzed the consequences of LMO2 knockdown in primary erythroblasts. Endogeneous LMO2 expression was upregulated along with the differentiation of cord blood cell-derived primary erythroblasts. shRNA-mediated knockdown of LMO2 in primary erythroblasts resulted in significant downregulation of HBB, HBA and SLC4A1. Conclusion: Our results suggest that LMO2 contributes to the expression of GATA-1 target genes in a context-dependent manner, through modulating the assembly of the components of GATA-SCL/TAL1 complex at endogeneous loci. Disclosures: No relevant conflicts of interest to declare.

scholarly journals KLF3 Represses the Inflammatory Response in Macrophages

Blood ◽  
2020 ◽  
Vol 136 (Supplement 1) ◽  
pp. 36-36
Author(s):  
Jessica M Salmon ◽  
Casie Leigh Reed ◽  
Maddyson Bender ◽  
Helen Lorraine Mitchell ◽  
Vanessa Fox ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcription Factor ◽  
Transcription Factors ◽  
Time Course ◽  
Target Genes ◽  
Wild Type ◽  
Cell Counts ◽  
Inflammatory Macrophages

Krüppel-like factors (KLFs) are a family of transcription factors that play essential roles in the development and differentiation of the hematopoietic system. These transcription factors possess highly conserved C-terminal zinc-finger motifs, which enable their binding to GC-rich, or CACC-box, motifs in promoter and enhancer regions of target genes. The N-terminal domains of these proteins are more varied and mediate the recruitment of various co-factors, which can form a complex with either activator or repressor function. Acting primarily as a gene repressor through its recruitment of CtBPs and histone deacetylases (HDACs) [1], we have recently shown that KLF3 competes with KLF1 bound sites in the genome to repress gene expression during erythropoiesis [2]. However, the function of Klf3 in other lineages has been less well studied. This widely expressed transcription factor has reported roles in the differentiation of marginal zone B cells, eosinophil function and inflammation [3]. We utilised the Klf3-null mouse model [4] to more closely examine the role of Klf3 in innate inflammatory cells. These mice exhibit elevated white cell counts, including monocytes (Figure 1A), and inflammation of the skin. Conditional knockout of Klf4 in myeloid cells leads to a deficiency of inflammatory macrophages [5]. To test our hypothesis KLF3 normally represses inflammation, perhaps by antagonising the action of KLF4, bone-marrow derived macrophages (BMDM) were generated from wild-type or Klf3-null mice and stimulated with the bacterial toxin lipopolysaccharide (LPS). In wild type BMDM, LPS induces Klf3 gene expression and activation then delayed repression of target genes such as Lgals3 (galectin-3) over a 21 hour time course (Figure 1B). Quantitative real-time PCR and mRNA-seq of WT v Klf3-null macrophages identified ~100 differentially expressed genes involved in proliferation, macrophage activation and inflammation. We transduced the monocyte cell line, RAW264.7 (that expresses Klf4, Klf3 and Klf2), with a retroviral vector expressing a tamoxifen-inducible KLF3-ER fusion construct. KLF3 induced cell cycle arrest and macrophage differentiation. We will report on KLF3-induced gene expression changes (repression and activation), and ChIP-seq for KLF3, in RAW cells. The results shed light on the mechanism by which KLF3 normally represses monocyte/macrophage responses to infection. This study highlights the importance of key transcriptional regulators that tightly control gene expression during inflammation. Loss of Klf3 leads to alterations in this process, resulting in hyper-activation of inflammatory macrophages, increased white cell counts and inflammation of the skin. A greater knowledge of the inflammatory process and how it is regulated is important for our understanding of acute infection and inflammatory disease. Further studies are planned to investigate the role of the KLF3 transcription factor in response to inflammation in vivo. References: 1. Pearson, R., et al., Kruppel-like transcription factors: A functional family. Int J Biochem Cell Biol, 2007. W2. Ilsley, M.D., et al., Kruppel-like factors compete for promoters and enhancers to fine-tune transcription. Nucleic Acids Res, 2017. 45(11): p. 6572-6588. W3. Knights, A.J., et al., Kruppel-like factor 3 (KLF3) suppresses NF-kappaB-driven inflammation in mice. J Biol Chem, 2020. 295(18): p. 6080-6091. W4. Sue, N., et al., Targeted disruption of the basic Kruppel-like factor gene (Klf3) reveals a role in adipogenesis. Mol Cell Biol, 2008. 28(12): p. 3967-78. W5. Alder, J.K., et al., Kruppel-like factor 4 is essential for inflammatory monocyte differentiation in vivo. J Immunol, 2008. 180(8): p. 5645-52. Figure 1: Elevated WCC (A) and inflammatory markers (B) in BMDM after LPS stimulation. 1. Total WCC in adult mice (3-6 months old) of the indicated genotypes. There is a statistically significant increase in the WCC in Klf3-/- v wild type mice (P<0.001 by student's t test). B. Time course (hours) after LPS stimulation of confluent BMDM. Klf3 is induced 3-fold by LPS and KLF3-target genes such as Lgals3 are not fully repressed by 21 hours in knockout mice. Figure 1 Disclosures Perkins: Novartis Oncology: Honoraria, Membership on an entity's Board of Directors or advisory committees.

scholarly journals Expression analysis of miRNAs and their putative target genes confirm a preponderant role of transcription factors in the early response of oil palm plants to salinity stress

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Fernanda Ferreira Salgado ◽  
Letícia Rios Vieira ◽  
Vivianny Nayse Belo Silva ◽  
André Pereira Leão ◽  
Priscila Grynberg ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcription Factors ◽  
Salinity Stress ◽  
Oil Palm ◽  
Functional Annotation ◽  
Target Genes ◽  
Early Response ◽  
Differentially Expressed ◽  
Putative Target

Abstract Background Several mechanisms regulating gene expression contribute to restore and reestablish cellular homeostasis so that plants can adapt and survive in adverse situations. MicroRNAs (miRNAs) play roles important in the transcriptional and post-transcriptional regulation of gene expression, emerging as a regulatory molecule key in the responses to plant stress, such as cold, heat, drought, and salt. This work is a comprehensive and large-scale miRNA analysis performed to characterize the miRNA population present in oil palm (Elaeis guineensis Jacq.) exposed to a high level of salt stress, to identify miRNA-putative target genes in the oil palm genome, and to perform an in silico comparison of the expression profile of the miRNAs and their putative target genes. Results A group of 79 miRNAs was found in oil palm, been 52 known miRNAs and 27 new ones. The known miRNAs found belonged to 28 families. Those miRNAs led to 229 distinct miRNA-putative target genes identified in the genome of oil palm. miRNAs and putative target genes differentially expressed under salinity stress were then selected for functional annotation analysis. The regulation of transcription, DNA-templated, and the oxidation-reduction process were the biological processes with the highest number of hits to the putative target genes, while protein binding and DNA binding were the molecular functions with the highest number of hits. Finally, the nucleus was the cellular component with the highest number of hits. The functional annotation of the putative target genes differentially expressed under salinity stress showed several ones coding for transcription factors which have already proven able to result in tolerance to salinity stress by overexpression or knockout in other plant species. Conclusions Our findings provide new insights into the early response of young oil palm plants to salinity stress and confirm an expected preponderant role of transcription factors - such as NF-YA3, HOX32, and GRF1 - in this response. Besides, it points out potential salt-responsive miRNAs and miRNA-putative target genes that one can utilize to develop oil palm plants tolerant to salinity stress.

Genome-Wide Chromatin Immunopreciptiation and Gene Expression Analysis Indicates That MMSET Is a Transcriptional Repressor in Vivo

Blood ◽  
2008 ◽  
Vol 112 (11) ◽  
pp. 627-627
Author(s):  
Dong-Joon Min ◽  
Julia Meyer ◽  
Eva Martinez-Garcia ◽  
Josh Lauring ◽  
Jonathan D. Licht
Keyword(s):  
Gene Expression ◽  
Cell Cycle ◽  
Multiple Myeloma ◽  
Cell Line ◽  
Signaling Pathway ◽  
Target Genes ◽  
Transcriptional Repressor ◽  
Low Levels

Abstract Multiple myeloma (MM) is a malignancy of plasma cells characterized by frequent chromosomal translocations of the immunoglobulin heavy chain (IgH) locus. The multiple myeloma SET domain (MMSET) gene is a recurrent chromosomal partner in the t(4;14) translocation, and MMSET levels are elevated in these patients relative to other myeloma cases and normal cells. Previously, we showed that MMSET is a histone methyltransferase with specific activity for lysine 20 on histone H4 and acts as a transcriptional repressor when tethered to a model target gene. To reveal the function of MMSET in t(4;14) MM in vivo, we identified MMSET target genes in the KMS11 t(4;14) MM cell line. Chromatin from these cells was subjected to immunoprecipitation with a polyclonal anti-MMSET antibody in biological replicate, amplified by ligation-mediated PCR and hybridized to NimbleGen 2.7kB promoter arrays, which represent 24,659 human promoters. Data analysis using the MaxFour algorithm ranked putative binding sites based upon intensities of 4 consecutive probes. The top 2000 promoters identified from each experiment were combined to yield a list of 1,412 putative MMSET target genes. This list was analyzed using the DAVID program (david.abcc.ncifcrf.gov/). Genes bound by MMSET includes those implicated in antigen processing and presentation (p<8.7×10-4), cell cycle (p<2.2×10-3), the p53 signaling pathway (p<0.03) apoptosis (p<1.6×10-6) and DNA repair (p<3.3×10-4) Among genes bound by MMSET were XBP1, IRF2, and BCL6, all important transcription factors regulating B cell development. Real-time quantitative PCR validated MMSET binding in 6/6 promoters tested so far. To investigate the role of MMSET in transcriptional regulation, we profiled gene expression in KMS11 cells using Illumina arrays to determine the expression of MMSET bound genes. Nearly 50% of genes bound by MMSET had very low levels of expression (≤100, Range on arrays 10–18,000) while only 13% of genes bound by MMSET were expressed at high levels (>1000). This supports the notion that MMSET represses target genes in vivo. Functional annotation of genes bound by MMSET and expressed at low levels showed over-representation of genes implicated in toll-like receptor signaling pathway (p<2.8×10-3), cytokine-signaling (p<3.3×10-3) and JAK2/STAT signaling (p<0.08), transmembrane receptor function (p<4×10-8), and apoptosis (p<0.01), while those bound yet expressed at high levels were implicated in oxidative phosphorylation (p<3.9×10-4) and protein synthesis (p<4.1×10-6). The effects of MMSET on gene expression were further investigated using KMS11KO cells in which the rearranged MMSET allele was ablated by homologous recombination. RNA from KMS11 and KMS11KO cells was profiled by Illumina arrays and genes showing a significant change in gene expression were determined by significance analysis of microarray (SAM) testing with 1% of false discovery rate. Among the 720 genes bound by MMSET and expressed at a level of >100 in the wild-type KMS11 cells, 35 genes were up-regulated and 20 genes were down-regulated (>1.5 fold) in the KMS11KO cell line. Among the 692 genes bound by MMSET and expressed at a level of ≤100, 9 genes were up-regulated in KMS11KO cells. The up-regulated genes (presumably bound and repressed by MMSET) were categorized in cytokine receptor (p<0.02) and JAK2/STAT signaling pathway (p<0.05), nucleosome assembly (p<6×10-4), apoptosis (p<0.01), and cell differentiation (p<0.05). Collectively these data suggest that MMSET may interfere with signal transduction, chromatin modulation and apoptosis pathways involved in the terminal differentiation of the plasma cell. Intriguingly MMSET also bound and was associated with repression of RB1 and RBL2 suggesting a role of MMSET in cell cycle control. Chromatin immunoprecipitation analysis of a MMSET bound gene (ARHGAP25) revealed that MMSET binding was correlated with increased tri-methylation of H4K20, a repression-associated chromatin mark. MMSET binding of this promoter was decreased but still detectable in the KMS11KO cells. Collectively these data suggest that MMSET binds and represses many target genes in vivo. However MMSET could still bind to genes expressed at a high level and MMSET ablation was associated with activation of some MMSET target genes, suggesting that its role in gene regulation may be complex and potentially gene-specific.

DNA methylation events in transcription factors and gene expression changes in colon cancer

Epigenomics ◽  
2020 ◽  
Vol 12 (18) ◽  
pp. 1593-1610
Author(s):  
Anna Díez-Villanueva ◽  
Rebeca Sanz-Pamplona ◽  
Robert Carreras-Torres ◽  
Ferran Moratalla-Navarro ◽  
M Henar Alonso ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Colon Cancer ◽  
Transcription Factors ◽  
Target Genes ◽  
Linear Models ◽  
Cpg Islands ◽  
Promoter Regions ◽  
Differential Gene

Aim: Gain insight about the role of DNA methylation in the malignant growth of colon cancer. Patients & methods: Methylation and gene expression from 90 adjacent-tumor paired tissues and 48 healthy tissues were analyzed. Tumor genes whose change in expression was explained by changes in methylation were identified using linear models adjusted for tumor stromal content. Results: No differences in methylation were found between adjacent and healthy tissues, but clear differences were found between adjacent and tumor samples. We identified hypermethylated CpG islands located in promoter regions that drive differential gene expression of transcription factors and their target genes. Conclusion: Changes in methylation of a few genes provoke important changes in gene expression, by expanding the signal through transcription activation/repression.

scholarly journals FgHtf1 Regulates Global Gene Expression towards Aerial Mycelium and Conidiophore Formation in the Cereal Fungal Pathogen Fusarium graminearum

2020 ◽  
Vol 86 (9) ◽  
Author(s):  
Gaili Fan ◽  
Huawei Zheng ◽  
Kai Zhang ◽  
Veena Devi Ganeshan ◽  
Stephen Obol Opiyo ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcription Factors ◽  
Gene Family ◽  
Fusarium Graminearum ◽  
Target Genes ◽  
Homeobox Gene ◽  
Global Gene Expression ◽  
Binding Motifs ◽  
Content Type ◽  
Aerial Growth

ABSTRACT The homeobox gene family of transcription factors (HTF) controls many developmental pathways and physiological processes in eukaryotes. We previously showed that a conserved HTF in the plant-pathogenic fungus Fusarium graminearum, Htf1 (FgHtf1), regulates conidium morphology in that organism. This study investigated the mechanism of FgHtf1-mediated regulation and identified putative FgHtf1 target genes by a chromatin immunoprecipitation assay combined with parallel DNA sequencing (ChIP-seq) and RNA sequencing. A total of 186 potential binding peaks, including 142 genes directly regulated by FgHtf1, were identified. Subsequent motif prediction analysis identified two DNA-binding motifs, TAAT and CTTGT. Among the FgHtf1 target genes were FgHTF1 itself and several important conidiation-related genes (e.g., FgCON7), the chitin synthase pathway genes, and the aurofusarin biosynthetic pathway genes. In addition, FgHtf1 may regulate the cAMP-protein kinase A (PKA)-Msn2/4 and Ca2+-calcineurin-Crz1 pathways. Taken together, these results suggest that, in addition to autoregulation, FgHtf1 also controls global gene expression and promotes a shift to aerial growth and conidiation in F. graminearum by activation of FgCON7 or other conidiation-related genes. IMPORTANCE The homeobox gene family of transcription factors is known to be involved in the development and conidiation of filamentous fungi. However, the regulatory mechanisms and downstream targets of homeobox genes remain unclear. FgHtf1 is a homeobox transcription factor that is required for phialide development and conidiogenesis in the plant pathogen F. graminearum. In this study, we identified FgHtf1-controlled target genes and binding motifs. We found that, besides autoregulation, FgHtf1 also controls global gene expression and promotes conidiation in F. graminearum by activation of genes necessary for aerial growth, FgCON7, and other conidiation-related genes.

Resveratrol Modulation of Gene Expression: The Role of Transcription Factors

2005 ◽  
pp. 168-191
Author(s):  
Fulvio Della Ragione ◽  
Valeria Cucciolla ◽  
Adriana Borriello ◽  
Vincenzo Zappia
Keyword(s):  
Gene Expression ◽  
Transcription Factors ◽  
Modulation Of Gene Expression

Role of the Hypoxia-Inducible Factor Pathway in Normal and Osteoarthritic Meniscus and in Mice after Destabilization of the Medial Meniscus

Cartilage ◽  
2020 ◽  
pp. 194760352095814
Author(s):  
Austin V. Stone ◽  
Richard F. Loeser ◽  
Michael F. Callahan ◽  
Margaret A. McNulty ◽  
David L. Long ◽  
...  
Keyword(s):  
Gene Expression ◽  
Target Genes ◽  
Medial Meniscus ◽  
Transforming Growth Factor ◽  
Hypoxia Inducible Factor ◽  
Early Time ◽  
Wild Type ◽  
Inflammatory Stimuli ◽  
Hif Pathway

Objective Meniscus injury and the hypoxia-inducible factor (HIF) pathway are independently linked to osteoarthritis pathogenesis, but the role of the meniscus HIF pathway remains unclear. We sought to identify and evaluate HIF pathway response in normal and osteoarthritic meniscus and to examine the effects of Epas1 (HIF-2α) insufficiency in mice on early osteoarthritis development. Methods Normal and osteoarthritic human meniscus specimens were obtained and used for immunohistochemical evaluation and cell culture studies for the HIF pathway. Meniscus cells were treated with pro-inflammatory stimuli, including interleukins (IL)-1β, IL-6, transforming growth factor (TGF)-α, and fibronectin fragments (FnF). Target genes were also evaluated with HIF-1α and HIF-2α (Epas1) overexpression and knockdown. Wild-type ( n = 36) and Epas1+/− ( n = 30) heterozygous mice underwent destabilization of the medial meniscus (DMM) surgery and were evaluated at 2 and 4 weeks postoperatively for osteoarthritis development using histology. Results HIF-1α and HIF-2α immunostaining and gene expression did not differ between normal and osteoarthritic meniscus. While pro-inflammatory stimulation significantly increased both catabolic and anabolic gene expression in the meniscus, HIF-1α and Epas1 expression levels were not significantly altered. Epas1 overexpression significantly increased Col2a1 expression. Both wild-type and Epas1+/− mice developed osteoarthritis following DMM surgery. There were no significant differences between genotypes at either time point. Conclusion The HIF pathway is likely not responsible for osteoarthritic changes in the human meniscus. Additionally, Epas1 insufficiency does not protect against osteoarthritis development in the mouse at early time points after DMM surgery. The HIF pathway may be more important for protection against catabolic stress.

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