Copper affects the binding of HIF-1α to the critical motifs of its target genes

Metallomics ◽  
2019 ◽  
Vol 11 (2) ◽  
pp. 429-438 ◽  
Author(s):  
Zhijuan Wu ◽  
Wenjing Zhang ◽  
Y. James Kang
Keyword(s):  
Dna Binding ◽  
Target Gene ◽  
Target Genes ◽  
Gene Selection ◽  
Hypoxic Conditions ◽  
Selection Of

Copper regulates the target gene selection of HIF-1α under hypoxic conditions by affecting HIF-1α-DNA binding patterns across the genome.

Mechanisms regulating target gene selection by the homeodomain-containing protein Fushi tarazu

Development ◽  
2000 ◽  
Vol 127 (13) ◽  
pp. 2965-2976 ◽  
Author(s):  
A. Nasiadka ◽  
A. Grill ◽  
H.M. Krause
Keyword(s):  
Transcription Factors ◽  
Dna Binding ◽  
Binding Site ◽  
Target Gene ◽  
Target Genes ◽  
Gene Selection ◽  
Activity Regulation ◽  
Fushi Tarazu ◽  
Activation Domain ◽  
Regulation Model

Homeodomain proteins are DNA-binding transcription factors that control major developmental patterning events. Although DNA binding is mediated by the homeodomain, interactions with other transcription factors play an unusually important role in the selection and regulation of target genes. A major question in the field is whether these cofactor interactions select target genes by modulating DNA binding site specificity (selective binding model), transcriptional activity (activity regulation model) or both. A related issue is whether the number of target genes bound and regulated is a small or large percentage of genes in the genome. In this study, we have addressed these issues using a chimeric protein that contains the strong activation domain of the viral VP16 protein fused to the Drosophila homeodomain-containing protein Fushi tarazu (Ftz). We find that genes previously thought not to be direct targets of Ftz remain unaffected by FtzVP16. Addition of the VP16 activation domain to Ftz does, however, allow it to regulate previously identified target genes at times and in regions that Ftz alone cannot. It also changes Ftz into an activator of two genes that it normally represses. Taken together, the results suggest that Ftz binds and regulates a relatively limited number of target genes, and that cofactors affect target gene specificity primarily by controlling binding site selection. Activity regulation then fine-tunes the temporal and spatial domains of promoter responses, the magnitude of these responses, and whether they are positive or negative.

Genome-wide discovery of Pax7 target genes during development

2008 ◽  
Vol 33 (1) ◽  
pp. 41-49 ◽  
Author(s):  
Robert B. White ◽  
Melanie R. Ziman
Keyword(s):  
Dna Binding ◽  
Embryonic Development ◽  
Functional Role ◽  
Target Gene ◽  
Target Genes ◽  
Gene Selection ◽  
Cultured Cells ◽  
Expression Vectors ◽  
Genes Encoding

Pax7 plays critical roles in development of brain, spinal cord, neural crest, and skeletal muscle. As a sequence-specific DNA-binding transcription factor, any direct functional role played by Pax7 during development is mediated through target gene selection. Thus, we have sought to identify genes targeted by Pax7 during embryonic development using an unbiased chromatin immunoprecipitation (ChIP) cloning assay to isolate cis-regulatory regions bound by Pax7 in vivo. Sequencing and genomic localization of a library of chromatin-DNA fragments bound by Pax7 has identified 34 candidate Pax7 target genes, with occupancy of a selection confirmed with independent chromatin enrichment tests (ChIP-PCR). To assess the capacity of Pax7 to regulate transcription from these loci, we have cloned alternate transcripts of Pax7 (differing significantly in their DNA binding domain) into expression vectors and transfected cultured cells with these constructs, then analyzed target gene expression levels using RT-PCR. We show that Pax7 directly occupies sites within genes encoding transcription factors Gbx1 and Eya4, the neurogenic cytokine receptor ciliary neurotrophic factor receptor, the neuronal potassium channel Kcnk2, and the signal transduction kinase Camk1d in vivo and regulates the transcriptional state of these genes in cultured cells. This analysis gives us greater insight into the direct functional role played by Pax7 during embryonic development.

scholarly journals Differential Contribution of N- and C-Terminal Regions of HIF1α and HIF2α to Their Target Gene Selectivity

2020 ◽  
Vol 21 (24) ◽  
pp. 9401
Author(s):  
Antonio Bouthelier ◽  
Florinda Meléndez-Rodríguez ◽  
Andrés A. Urrutia ◽  
Julián Aragonés
Keyword(s):  
Transcription Factors ◽  
Dna Binding ◽  
Cellular Response ◽  
Target Gene ◽  
Target Genes ◽  
Transactivation Domain ◽  
Transactivation Domains ◽  
Relative Contribution

Cellular response to hypoxia is controlled by the hypoxia-inducible transcription factors HIF1α and HIF2α. Some genes are preferentially induced by HIF1α or HIF2α, as has been explored in some cell models and for particular sets of genes. Here we have extended this analysis to other HIF-dependent genes using in vitro WT8 renal carcinoma cells and in vivo conditional Vhl-deficient mice models. Moreover, we generated chimeric HIF1/2 transcription factors to study the contribution of the HIF1α and HIF2α DNA binding/heterodimerization and transactivation domains to HIF target specificity. We show that the induction of HIF1α-dependent genes in WT8 cells, such as CAIX (CAR9) and BNIP3, requires both halves of HIF, whereas the HIF2α transactivation domain is more relevant for the induction of HIF2 target genes like the amino acid carrier SLC7A5. The HIF selectivity for some genes in WT8 cells is conserved in Vhl-deficient lung and liver tissue, whereas other genes like Glut1 (Slc2a1) behave distinctly in these tissues. Therefore the relative contribution of the DNA binding/heterodimerization and transactivation domains for HIF target selectivity can be different when comparing HIF1α or HIF2α isoforms, and that HIF target gene specificity is conserved in human and mouse cells for some of the genes analyzed.

scholarly journals Unusual DNA-binding properties of the Arabidopsis thaliana WRKY50 transcription factor at target gene promoters

2020 ◽  
Author(s):  
Konstantin Kanofsky ◽  
Jendrik Rusche ◽  
Lea Eilert ◽  
Fabian Machens ◽  
Reinhard Hehl
Keyword(s):  
Dna Binding ◽  
Binding Site ◽  
Target Gene ◽  
Target Genes ◽  
Specific Binding ◽  
Gene Promoters ◽  
Molecular Pattern ◽  
High Flexibility ◽  
Site Recognition

Abstract Key message WRKY50 from A. thaliana requires WT-boxes at target gene promoters for activation and binding. Abstract Based on the genome-wide prediction of WRKY50 target genes and the similarity of a WRKY50 binding site to WT-boxes in microbe-associated molecular pattern (MAMP)-responsive cis-regulatory modules (CRM), four WT-box containing CRMs from the promoter region of three WRKY50 target genes were investigated for their interaction with WRKY50. These target genes are DJ1E, WRKY30 and ATBBE4. Two of the four CRMs, one from DJ1E and one from WRKY30, were able to activate reporter gene expression in the presence of WRKY50. Activation requires the WT-boxes GGACTTTT, GGACTTTG from DJ1E and GGACTTTC from WRKY30. WRKY50 does not activate a second CRM from WRKY30 and the CRM from ATBBE4, both containing the WT-box TGACTTTT. In vitro gel-shift assays demonstrate WT-box-specific binding of the WRKY50 DNA-binding domain to all four CRMs. This work shows a high flexibility of WRKY50 binding site recognition beyond the classic W-box TTGACC/T.

scholarly journals Cathepsin L, a Target of Hypoxia-Inducible Factor-1-α, Is Involved in Melanosome Degradation in Melanocytes

2021 ◽  
Vol 22 (16) ◽  
pp. 8596
Author(s):  
Ji Young Kim ◽  
Eun Jung Lee ◽  
Yuri Ahn ◽  
Sujin Park ◽  
Yu Jeong Bae ◽  
...  
Keyword(s):  
Target Gene ◽  
Target Genes ◽  
Cathepsin L ◽  
Hypoxia Inducible Factor ◽  
Luciferase Reporter ◽  
Lysosomal Activity ◽  
Hypoxia Inducible Factor 1 ◽  
Lysosomal Protease ◽  
Hypoxic Conditions ◽  
Novel Target

Hypoxic conditions induce the activation of hypoxia-inducible factor-1α (HIF-1α) to restore the supply of oxygen to tissues and cells. Activated HIF-1α translocates into the nucleus and binds to hypoxia response elements to promote the transcription of target genes. Cathepsin L (CTSL) is a lysosomal protease that degrades cellular proteins via the endolysosomal pathway. In this study, we attempted to determine if CTSL is a hypoxia responsive target gene of HIF-1α, and decipher its role in melanocytes in association with the autophagic pathway. The results of our luciferase reporter assay showed that the expression of CTSL is transcriptionally activated through the binding of HIF1-α at its promoter. Under autophagy-inducing starvation conditions, HIF-1α and CTSL expression is highly upregulated in melan-a cells. The mature form of CTSL is closely involved in melanosome degradation through lysosomal activity upon autophagosome–lysosome fusion. The inhibition of conversion of pro-CTSL to mature CTSL leads to the accumulation of gp100 and tyrosinase in addition to microtubule-associated protein 1 light chain 3 (LC3) II, due to decreased lysosomal activity in the autophagic pathway. In conclusion, we have identified that CTSL, a novel target of HIF-1α, participates in melanosome degradation in melanocytes through lysosomal activity during autophagosome–lysosome fusion.

scholarly journals Mediator complex subunit Med19 binds directly GATA DNA-binding zinc finger and functions with Med1 in GATA-driven gene regulation in vivo

2020 ◽  
Author(s):  
Clément Immarigeon ◽  
Sandra Bernat-Fabre ◽  
Emmanuelle Guillou ◽  
Alexis Verger ◽  
Elodie Prince ◽  
...  
Keyword(s):  
Dna Binding ◽  
Rna Polymerase Ii ◽  
Zinc Finger ◽  
Target Gene ◽  
Target Genes ◽  
Mediator Complex ◽  
Transcriptional Responses ◽  
Evolutionarily Conserved

AbstractThe evolutionarily-conserved multiprotein Mediator complex (MED) serves as an interface between DNA-bound transcription factors (TFs) and the RNA Polymerase II machinery. It has been proposed that each TF interacts with a dedicated MED subunit to induce specific transcriptional responses. However, binary MED subunit - TF partnerships are probably oversimplified models. Using Drosophila TFs of the GATA family - Pannier (Pnr) and Serpent (Srp) - as a model, we have previously established GATA cofactor evolutionarily-conserved function for the Med1 Mediator subunit. Here, we show that another subunit, Med19, is required for GATA-dependent gene expression and interacts physically with Pnr and Srp in cellulo, in vivo and in vitro through their conserved C-zinc finger (ZF), indicating general GATA co-activator functions. Interestingly, Med19 is critical for the regulation of all tested GATA target genes which is not the case for Med1, suggesting differential use of MED subunits by GATAs depending on the target gene. Lastly, despite their presumed distant position within the MED middle module, both subunits interact physically. In conclusion, our data shed new light first on the MED complex, engaging several subunits to mediate TF-driven transcriptional responses and second, on GATA TFs, showing that ZF DNA-binding domain also serves for transactivation.

scholarly journals GFI1 tethers the NuRD complex to open and transcriptionally active chromatin in myeloid progenitors

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Anne Helness ◽  
Jennifer Fraszczak ◽  
Charles Joly-Beauparlant ◽  
Halil Bagci ◽  
Christian Trahan ◽  
...  
Keyword(s):  
Dna Binding ◽  
Target Gene ◽  
Molecular Mechanisms ◽  
Target Genes ◽  
Myeloid Differentiation ◽  
Nurd Complex ◽  
Nucleosome Remodeling ◽  
Chromatin Remodeling Complexes ◽  
Active Transcription ◽  
Neutrophil Differentiation

AbstractGrowth factor indepdendent 1 (GFI1) is a SNAG-domain, DNA binding transcriptional repressor which controls myeloid differentiation through molecular mechanisms and co-factors that still remain to be clearly identified. Here we show that GFI1 associates with the chromodomain helicase DNA binding protein 4 (CHD4) and other components of the Nucleosome remodeling and deacetylase (NuRD) complex. In granulo-monocytic precursors, GFI1, CHD4 or GFI1/CHD4 complexes occupy sites enriched for histone marks associated with active transcription suggesting that GFI1 recruits the NuRD complex to target genes regulated by active or bivalent promoters and enhancers. GFI1 and GFI1/CHD4 complexes occupy promoters that are either enriched for IRF1 or SPI1 consensus binding sites, respectively. During neutrophil differentiation, chromatin closure and depletion of H3K4me2 occurs at different degrees depending on whether GFI1, CHD4 or both are present, indicating that GFI1 is more efficient in depleting of H3K4me2 and -me1 marks when associated with CHD4. Our data suggest that GFI1/CHD4 complexes regulate histone modifications differentially to enable regulation of target genes affecting immune response, nucleosome organization or cellular metabolic processes and that both the target gene specificity and the activity of GFI1 during myeloid differentiation depends on the presence of chromatin remodeling complexes.

scholarly journals Myrf guides target gene selection of transcription factor Sox10 during oligodendroglial development

2019 ◽  
Vol 48 (3) ◽  
pp. 1254-1270 ◽  
Author(s):  
Jessica Aprato ◽  
Elisabeth Sock ◽  
Matthias Weider ◽  
Olga Elsesser ◽  
Franziska Fröb ◽  
...  
Keyword(s):  
Target Gene ◽  
Gene Selection ◽  
Gene Activation ◽  
Terminal Differentiation ◽  
Physical Interaction ◽  
Oligodendrocyte Precursor ◽  
Cooperative Activation ◽  
Vertebrate Central Nervous System ◽  
Selection Of

Abstract Oligodendrocytes generate myelin in the vertebrate central nervous system and thus ensure rapid propagation of neuronal activity. Their development is controlled by a network of transcription factors that function as determinants of cell identity or as temporally restricted stage-specific regulators. The continuously expressed Sox10 and Myrf, a factor induced during late development, are particularly important for terminal differentiation. How these factors function together mechanistically and influence each other, is not well understood. Here we show that Myrf not only cooperates with Sox10 during the induction of genes required for differentiation and myelin formation. Myrf also inhibits the activity of Sox10 on genes that are essential during earlier phases of oligodendroglial development. By characterization of the exact DNA-binding requirements of Myrf, we furthermore show that cooperative activation is a consequence of joint binding of Sox10 and Myrf to the same regulatory regions. In contrast, inhibition of Sox10-dependent gene activation occurs on genes that lack Myrf binding sites and likely involves physical interaction between Myrf and Sox10 followed by sequestration. These two opposite activities allow Myrf to redirect Sox10 from genes that it activates in oligodendrocyte precursor cells to genes that need to be induced during terminal differentiation.

scholarly journals Agrobacterium-mediated Genetic Transformation of Lentil (Lens culinaris Medik.) with Chitinase Gene followed by In vitro Flower and Pod Formation

2019 ◽  
Vol 29 (1) ◽  
pp. 99-109
Author(s):  
Subroto K Das ◽  
Kishwar Jahan Shethi ◽  
MI Hoque ◽  
RH Sarker
Keyword(s):  
Genetic Transformation ◽  
Lens Culinaris ◽  
Target Gene ◽  
Gene Selection ◽  
Chitinase Gene ◽  
Pcr Analysis ◽  
Agrobacterium Strain ◽  
Half Strength ◽  
Selection Of

To investigate the integration of chitinase gene in lentil (Lens culinaris Medik.) namely, BARI masur-4 (BM-4), BARI masur-5 (BM-5) and BARI masur-6 (BM-6) through Agrobacterium-mediated genetic transformation was performed using Agrobacterium strain EHA 105 harboring bar (resistant to phosphinotrycin) and chitinase (gene of interest) gene. Selection of transformed shoots was carried out by gradually increasing the concentration of phosphinotrycin (PPT) up to 2.0 mg/l. Transgenic lentil shoots were produced with an overall frequency of 0.36 in case of BM-4 and BM-6 and 0.34 in case of BM-5, respectively. Most of the selected shoots developed in vitro flowers and pods following their sub-culture on half strength of MS supplemented with 20 mg/l IBA, 0.5 mg/l NAA with 50 mg/l ticarcillin. Seedlings germinated from the seeds were successfully transferred to soil for the development of further progeny. Stable integration of target gene was confirmed through PCR analysis. Plant Tissue Cult. & Biotech. 29(1): 99-109, 2019 (June)

An Ignored Pitfall in Selecting Reference Genes and the Solution with Emphasis on Subtypes and Sex of Thyroid Cancer Patients

2021 ◽  
Author(s):  
Ghazal Esfandiarpour ◽  
Mohammad Mokhtari ◽  
seyed-Morteza Javadirad ◽  
Mohsen Kolahdouzan ◽  
Ahmed Almuslimawi
Keyword(s):  
Thyroid Cancer ◽  
Statistical Analysis ◽  
Reference Genes ◽  
Target Gene ◽  
Target Genes ◽  
Meta Analysis ◽  
Specific Reference ◽  
Cancer Subtypes ◽  
Common Reference ◽  
Selection Of

Abstract Routine tissue specific reference genes are widely used in transcriptomics studies without concerning their target genes, sex of patients, and diseases subtype. We proposed the concept of specific reference genes for each target gene after considering sex of patients and thyroid cancer subtypes. RT-qPCR technique was coupled with expression meta-analysis of samples with different races and ethnicities, in both sexes, and in different thyroid cancer subtypes. Eight common reference genes were evaluated and some of them undoubtedly ruled out. We found that mean and SD values of the genes must be considered carefully before the selection of reference genes. A formula was also developed accordingly and we equipped it with statistical analysis of more than 25000 genes. In conclusion, the reckless selection of reference genes can distort the output and must be prohibited.

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