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1.
Nat Neurosci ; 22(9): 1413-1423, 2019 09.
Artigo em Inglês | MEDLINE | ID: mdl-31427770

RESUMO

Understanding the transcriptional changes that are engaged in stress resilience may reveal novel antidepressant targets. Here we use gene co-expression analysis of RNA-sequencing data from brains of resilient mice to identify a gene network that is unique to resilience. Zfp189, which encodes a previously unstudied zinc finger protein, is the highest-ranked key driver gene in the network, and overexpression of Zfp189 in prefrontal cortical neurons preferentially activates this network and promotes behavioral resilience. The transcription factor CREB is a predicted upstream regulator of this network and binds to the Zfp189 promoter. To probe CREB-Zfp189 interactions, we employ CRISPR-mediated locus-specific transcriptional reprogramming to direct CREB or G9a (a repressive histone methyltransferase) to the Zfp189 promoter in prefrontal cortex neurons. Induction of Zfp189 with site-specific CREB is pro-resilient, whereas suppressing Zfp189 expression with G9a increases susceptibility. These findings reveal an essential role for Zfp189 and CREB-Zfp189 interactions in mediating a central transcriptional network of resilience.


Assuntos
Adaptação Psicológica/fisiologia , Estresse Psicológico/genética , Dedos de Zinco/genética , Animais , Redes Reguladoras de Genes/genética , Camundongos , Camundongos Endogâmicos C57BL , Córtex Pré-Frontal/metabolismo , Transcrição Genética
2.
BMC Plant Biol ; 19(1): 329, 2019 Jul 23.
Artigo em Inglês | MEDLINE | ID: mdl-31337346

RESUMO

BACKGROUND: Zinc finger proteins (ZFPs) containing only a single zinc finger domain play important roles in the regulation of plant growth and development, as well as in biotic and abiotic stress responses. To date, the evolutionary history and functions of the ZFP gene family have not been identified in cotton. RESULTS: In this paper, we identified 29 ZFP genes in Gossypium hirsutum. This gene family was divided into seven subfamilies, 22 of which were distributed over 17 chromosomes. Bioinformatic analysis revealed that 20 GhZFP genes originated from whole genome duplications and two originated from dispersed duplication events, indicating that whole genome duplication is the main force in the expansion of the GhZFP gene family. Most GhZFP8 subfamily genes, except for GhZFP8-3, were highly expressed during fiber cell growth, and were induced by brassinosteroids in vitro. Furthermore, we found that a large number of GhZFP genes contained gibberellic acid responsive elements, auxin responsive elements, and E-box elements in their promoter regions. Exogenous application of these hormones significantly stimulated the expression of these genes. CONCLUSIONS: Our findings reveal that GhZFP8 genes are involved in cotton fiber development and widely induced by auxin, gibberellin and BR, which provides a foundation for the identification of more downstream genes with potential roles in phytohormone stimuli, and a basis for breeding better cotton varieties in the future.


Assuntos
Gossypium/genética , Reguladores de Crescimento de Planta/fisiologia , Proteínas de Plantas/genética , Dedos de Zinco/genética , Brassinosteroides/metabolismo , Mapeamento Cromossômico , Sequência Conservada/genética , Giberelinas/fisiologia , Gossypium/fisiologia , Ácidos Indolacéticos/metabolismo , Filogenia , Proteínas de Plantas/fisiologia , Reação em Cadeia da Polimerase , Alinhamento de Sequência , Transcriptoma , Dedos de Zinco/fisiologia
3.
Biotechnol Appl Biochem ; 66(5): 808-814, 2019 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-31195426

RESUMO

Nonsteroidal anti-inflammatory drugs (NSAIDs) are known to exhibit antitumor activities. Among the very well-known oncogenes in breast cancer is zinc finger protein 703 (ZNF703) and cyclooxygenase-2 (COX-2). Numerous reports indicate a direct link among apoptosis resistance, chemotherapy resistance, and increased expression of ZNF703. In the present study, the expression level of ZNF703 was compared in human breast cancer tissue, healthy breast tissue, and MCF-7 breast cancer cell line by a real-time PCR. We also investigated the inhibitory effect of anti-ZNF703 RNAi interference (RNAi) and ibuprofen, either individually or in combination, on MCF-7 cell survival and apoptosis. Results showed a 93.3% and fourfold increase in the expression of ZNF703 in breast cancer tissue and MCF-7 cell line, respectively. Ibuprofen inhibited the viability of MCF-7 cells in a concentration-dependent manner. Ibuprofen alone or in combination with anti-ZNF703 RNA reduced the expression of ZNF703, induced apoptosis, reduced mitochondrial membrane potential, and elevated BAX and LC3A in MCF-7 cells. Our results show that the combination of ibuprofen and anti-ZNF703 siRNA is more effective in promoting apoptosis than each treatment alone. We report that the combination of anti-ZNF703 RNAi with ibuprofen as the inhibitor of COX-2 is highly effective in inhibiting MCF-7 as a breast cancer cell line and shows therapeutic potential for breast cancer.


Assuntos
Anti-Inflamatórios não Esteroides/farmacologia , Neoplasias da Mama/tratamento farmacológico , Regulação Neoplásica da Expressão Gênica/efeitos dos fármacos , Interferência de RNA , Dedos de Zinco/efeitos dos fármacos , Apoptose/efeitos dos fármacos , Neoplasias da Mama/genética , Neoplasias da Mama/patologia , Quimioterapia Combinada , Feminino , Regulação Neoplásica da Expressão Gênica/genética , Humanos , Células MCF-7 , Dedos de Zinco/genética
4.
Plant Sci ; 285: 55-67, 2019 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-31203894

RESUMO

C2H2-type zinc finger proteins play important roles in plant growth, development, and abiotic stress tolerance. Here, we explored the role of the C2H2-type zinc finger protein SALT INDUCED ZINC FINGER PROTEIN1 (AtSIZ1; At3G25910) in Arabidopsis thaliana under salt stress. AtSIZ1 expression was induced by salt treatment. During the germination stage, the germination rate, germination energy, germination index, cotyledon growth rate, and root length were significantly higher in AtSIZ1 overexpression lines than in the wild type under various stress treatments, whereas these indices were significantly reduced in AtSIZ1 loss-of-function mutants. At the mature seedling stage, the overexpression lines maintained higher levels of K+, proline, and soluble sugar, lower levels of Na+ and MDA, and lower Na+/K+ ratios than the wild type. Stress-related marker genes such as SOS1, AtP5CS1, AtGSTU5, COR15A, RD29A, and RD29B were expressed at higher levels in the overexpression lines than the wild type and loss-of-function mutants under salt treatment. These results indicate that AtSIZ1 improves salt tolerance in Arabidopsis by helping plants maintain ionic homeostasis and osmotic balance.


Assuntos
Proteínas de Arabidopsis/fisiologia , Arabidopsis/metabolismo , Ligases/fisiologia , Dedos de Zinco/fisiologia , Arabidopsis/genética , Arabidopsis/fisiologia , Proteínas de Arabidopsis/genética , Homeostase , Ligases/genética , Filogenia , Potássio/metabolismo , Prolina/metabolismo , Estresse Salino , Tolerância ao Sal , Sódio/metabolismo , Dedos de Zinco/genética
5.
J Dairy Sci ; 102(8): 7226-7236, 2019 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-31202648

RESUMO

The mammalian Y chromosome gene families in the ampliconic region are expressed predominantly or exclusively in the testis, and their copy number variations (CNV) are significantly associated with male reproductive traits, suggesting they have important roles in spermatogenesis and testicular development. ZNF280AY (zinc finger protein 280A, Y-linked) is a member of the zinc finger protein family and has been identified as a bovid-specific Y-chromosome gene. The current study applied a reliable quantitative real-time PCR method to estimate the CNV of ZNF280AY in 715 bulls across 21 cattle breeds and to further investigate the association of the CNV of ZNF280AY with bull reproductive traits and ZNF280AY mRNA expression levels in adult testis. The results revealed that the median copy number of ZNF280AY was 47, and the copy number varied from 11 to 154, showing significant CNV between and within the investigated cattle breeds. In addition, all 715 bulls were classified into Y1, Y2, and Y3 lineage groups based on a rapid genotyping method described previously. Pairwise comparisons indicated that bulls belonging to the Y1 lineage had a significantly lower median copy number (40) than bulls belonging to the Y2 (52) and Y3 lineages (57). Association analysis revealed that the CNV of ZNF280AY was correlated negatively with the percentage of normal sperm and sperm concentration in Holstein bulls, whereas no significant correlation was observed with ejaculation volume, total sperm count, sperm motility, postthaw motility (PTM), and scrotal circumference in Holstein and Simmental bulls. Furthermore, no correlation was observed between ZNF280AY copy number and ZNF280AY mRNA expression levels in the testis. The current study suggests that the CNV of the ZNF280AY gene family is associated with male reproductive traits and may serve as a valuable marker for early bull fertility selection in Holstein breeding programs.


Assuntos
Bovinos/genética , Variações do Número de Cópias de DNA , Fertilidade/genética , Regulação da Expressão Gênica , Genes Ligados ao Cromossomo Y/genética , Reprodução/genética , Cromossomo Y/genética , Animais , Cruzamento , Bovinos/fisiologia , Marcadores Genéticos/genética , Genótipo , Masculino , Especificidade de Órgãos , Fenótipo , Reação em Cadeia da Polimerase em Tempo Real/veterinária , Especificidade da Espécie , Contagem de Espermatozoides/veterinária , Motilidade Espermática/genética , Espermatogênese/genética , Testículo/fisiologia , Dedos de Zinco/genética
6.
Plant Sci ; 283: 355-365, 2019 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-31128706

RESUMO

Despite recent evidence that HDACs are involved in the environmental stress responses of plants, their roles in the abiotic stress responses of monocot plants remain largely unexplored. We investigated a HDAC gene, Bradi3g08060 (BdHD1), in Brachypodium distachyon. The Brachypodium BdHD1-overexpression plants displayed a hypersensitive phenotype to ABA and exhibited better survival under drought conditions. On the other hand, the RNA-interference plants were insensitive to ABA and showed low survival under drought stress. At the genome-wide level, overexpression of BdHD1 led to lower H3K9 acetylation at the transcriptional start sites of 230 genes than in the wild type plants under the drought treatment. We validated our ChIP-Seq data on 10 selected transcription factor genes from the 230 drought-specific genes. These genes exhibited much lower expression in the BdHD1-overexpression plants compared to the wild type plants under drought stress. We further identified an ABA-inducible transcription factor gene BdWRKY24 that was repressed in BdHD1-OE plants, but highly expressed in RNA-interference plants under drought stress. These results indicate that BdHD1 plays a positive role in ABA sensitivity and drought stress tolerance and they provide a link between the role of BdHD1 and the drought stress response at a genome-wide level in Brachypodium.


Assuntos
Ácido Abscísico/fisiologia , Brachypodium/metabolismo , Histona Desacetilases/fisiologia , Reguladores de Crescimento de Planta/fisiologia , Proteínas de Plantas/fisiologia , Ácido Abscísico/metabolismo , Arabidopsis/enzimologia , Arabidopsis/genética , Brachypodium/enzimologia , Brachypodium/genética , Brachypodium/fisiologia , Desidratação , Regulação da Expressão Gênica de Plantas , Técnicas de Silenciamento de Genes , Histona Desacetilases/metabolismo , Filogenia , Reguladores de Crescimento de Planta/metabolismo , Proteínas de Plantas/metabolismo , Plantas Geneticamente Modificadas , Dedos de Zinco/genética , Dedos de Zinco/fisiologia
7.
Biochim Biophys Acta Gene Regul Mech ; 1862(6): 643-656, 2019 06.
Artigo em Inglês | MEDLINE | ID: mdl-30959128

RESUMO

Gluconeogenesis is essential for blood glucose homeostasis during fasting and is regulated by various enzymes, which are encoded by gluconeogenic genes. Those genes are controlled by various transcription factors. Zinc finger and BTB domain-containing 7c (Zbtb7c, also called Kr-pok) is a BTB-POZ family transcription factor with proto-oncogenic activity. Previous findings have indicated that Zbtb7c is involved in the regulation of fatty acid biosynthesis, suggesting an involvement also in primary metabolism. We found here that fasting induced Zbtb7c expression in the mouse liver and in primary liver hepatocytes. We also observed that Zbtb7c-knockout mice have decreased blood glucose levels, so we investigated whether Zbtb7c plays a role in gluconeogenesis. Indeed, differential gene expression analysis of Zbtb7c-knockout versus wild type mouse livers showed downregulated transcription of gluconeogenic genes encoding the glucose 6-phosphatase catalytic subunit (G6pc) and phosphoenolpyruvate carboxykinase 1 (Pck1), while Zbtb7c expression upregulated these two genes, under fasting conditions. Mechanistically, we found that when complexed with histone deacetylase 3 (Hdac3), Zbtb7c binds insulin response elements (IREs) within the G6pc and Pck1 promoters. Moreover, complexed Zbtb7c deacetylated forkhead box O1 (Foxo1), thereby increasing Foxo1 binding to the G6pc and Pck1 IREs, resulting in their transcriptional activation. These results demonstrate Zbtb7c to be a crucial metabolic regulator of blood glucose homeostasis, during mammalian fasting.


Assuntos
Jejum , Regulação da Expressão Gênica , Gluconeogênese/fisiologia , Glucose-6-Fosfatase/genética , Peptídeos e Proteínas de Sinalização Intracelular/genética , Fosfoenolpiruvato Carboxiquinase (GTP)/genética , Proteínas/metabolismo , Fatores de Transcrição/metabolismo , Dedos de Zinco/fisiologia , Animais , Glicemia , Proteínas de Ligação a DNA/metabolismo , Ácidos Graxos/biossíntese , Proteína Forkhead Box O1/metabolismo , Gluconeogênese/genética , Glucose/metabolismo , Glucose-6-Fosfatase/metabolismo , Células HEK293 , Células Hep G2 , Hepatócitos/metabolismo , Histona Desacetilases/metabolismo , Homeostase , Humanos , Peptídeos e Proteínas de Sinalização Intracelular/metabolismo , Fígado/metabolismo , Masculino , Camundongos , Camundongos Endogâmicos C57BL , Camundongos Knockout , Modelos Animais , Mutagênese Sítio-Dirigida , Fosfoenolpiruvato Carboxiquinase (GTP)/metabolismo , Regiões Promotoras Genéticas , Proteínas/genética , Transcriptoma , Dedos de Zinco/genética
8.
Mol Biotechnol ; 61(6): 421-426, 2019 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-30937688

RESUMO

The B-box proteins (BBXs) are zinc finger proteins containing one or two B-box domain(s) and involved in regulation of development processes as transcription factors in plants. Here, seven BBX genes in Malus domestica genome (MdBBXs) were identified and found to be up-regulated under abiotic stresses, with 2-12 folds in roots. All recombinant MdBBXs expressed in Escherichia coli (E. coli) enhanced the cell's tolerance to salt and osmotic stresses, respectively. Deficiency of B-box domain of MdBBX10 led to the loss of anti-stress functions. Five conservative cysteines in B-box domain played crucial roles in stress resistance, which are involved in two of metal iron binding sites of zinc finger motifs in BBXs. All the above results suggested MdBBXs confer stress tolerance to E. coli cell against abiotic stresses.


Assuntos
Escherichia coli/genética , Regulação da Expressão Gênica de Plantas , Malus/genética , Proteínas de Plantas/genética , Tolerância ao Sal/genética , Fatores de Transcrição/genética , Sequência de Aminoácidos , Clonagem Molecular , Escherichia coli/efeitos dos fármacos , Escherichia coli/metabolismo , Expressão Gênica , Vetores Genéticos/química , Vetores Genéticos/metabolismo , Malus/metabolismo , Proteínas de Plantas/metabolismo , Raízes de Plantas/genética , Raízes de Plantas/metabolismo , Polietilenoglicóis/farmacologia , Domínios Proteicos , Proteínas Recombinantes/genética , Proteínas Recombinantes/metabolismo , Alinhamento de Sequência , Homologia de Sequência de Aminoácidos , Cloreto de Sódio/farmacologia , Estresse Fisiológico/genética , Fatores de Transcrição/metabolismo , Dedos de Zinco/genética
9.
Proc Natl Acad Sci U S A ; 116(13): 5892-5901, 2019 03 26.
Artigo em Inglês | MEDLINE | ID: mdl-30850530

RESUMO

Gene-regulatory networks are ubiquitous in nature and critical for bottom-up engineering of synthetic networks. Transcriptional repression is a fundamental function that can be tuned at the level of DNA, protein, and cooperative protein-protein interactions, necessitating high-throughput experimental approaches for in-depth characterization. Here, we used a cell-free system in combination with a high-throughput microfluidic device to comprehensively study the different tuning mechanisms of a synthetic zinc-finger repressor library, whose affinity and cooperativity can be rationally engineered. The device is integrated into a comprehensive workflow that includes determination of transcription-factor binding-energy landscapes and mechanistic modeling, enabling us to generate a library of well-characterized synthetic transcription factors and corresponding promoters, which we then used to build gene-regulatory networks de novo. The well-characterized synthetic parts and insights gained should be useful for rationally engineering gene-regulatory networks and for studying the biophysics of transcriptional regulation.


Assuntos
Sistema Livre de Células , Redes Reguladoras de Genes , Engenharia Genética/métodos , Fatores de Transcrição/síntese química , Biblioteca Gênica , Redes Reguladoras de Genes/genética , Dispositivos Lab-On-A-Chip , Regiões Promotoras Genéticas/genética , Dedos de Zinco/genética
10.
Gene ; 695: 92-98, 2019 May 05.
Artigo em Inglês | MEDLINE | ID: mdl-30769141

RESUMO

Zinc finger proteins are a class of transcription factors with finger-like domains and have diverse uses in biological processes, including development, differentiation, and metabolism. In this study, we identified the absence of the 24 bp sequence in the third exon of the zinc finger protein 764-like (ZNF764L) gene that lead to the production of two new transcripts, ZNF764L-SV1 and ZNF764L-SV2, and the sum of the expression levels of the two transcripts is approximately equal the total RNA expression level. Temporal and spatial expression showed that ZNF764L had higher expression during the embryonic stage. Moreover, the research study revealed a 22-bp indel mutation in the first exon region of ZNF764L gene. Statistically significant results (P < 0.05) were encountered for this indel for chicken growth and carcass traits, which include birth weight, chest breadth and body slanting length at 4 weeks of age and subcutaneous fat weight and others. Genetic parameter analysis showed that D is the predominant allele in the commercial chicken population. Gene expression for each genotype showed that birds carrying the II allele had a higher expression level than the other genotypes. These findings enrich the understanding of ZNF764L gene function and enhance reproduction in the chicken industry.


Assuntos
Galinhas/genética , Dedos de Zinco/genética , Alelos , Processamento Alternativo/genética , Animais , Éxons , Estudos de Associação Genética , Genótipo , Mutação INDEL/genética , Carne , Fenótipo , Polimorfismo de Nucleotídeo Único/genética , RNA Mensageiro/genética , Fatores de Transcrição/genética
11.
PLoS One ; 14(2): e0212492, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-30768627

RESUMO

BACKGROUND: B-cell lymphoma/leukaemia 11A (BCL11A) is a C2H2-type zinc-finger transcription factor protein that is a critical modulator of haemoglobin switching and suppresses the production of foetal haemoglobin. Variation in the BCL11A gene ameliorates the severity of sickle cell disease (SCD) and ß-thalassemia (ß-thal). The BCL11A gene is located on chromosome 2p16.1 and encodes an 835-amino acid protein. METHOD: Using state-of-the-art in silico tools, this study examined the most pathogenic non-synonymous single nucleotide polymorphisms (nsSNPs) that disrupt the BCL11A protein and mediate foetal-to-adult globin switching. A total of 11,463 SNPs were retrieved from the Single Nucleotide Polymorphism database (dbSNP). These included 799 in the 5' untranslated region (UTR), 486 in the 3' UTR, and 266 non-synonymous, 189 coding synonymous, six nonsense, and six stop-gained SNPs. RESULTS AND DISCUSSION: In silico tools (SIFT, SNAP, PolyPhen-2, PANTHER, I-Mutant, PROVEAN, SNPs&GO, mCSM, and PhD-SNP) predicted the five most-deleterious nsSNPs: rs61742690, rs62142605, rs17028351, rs115666026, and rs74987258. Molecular dynamic simulation and homology modelling of the mutated proteins (S783N, D643N, G451S, K670R, and M313L) of the most deleterious nsSNPs revealed their functional and structural impact. nsSNP rs61742690 was predicted to be the most deleterious, as supported by eight of the nine in silico tools. CONCLUSIONS: Complete failure in the protein-protein interactions with functional partners (KLF1 and others) and significant changes (±100% variation) in the interface energy revealed that rs61742690 (S783N) in the zinc-finger domain is a suitable target for disrupting BCL11A-mediated foetal-to-adult globin switching.


Assuntos
Proteínas de Transporte/genética , Globinas/genética , Proteínas Nucleares/genética , Algoritmos , Proteínas de Transporte/química , Proteínas de Transporte/metabolismo , Simulação por Computador , Bases de Dados de Ácidos Nucleicos , Hemoglobina Fetal/biossíntese , Hemoglobina Fetal/genética , Globinas/metabolismo , Humanos , Simulação de Dinâmica Molecular , Proteínas Mutantes/química , Proteínas Mutantes/genética , Proteínas Mutantes/metabolismo , Proteínas Nucleares/química , Proteínas Nucleares/metabolismo , Polimorfismo de Nucleotídeo Único , Domínios e Motivos de Interação entre Proteínas/genética , Homologia de Sequência de Aminoácidos , Dedos de Zinco/genética
12.
Fungal Genet Biol ; 124: 59-72, 2019 03.
Artigo em Inglês | MEDLINE | ID: mdl-30630094

RESUMO

Cryptococcus neoformans is a ubiquitous yeast pathogen that often infects the human central nervous system (CNS) to cause meningitis in immunocompromised individuals. Although numerous signaling pathways and factors important for fungal sexual reproduction and virulence have been investigated, their precise mechanism of action remains to be further elucidated. In this study, we identified and characterized a novel zinc finger protein Zfp1 that regulates fungal sexual reproduction and virulence in C. neoformans. qRT-PCR and ZFP1 promoter regulatory activity assays revealed a ubiquitous expression pattern of ZFP1 in all stages during mating. Subcellular localization analysis indicates that Zfp1 is targeted to the cytoplasm of C. neoformans. In vitro assays of stress responses showed that zfp1Δ mutants and the ZFP1 overexpressed strains ZFP1OE are hypersensitive to SDS, but not Congo red, indicating that Zfp1 may regulate cell membrane integrity. Zfp1 is also essential for fungal sexual reproduction because basidiospore production was blocked in bilateral mating between zfp1Δ mutants or ZFP1 overexpressed strains. Fungal nuclei development assay showed that nuclei in the bilateral mating of zfp1Δ mutants or ZFP1 overexpressed strains failed to undergo meiosis after fusion, indicating Zfp1 is important for regulating meiosis during mating. Although zfp1Δ mutants showed normal growth and produced normal major virulence factors, virulence was attenuated in a murine model. Interestingly, we found that the ZFP1 overexpressed strains were avirulent in a murine systemic-infection model. Overall, our study showed that the zinc finger protein Zfp1 is essential for fungal sporulation and virulence in C. neoformans.


Assuntos
Cryptococcus neoformans/fisiologia , Cryptococcus neoformans/patogenicidade , Proteínas Fúngicas/fisiologia , Dedos de Zinco/fisiologia , Motivos de Aminoácidos , Animais , Western Blotting , Membrana Celular/metabolismo , Divisão do Núcleo Celular/fisiologia , Criptococose/microbiologia , Criptococose/patologia , Cryptococcus neoformans/genética , Feminino , Cápsulas Fúngicas/metabolismo , Proteínas Fúngicas/química , Proteínas Fúngicas/genética , Perfilação da Expressão Gênica , Meiose/fisiologia , Camundongos Endogâmicos BALB C , Reação em Cadeia da Polimerase em Tempo Real , Virulência , Zinco/metabolismo , Dedos de Zinco/genética
13.
BMC Plant Biol ; 18(1): 373, 2018 Dec 27.
Artigo em Inglês | MEDLINE | ID: mdl-30587139

RESUMO

BACKGROUND: Ubiquitous CCCH nucleic acid-binding motif is found in a wide-variety of organisms. CCCH genes are involved in plant developmental processes and biotic and abiotic stress responses. Brassica rapa is a vital economic crop and classical model plant of polyploidy evolution, but the functions of CCCH genes in B. rapa are unclear. RESULTS: In this study, 103 CCCH genes in B. rapa were identified. A comparative analysis of the chromosomal position, gene structure, domain organization and duplication event between B. rapa and Arabidopsis thaliana were performed. Results showed that CCCH genes could be divided into 18 subfamilies, and segmental duplication might mainly contribute to this family expansion. C-X7/8-C-X5-C3-H was the most commonly found motif, but some novel CCCH motifs were also found, along with some loses of typical CCCH motifs widespread in other plant species. The multifarious gene structures and domain organizations implicated functional diversity of CCCH genes in B. rapa. Evidence also suggested functional redundancy in at least one subfamily due to high conservation between members. Finally, the expression profiles of subfamily-IX genes indicated that they are likely involved in various stress responses. CONCLUSION: This study provides the first genome-wide characterization of the CCCH genes in B. rapa. The results suggest that B. rapa CCCH genes are likely functionally divergent, but mostly involved in plant development and stress response. These results are expected to facilitate future functional characterization of this potential RNA-binding protein family in Brassica crops.


Assuntos
Brassica rapa/genética , Proteínas de Ligação a DNA/genética , Genes de Plantas/genética , Proteínas de Plantas/genética , Dedos de Zinco/genética , Arabidopsis/genética , Brassica rapa/fisiologia , Mapeamento Cromossômico , Sequência Conservada/genética , Proteínas de Ligação a DNA/fisiologia , Regulação da Expressão Gênica de Plantas/genética , Genes de Plantas/fisiologia , Estudo de Associação Genômica Ampla , Filogenia , Proteínas de Plantas/fisiologia , Alinhamento de Sequência , Estresse Fisiológico , Dedos de Zinco/fisiologia
14.
Int J Mol Sci ; 19(8)2018 Jul 25.
Artigo em Inglês | MEDLINE | ID: mdl-30044387

RESUMO

Longan is an important fruit tree in the subtropical region of Southeast Asia and Australia. However, its blooming and its yield are susceptible to stresses such as droughts, high salinity, and high and low temperature. To date, the molecular mechanisms of abiotic stress tolerance and flower induction in longan have not been elucidated. WRKY transcription factors (TFs), which have been studied in various plant species, play important regulatory roles in plant growth, development, and responses to stresses. However, there is no report about WRKYs in longan. In this study, we identified 55 WRKY genes with the conserved WRKY domain and zinc finger motif in the longan genome. Based on the structural features of WRKY proteins and topology of the phylogenetic tree, the longan WRKY (DlWRKY) family was classified into three major groups (I⁻III) and five subgroups (IIa⁻IIe) in group II. Tissue expression analysis showed that 25 DlWRKYs were highly expressed in almost all organs, suggesting that these genes may be important for plant growth and organ development in longan. Comparative RNA-seq and qRT-PCR-based gene expression analysis revealed that 18 DlWRKY genes showed a specific expression during three stages of flower induction in "Sijimi" ("SJ"), which exhibited the "perpetual flowering" (PF) habit, indicating that these 18 DlWRKY genes may be involved in the flower induction and the genetic control of the perpetual flowering trait in longan. Furthermore, the RT-qPCR analysis illustrated the significant variation of 27, 18, 15, 17, 27, and 23 DlWRKY genes under SA (Salicylic acid), MeJA (Methyl Jasmonate), heat, cold, drought, or high salinity treatment, respectively, implicating that they might be stress- or hormone-responsive genes. In summary, we systematically and comprehensively analyzed the structure, evolution, and expression pattern of the DlWRKY genes. The results presented here increase our understanding of the WRKY family in fruit trees and provide a basis for the further elucidation of the biological function of DlWRKY genes in longan.


Assuntos
Flores/crescimento & desenvolvimento , Proteínas de Plantas/genética , Sapindaceae/genética , Estresse Fisiológico/genética , Temperatura Baixa , Secas , Perfilação da Expressão Gênica , Genoma de Planta/genética , Estudo de Associação Genômica Ampla , Família Multigênica , Filogenia , Proteínas de Plantas/metabolismo , Alinhamento de Sequência , Análise de Sequência de RNA , Fatores de Transcrição/genética , Fatores de Transcrição/metabolismo , Dedos de Zinco/genética
15.
PLoS Comput Biol ; 14(6): e1006290, 2018 06.
Artigo em Inglês | MEDLINE | ID: mdl-29953437

RESUMO

A major goal of cancer genomics is to identify somatic mutations that play a role in tumor initiation or progression. Somatic mutations within transcription factors are of particular interest, as gene expression dysregulation is widespread in cancers. The substantial gene expression variation evident across tumors suggests that numerous regulatory factors are likely to be involved and that somatic mutations within them may not occur at high frequencies across patient cohorts, thereby complicating efforts to uncover which ones are cancer-relevant. Here we analyze somatic mutations within the largest family of human transcription factors, namely those that bind DNA via Cys2His2 zinc finger domains. Specifically, to hone in on important mutations within these genes, we aggregated somatic mutations across all of them by their positions within Cys2His2 zinc finger domains. Remarkably, we found that for three classes of cancers profiled by The Cancer Genome Atlas (TCGA)-Uterine Corpus Endometrial Carcinoma, Colon and Rectal Adenocarcinomas, and Skin Cutaneous Melanoma-two specific, functionally important positions within zinc finger domains are mutated significantly more often than expected by chance, with alterations in 18%, 10% and 43% of tumors, respectively. Numerous zinc finger genes are affected, with those containing Krüppel-associated box (KRAB) repressor domains preferentially targeted by these mutations. Further, the genes with these mutations also have high overall missense mutation rates, are expressed at levels comparable to those of known cancer genes, and together have biological process annotations that are consistent with roles in cancers. Altogether, we introduce evidence broadly implicating mutations within a diverse set of zinc finger proteins as relevant for cancer, and propose that they contribute to the widespread transcriptional dysregulation observed in cancer cells.


Assuntos
Dedos de Zinco CYS2-HIS2/genética , Dedos de Zinco/genética , Polipose Adenomatosa do Colo/genética , Sequência de Aminoácidos/genética , Sítios de Ligação/genética , Dedos de Zinco CYS2-HIS2/fisiologia , DNA/metabolismo , Proteínas de Ligação a DNA/metabolismo , Feminino , Humanos , Masculino , Neoplasias/genética , Proteínas Repressoras/genética , Homologia de Sequência de Aminoácidos , Neoplasias Cutâneas/genética , Fatores de Transcrição/genética , Fatores de Transcrição/metabolismo , Neoplasias Uterinas/genética , Dedos de Zinco/fisiologia
16.
Dev Growth Differ ; 60(3): 158-173, 2018 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-29664133

RESUMO

During early vertebrate embryogenesis, bone morphogenetic proteins (BMPs) belonging to the transforming growth factor-ß (TGF-ß) family of growth factors play a central role in dorsal-ventral (DV) patterning of embryos, while other growth factors such as Wnt and fibroblast growth factor (FGF) family members regulate formation of the anterior-posterior (AP) axis. Although the establishment of body plan is thought to require coordinated formation of the DV and AP axes, the mechanistic details underlying this coordination are not well understood. Here, we show that a Xenopus homologue of zbtb14 plays an essential role in the regulation of both DV and AP patterning during early Xenopus development. We show that overexpression of Zbtb14 promotes neural induction and inhibits epidermal differentiation, thereby regulating DV patterning. In addition, Zbtb14 promotes the formation of posterior neural tissue and suppresses anterior neural development. Consistent with this, knock-down experiments show that Zbtb14 is required for neural development, especially for the formation of posterior neural tissues. Mechanistically, Zbtb14 reduces the levels of phosphorylated Smad1/5/8 to suppress BMP signaling and induces an accumulation of ß-Catenin to promote Wnt signaling. Collectively, these results suggest that Zbtb14 plays a crucial role in the formation of DV and AP axes by regulating both the BMP and Wnt signaling pathways during early Xenopus embryogenesis.


Assuntos
Embrião não Mamífero/metabolismo , Proteínas de Xenopus/metabolismo , Xenopus laevis/metabolismo , Animais , Padronização Corporal , Fatores de Crescimento de Fibroblastos/metabolismo , Regulação da Expressão Gênica no Desenvolvimento , Fatores de Transcrição Kruppel-Like/genética , Fatores de Transcrição Kruppel-Like/metabolismo , Proteína Smad1/metabolismo , Proteína Smad5/metabolismo , Proteína Smad8/metabolismo , Proteínas de Xenopus/genética , Xenopus laevis/embriologia , Dedos de Zinco/genética , Dedos de Zinco/fisiologia
17.
Biochem Biophys Res Commun ; 498(4): 954-959, 2018 04 15.
Artigo em Inglês | MEDLINE | ID: mdl-29548822

RESUMO

Functional studies of CCCH-type zinc finger proteins in abiotic stress responses have largely focused on tandem CCCH-type zinc finger (TZF) genes, whereas the study of functional roles of non-TZF genes in abiotic stress responses has largely been neglected. Here, we investigated the functional roles of AtC3H17, a non-TZF gene of Arabidopsis, in salt stress responses. AtC3H17 expression significantly increased under NaCl, mannitol, and ABA treatments. AtC3H17-overexpressing transgenic plants (OXs) were more tolerant under NaCl and MV treatment conditions than the wild type (WT). atc3h17 mutants were more sensitive under NaCl and MV treatment conditions compared with the WT. The transcription of the salt stress-responsive genes in ABA-dependent pathway, such as RAB18, COR15A, and RD22, was significantly higher in AtC3H17 OXs than in WT both under NaCl-free condition and after NaCl treatment. Our results demonstrate that AtC3H17 functions as a positive regulator in salt stress response, via the up-regulation of ABA-dependent salt stress-response pathway.


Assuntos
Proteínas de Arabidopsis/genética , Arabidopsis/genética , Genes de Plantas/fisiologia , Cloreto de Sódio/farmacologia , Estresse Fisiológico/genética , Transativadores/genética , Ácido Abscísico/metabolismo , Regulação da Expressão Gênica de Plantas/efeitos dos fármacos , Redes e Vias Metabólicas/genética , Dedos de Zinco/genética
18.
Development ; 145(7)2018 03 29.
Artigo em Inglês | MEDLINE | ID: mdl-29511024

RESUMO

Connective tissues support organs and play crucial roles in development, homeostasis and fibrosis, yet our understanding of their formation is still limited. To gain insight into the molecular mechanisms of connective tissue specification, we selected five zinc-finger transcription factors - OSR1, OSR2, EGR1, KLF2 and KLF4 - based on their expression patterns and/or known involvement in connective tissue subtype differentiation. RNA-seq and ChIP-seq profiling of chick limb micromass cultures revealed a set of common genes regulated by all five transcription factors, which we describe as a connective tissue core expression set. This common core was enriched with genes associated with axon guidance and myofibroblast signature, including fibrosis-related genes. In addition, each transcription factor regulated a specific set of signalling molecules and extracellular matrix components. This suggests a concept whereby local molecular niches can be created by the expression of specific transcription factors impinging on the specification of local microenvironments. The regulatory network established here identifies common and distinct molecular signatures of limb connective tissue subtypes, provides novel insight into the signalling pathways governing connective tissue specification, and serves as a resource for connective tissue development.


Assuntos
Diferenciação Celular/genética , Galinhas/metabolismo , Tecido Conjuntivo/metabolismo , Fatores de Transcrição/metabolismo , Animais , Galinhas/genética , Clonagem Molecular , Extremidades , Perfilação da Expressão Gênica , Regulação da Expressão Gênica no Desenvolvimento , Imuno-Histoquímica , Hibridização In Situ , Morfogênese/genética , Reação em Cadeia da Polimerase em Tempo Real , Análise de Sequência de RNA , Transdução de Sinais , Dedos de Zinco/genética
19.
J Virol ; 92(10)2018 05 15.
Artigo em Inglês | MEDLINE | ID: mdl-29491167

RESUMO

In addition to specific RNA-binding zinc finger domains, the retroviral Gag polyprotein contains clusters of basic amino acid residues that are thought to support Gag-viral genomic RNA (gRNA) interactions. One of these clusters is the basic K16NK18EK20 region, located upstream of the first zinc finger of the Mason-Pfizer monkey virus (M-PMV) nucleocapsid (NC) protein. To investigate the role of this basic region in the M-PMV life cycle, we used a combination of in vivo and in vitro methods to study a series of mutants in which the overall charge of this region was more positive (RNRER), more negative (AEAEA), or neutral (AAAAA). The mutations markedly affected gRNA incorporation and the onset of reverse transcription. The introduction of a more negative charge (AEAEA) significantly reduced the incorporation of M-PMV gRNA into nascent particles. Moreover, the assembly of immature particles of the AEAEA Gag mutant was relocated from the perinuclear region to the plasma membrane. In contrast, an enhancement of the basicity of this region of M-PMV NC (RNRER) caused a substantially more efficient incorporation of gRNA, subsequently resulting in an increase in M-PMV RNRER infectivity. Nevertheless, despite the larger amount of gRNA packaged by the RNRER mutant, the onset of reverse transcription was delayed in comparison to that of the wild type. Our data clearly show the requirement for certain positively charged amino acid residues upstream of the first zinc finger for proper gRNA incorporation, assembly of immature particles, and proceeding of reverse transcription.IMPORTANCE We identified a short sequence within the Gag polyprotein that, together with the zinc finger domains and the previously identified RKK motif, contributes to the packaging of genomic RNA (gRNA) of Mason-Pfizer monkey virus (M-PMV). Importantly, in addition to gRNA incorporation, this basic region (KNKEK) at the N terminus of the nucleocapsid protein is crucial for the onset of reverse transcription. Mutations that change the positive charge of the region to a negative one significantly reduced specific gRNA packaging. The assembly of immature particles of this mutant was reoriented from the perinuclear region to the plasma membrane. On the contrary, an enhancement of the basic character of this region increased both the efficiency of gRNA packaging and the infectivity of the virus. However, the onset of reverse transcription was delayed even in this mutant. In summary, the basic region in M-PMV Gag plays a key role in the packaging of genomic RNA and, consequently, in assembly and reverse transcription.


Assuntos
Produtos do Gene gag/genética , Vírus dos Macacos de Mason-Pfizer/fisiologia , Proteínas do Nucleocapsídeo/genética , Transcrição Reversa/genética , Montagem de Vírus/genética , Sequência de Aminoácidos/genética , Linhagem Celular , Células HEK293 , Humanos , Vírus dos Macacos de Mason-Pfizer/genética , Mutação/genética , RNA Viral/genética , Dedos de Zinco/genética
20.
Gene ; 650: 68-76, 2018 Apr 15.
Artigo em Inglês | MEDLINE | ID: mdl-29408733

RESUMO

Kruppel-like Factors (KLF) are responsible for regulating many genes involved in physiological and pathological processes. They are characterized by three conserved zinc-fingers in the DNA-binding domain, wherein mutations could affect the binding efficiency and transcription regulation. This study aimed to perform bioinformatics analysis to determine the most deleterious non-synonymous variants in KLFs involved in cardiac development and diseases, and their effects over the protein structure and stability. Eight hundred and fifty non-synonymous variants were found in seven KLFs related to cardiac diseases. Seventeen algorithms were used to predict the effect of selected variants over the structure and function of seven KLFs. The Top3 variants were selected in each category of conserved and non-conserved residues in the zinc-finger (ZF) domain. KLF5 p.Cys410Phe was the only variant predicted as deleterious in all algorithms, occurring in a conserved residue of zinc ion interaction. KLF15 p.Arg364Pro was the only variant predicted to affect the DNA-binding, and also occurs in a conserved ZF-domain. Our bioinformatics analysis determined potential variants that may lead to development of cardiac diseases, as well as reinforced the importance of KLF analysis in vitro and in vivo.


Assuntos
Cardiopatias/genética , Fatores de Transcrição Kruppel-Like/genética , Mutação de Sentido Incorreto , Homologia de Sequência de Aminoácidos , Sequência de Aminoácidos , Substituição de Aminoácidos , Sítios de Ligação/genética , Biologia Computacional , Sequência Conservada , Humanos , Fatores de Transcrição Kruppel-Like/química , Fatores de Transcrição Kruppel-Like/metabolismo , Modelos Moleculares , Polimorfismo de Nucleotídeo Único , Análise de Sequência de DNA , Dedos de Zinco/genética
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