scholarly journals Genome-Wide Identification, Comparison, and Expression Analysis of Transcription Factors in Ascidian Styela clava

2021 ◽  
Vol 22 (9) ◽  
pp. 4317
Author(s):  
Jin Zhang ◽  
Jiankai Wei ◽  
Haiyan Yu ◽  
Bo Dong
Keyword(s):  
Transcription Factors ◽  
Zinc Finger ◽  
Hox Genes ◽  
Zinc Finger Protein ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Environmental Adaptation ◽  
Species Differentiation ◽  
Significant Discrepancy ◽  
Styela Clava

Tunicates include diverse species, as they are model animals for evolutionary developmental biology study. The embryonic development of tunicates is known to be extensively regulated by transcription factors (TFs). Styela clava, the globally distributed invasive tunicate, exhibits a strong capacity for environmental adaptation. However, the TFs were not systematically identified and analyzed. In this study, we reported 553 TFs categorized into 60 families from S. clava, based on the whole genome data. Comparison of TFs analysis among the tunicate species revealed that the gene number in the zinc finger superfamily displayed the most significant discrepancy, indicating this family was under the highly evolutionary selection and might be related to species differentiation and environmental adaptation. The greatest number of TFs was discovered in the Cys2His2-type zinc finger protein (zf-C2H2) family in S. clava. From the point of temporal view, more than half the TFs were expressed at the early embryonic stage. The expression correlation analysis revealed the existence of a transition for TFs expression from early embryogenesis to the later larval development in S. clava. Eight Hox genes were identified to be located on one chromosome, exhibiting different arrangement and expression patterns, compared to Ciona robusta (C. intestinalis type A). In addition, a total of 23 forkhead box (fox) genes were identified in S. clava, and their expression profiles referred to their potential roles in neurodevelopment and sensory organ development. Our data, thus, provides crucial clues to the potential functions of TFs in development and environmental adaptation in the leathery sea squirt.

Single zinc-finger extension: enhancing transcriptional activity and specificity of three-zinc-finger proteins

2005 ◽  
Vol 386 (2) ◽  
pp. 95-99 ◽  
Author(s):  
Alexander E.F. Smith ◽  
Farzin Farzaneh ◽  
Kevin G. Ford
Keyword(s):  
Transcription Factors ◽  
Fusion Protein ◽  
Zinc Finger ◽  
Protein Interactions ◽  
Transcriptional Activation ◽  
Zinc Finger Protein ◽  
Zinc Finger Proteins ◽  
Finger Protein ◽  
Finger Extension ◽  
Vp16 Fusion

AbstractIn order to demonstrate that an existing zinc-finger protein can be simply modified to enhance DNA binding and sequence discrimination in both episomal and chromatin contexts using existing zinc-finger DNA recognition code data, and without recourse to phage display and selection strategies, we have examined the consequences of a single zinc-finger extension to a synthetic three-zinc-finger VP16 fusion protein, on transcriptional activation from model target promoters harbouring the zinc-finger binding sequences. We report a nearly 10-fold enhanced transcriptional activation by the four-zinc-finger VP16 fusion protein relative to the progenitor three-finger VP16 protein in transient assays and a greater than five-fold enhancement in stable reporter-gene expression assays. A marked decrease in transcriptional activation was evident for the four-zinc-finger derivative from mutated regulatory regions compared to the progenitor protein, as a result of recognition site-size extension. This discriminatory effect was shown to be protein concentration-dependent. These observations suggest that four-zinc-finger proteins are stable functional motifs that can be a significant improvement over the progenitor three-zinc-finger protein, both in terms of specificity and the ability to target transcriptional function to promoters, and that single zinc-finger extension can therefore have a significant impact on DNA zinc-finger protein interactions. This is a simple route for modifying or enhancing the binding properties of existing synthetic zinc-finger-based transcription factors and may be particularly suited for the modification of endogenous zinc-finger transcription factors for promoter biasing applications.

CCCH Zinc Finger Genes in Barley: Genome-Wide Identification, Evolution, Expression and Haplotype Analysis

2021 ◽  
Author(s):  
Qi Ai ◽  
Wenqiu Pan ◽  
Yan Zeng ◽  
Yihan Li ◽  
Licao Cui
Keyword(s):  
Transcription Factors ◽  
Abiotic Stress ◽  
Zinc Finger ◽  
Molecular Breeding ◽  
Animal Feed ◽  
Expression Profiles ◽  
Exome Capture ◽  
Biotic And Abiotic Stress ◽  
Motif Analysis ◽  
Developmental Processes

Abstract Background: CCCH transcription factors are important zinc finger transcription factors involved in the response to biotic and abiotic stress and physiological and developmental processes. Barley (Hordeum vulgare) is an agriculturally important cereal crop with multiple uses, such as brewing production, animal feed, and human food. The identification and assessment of new functional genes are important for the molecular breeding of barley. Results: In this study, a total of 35 protein-encoding CCCH genes unevenly dispersed on seven different chromosomes were identified in barley. Phylogenetic analysis categorized the barley CCCH genes (HvC3Hs) into seven subfamilies according to their distinct features, and this classification was supported by intron–exon structure and conserved motif analysis. Despite the large genome size of barley, the lower number of CCCH genes in barley might be attributed to the low frequency of segmental and tandem duplication events. Furthermore, the HvC3H genes displayed distinct expression profiles for different developmental processes and in response to various types of stresses. The expression of HvC3H9 was significantly induced by multiple types of abiotic stress and/or phytohormone treatment, which might make it an excellent target for the molecular breeding of barley. Genetic variation of HvC3Hs was characterized using publicly available exome-capture sequencing datasets. Clear genetic divergence was observed between wild and landrace barley populations in HvC3H genes. For most HvC3Hs, nucleotide diversity and the number of haplotype polymorphisms decreased during barley domestication. Conclusion: Overall, our study provides a comprehensive characterization of barley CCCH transcription factors, their diversity, and their biological functions.

scholarly journals Major Latex Protein MdMLP423 Negatively Regulates Defense against Fungal Infections in Apple

2020 ◽  
Vol 21 (5) ◽  
pp. 1879 ◽  
Author(s):  
Shanshan He ◽  
Gaopeng Yuan ◽  
Shuxun Bian ◽  
Xiaolei Han ◽  
Kai Liu ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Stress Responses ◽  
Zinc Finger Protein ◽  
Fungal Infections ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Genes Encoding ◽  
Pathogenesis Related Gene ◽  
Stress Related Genes ◽  
Related Proteins

Major latex proteins (MLPs) play critical roles in plants defense and stress responses. However, the roles of MLPs from apple (Malus × domestica) have not been clearly identified. In this study, we focused on the biological role of MdMLP423, which had been previously characterized as a potential pathogenesis-related gene. Phylogenetic analysis and conserved domain analysis indicated that MdMLP423 is a protein with a ‘Gly-rich loop’ (GXGGXG) domain belonging to the Bet v_1 subfamily. Gene expression profiles showed that MdMLP423 is mainly expressed in flowers. In addition, the expression of MdMLP423 was significantly inhibited by Botryosphaeria berengeriana f. sp. piricola (BB) and Alternaria alternata apple pathotype (AAAP) infections. Apple calli overexpressing MdMLP423 had lower expression of resistance-related genes, and were more sensitive to infection with BB and AAAP compared with non-transgenic calli. RNA-seq analysis of MdMLP423-overexpressing calli and non-transgenic calli indicated that MdMLP423 regulated the expression of a number of differentially expressed genes (DEGs) and transcription factors, including genes involved in phytohormone signaling pathways, cell wall reinforcement, and genes encoding the defense-related proteins, AP2-EREBP, WRKY, MYB, NAC, Zinc finger protein, and ABI3. Taken together, our results demonstrate that MdMLP423 negatively regulates apple resistance to BB and AAAP infections by inhibiting the expression of defense- and stress-related genes and transcription factors.

scholarly journals On the prediction of DNA-binding preferences of C2H2-ZF domains using structural models: application on human CTCF

2020 ◽  
Vol 2 (3) ◽  
Author(s):  
Alberto Meseguer ◽  
Filip Årman ◽  
Oriol Fornes ◽  
Ruben Molina-Fernández ◽  
Jaume Bonet ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Dna Binding ◽  
Binding Site ◽  
Zinc Finger ◽  
Zinc Finger Protein ◽  
Computational Method ◽  
Chromatin Binding ◽  
Input Structure ◽  
Binding Factor ◽  
Potential Binding

Abstract Cis2-His2 zinc finger (C2H2-ZF) proteins are the largest family of transcription factors in human and higher metazoans. To date, the DNA-binding preferences of many members of this family remain unknown. We have developed a computational method to predict their DNA-binding preferences. We have computed theoretical position weight matrices (PWMs) of proteins composed by C2H2-ZF domains, with the only requirement of an input structure. We have predicted more than two-third of a single zinc-finger domain binding site for about 70% variants of Zif268, a classical member of this family. We have successfully matched between 60 and 90% of the binding-site motif of examples of proteins composed by three C2H2-ZF domains in JASPAR, a standard database of PWMs. The tests are used as a proof of the capacity to scan a DNA fragment and find the potential binding sites of transcription-factors formed by C2H2-ZF domains. As an example, we have tested the approach to predict the DNA-binding preferences of the human chromatin binding factor CTCF. We offer a server to model the structure of a zinc-finger protein and predict its PWM.

Generation of Two Homologous and Intronless Zinc-Finger Protein Genes, Zfp352 and Zfp353, with Different Expression Patterns by Retrotransposition

Genomics ◽  
2002 ◽  
Vol 79 (1) ◽  
pp. 18-23 ◽  
Author(s):  
Huang-Hui Chen ◽  
Tiffany Yi-Chen Liu ◽  
Chiu-Jung Huang ◽  
Kong-Bung Choo
Keyword(s):  
Zinc Finger ◽  
Zinc Finger Protein ◽  
Expression Patterns ◽  
Finger Protein

scholarly journals Transcriptional Regulation of the AP-2α Promoter by BTEB-1 and AP-2rep, a Novel wt-1/egr-Related Zinc Finger Repressor

1999 ◽  
Vol 19 (1) ◽  
pp. 194-204 ◽  
Author(s):  
Axel Imhof ◽  
Marion Schuierer ◽  
Oliver Werner ◽  
Markus Moser ◽  
Christina Roth ◽  
...  
Keyword(s):  
Transcriptional Regulation ◽  
Transcription Factors ◽  
Zinc Finger ◽  
Transcriptional Repression ◽  
Promoter Activity ◽  
Zinc Finger Protein ◽  
Cdna Expression Library ◽  
Neuro2a Cell ◽  
Expression Library ◽  
Cell Extracts

ABSTRACT AP-2 transcription factors have been suggested to exert key regulatory functions in vertebrate embryonic development, in tumorigenicity of various cancer cell types, and in controlling cell cycle and apoptotic effector genes. In this study, we investigated transcriptional regulation of the AP-2α gene promoter mediated by an autoregulatory element (referred to as A32) with a core consensus AP-2 binding site at position −336 relative to the mRNA initiation site. AP-2 and multiple different nuclear proteins in HeLa and Neuro2A cell extracts form specific bandshifts with the A32 element. By screening a mouse brain cDNA expression library, we isolated two different cDNAs encoding the transcription factor BTEB-1 and a novel zinc finger protein, AP-2rep. AP-2rep reveals a modular structure with homology to transcription factors of the wt-1/egr-1-family. AP-2rep, BTEB-1, and AP-2 interact in a mutually exclusive manner with overlapping binding sites in the A32 element. Transfection studies revealed that BTEB-1 is a strong activator of AP-2α promoter activity, whereas cotransfected AP-2α resulted in moderate autoactivation of promoter activity. In contrast, AP-2rep confers strong transcriptional repression to the AP-2α gene, and we observed an excellent correlation between induction of AP-2rep mRNA expression and downregulation of AP-2α mRNA during development of the kidney. In summary, we have identified multiple transcription factors and cloned from an expression library a novel zinc finger silencing factor, AP-2rep, mediating positive and negative regulation of AP-2α expression through a set of overlappingcis-regulatory promoter elements.

scholarly journals Genome-Wide Characterization, Expression Profile Analysis of WRKY Family Genes in Santalum album and Functional Identification of Their Role in Abiotic Stress

2019 ◽  
Vol 20 (22) ◽  
pp. 5676 ◽  
Author(s):  
Haifeng Yan ◽  
Mingzhi Li ◽  
Yuping Xiong ◽  
Jianming Wu ◽  
Jaime A. Teixeira da Silva ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Abiotic Stress ◽  
Stress Responses ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Protein Sequences ◽  
Santalum Album ◽  
Biotic And Abiotic Stress ◽  
Functional Identification ◽  
Wrky Protein

WRKY proteins are a large superfamily of transcription factors that are involved in diverse biological processes including development, as well as biotic and abiotic stress responses in plants. WRKY family proteins have been extensively characterized and analyzed in many plant species, including Arabidopsis, rice, and poplar. However, knowledge on WRKY transcription factors in Santalum album is scarce. Based on S. album genome and transcriptome data, 64 SaWRKY genes were identified in this study. A phylogenetic analysis based on the structures of WRKY protein sequences divided these genes into three major groups (I, II, III) together with WRKY protein sequences from Arabidopsis. Tissue-specific expression patterns showed that 37 SaWRKY genes were expressed in at least one of five tissues (leaves, roots, heartwood, sapwood, or the transition zone), while the remaining four genes weakly expressed in all of these tissues. Analysis of the expression profiles of the 42 SaWRKY genes after callus was initiated by salicylic acid (SA) and methyl jasmonate (MeJA) revealed that 25 and 24 SaWRKY genes, respectively, were significantly induced. The function of SaWRKY1, which was significantly up-regulated by SA and MeJA, was analyzed. SaWRKY1 was localized in the nucleus and its overexpression improved salt tolerance in transgenic Arabidopsis. Our study provides important information to further identify the functions of SaWRKY genes and to understand the roles of SaWRKY family genes involved in the development and in SA- and MeJA-mediated stress responses.

scholarly journals 1000. Down-Regulating the Epithelial Glycoprotein-2 Promoter Utilizing Engineered Zinc Finger Protein Transcription Factors

2006 ◽  
Vol 13 ◽  
pp. S385
Author(s):  
Willemijn M. Gommans ◽  
Pamela M.J. McLaughlin ◽  
Robbert Cool ◽  
Beatrice I. Lindhout ◽  
Bert van der Zaal ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Zinc Finger ◽  
Zinc Finger Protein ◽  
Finger Protein ◽  
Protein Transcription
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