scholarly journals Differential expression of transcription factor- and further growth-related genes correlates with contrasting cluster architecture in Vitis vinifera ‘Pinot Noir’ and Vitis spp. genotypes

2020 ◽  
Vol 133 (12) ◽  
pp. 3249-3272
Author(s):  
Robert Richter ◽  
Susanne Rossmann ◽  
Doreen Gabriel ◽  
Reinhard Töpfer ◽  
Klaus Theres ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcription Factor ◽  
Vitis Vinifera ◽  
Differential Expression ◽  
Fungal Infections ◽  
Clonal Selection ◽  
Interspecific Cross ◽  
Pinot Noir ◽  
Wine Production ◽  
Cluster Architecture

Abstract Grapevine (Vitis vinifera L.) is an economically important crop that needs to comply with high quality standards for fruit, juice and wine production. Intense plant protection is required to avoid fungal damage. Grapevine cultivars with loose cluster architecture enable reducing protective treatments due to their enhanced resilience against fungal infections, such as Botrytis cinerea-induced gray mold. A recent study identified transcription factor gene VvGRF4 as determinant of pedicel length, an important component of cluster architecture, in samples of two loose and two compact quasi-isogenic ‘Pinot Noir’ clones. Here, we extended the analysis to 12 differently clustered ‘Pinot Noir’ clones from five diverse clonal selection programs. Differential gene expression of these clones was studied in three different locations over three seasons. Two phenotypically opposite clones were grown at all three locations and served for standardization. Data were correlated with the phenotypic variation of cluster architecture sub-traits. A set of 14 genes with consistent expression differences between loosely and compactly clustered clones—independent from season and location—was newly identified. These genes have annotations related to cellular growth, cell division and auxin metabolism and include two more transcription factor genes, PRE6 and SEP1-like. The differential expression of VvGRF4 in relation to loose clusters was exclusively found in ‘Pinot Noir’ clones. Gene expression studies were further broadened to phenotypically contrasting F1 individuals of an interspecific cross and OIV reference varieties of loose cluster architecture. This investigation confirmed PRE6 and six growth-related genes to show differential expression related to cluster architecture over genetically divergent backgrounds.

scholarly journals Same same but different: Cluster architecture variation in five ‘Pinot Noir’ clonal selection lines correlates with differential expression of three transcription factors and further growth related genes

2020 ◽  
Author(s):  
Robert Richter ◽  
Susanne Rossmann ◽  
Doreen Gabriel ◽  
Reinhard Töpfer ◽  
Klaus Theres ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcription Factor ◽  
Differential Gene Expression ◽  
Fungal Infections ◽  
Clonal Selection ◽  
Pinot Noir ◽  
Cellular Growth ◽  
Wine Production ◽  
Cluster Architecture ◽  
Differential Gene

AbstractGrapevine (Vitis vinifera L.) is an economically important crop that needs to comply with high quality standards for fruit, juice and wine production. Intense plant protection is required to avoid losses caused by fungal infections. Grapevine cultivars with loose cluster architecture enable to reduce protective chemical treatments due to their enhanced resilience against fungal infections such as Botrytis cinerea induced grey mold. A recent study identified transcription factor gene VvGRF4 as determinant of inflorescence structure in exemplary samples of loose and compact quasi-isogenic ‘Pinot Noir’ clones. Here, we extended the analysis to 12 differently clustered ‘Pinot Noir’ clones originating from five different clonal selection programs. Differential gene expression of these clones was studied in three different locations over three seasons in demonstrative vineyards. Two phenotypically contrasting clones were grown at all three locations and served for standardization of downstream analyses. Differential gene expression data were correlated to the phenotypic variation of cluster architecture sub-traits. A consistent differential gene expression of VvGRF4 in relation to loose clusters was verified over the different environments and in the extended set of ‘Pinot Noir’ clones. In addition, 14 more genes with consistent expression differences between loosely and compactly clustered clones independent from season and location were identified. These genes show annotations related to cellular growth, cell wall extension, cell division and auxin metabolism. They include two more transcription factor genes.

scholarly journals A multi-tool recipe to identify regions of protein-DNA binding and their influence on associated gene expression

F1000Research ◽  
2018 ◽  
Vol 6 ◽  
pp. 784
Author(s):  
Daniel E. Carlin ◽  
Kassi Kosnicki ◽  
Sara Garamszegi ◽  
Trey Ideker ◽  
Helga Thorvaldsdóttir ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcription Factor ◽  
Transcription Factors ◽  
User Interface ◽  
Dna Binding ◽  
Data Integration ◽  
Differential Expression ◽  
Regulation Of Transcription ◽  
Rna Seq ◽  
Functional Regulation

One commonly performed bioinformatics task is to infer functional regulation of transcription factors by observing differential expression under a knockout, and integrating DNA binding information of that transcription factor.   However, until now, this task has required dedicated bioinformatics support to perform the necessary data integration. GenomeSpace provides a protocol, or “recipe”, and a user interface with inter-operating software tools to identify protein occupancies along the genome from a ChIP-seq experiment and associated differentially regulated genes from a RNA-Seq experiment. By integrating RNA-Seq and ChIP-seq analyses, a user is easily able to associate differing expression phenotypes with changing epigenetic landscapes.

scholarly journals A banned variety was the mother of several major wine grapes

2009 ◽  
Vol 6 (3) ◽  
pp. 367-369 ◽  
Author(s):  
Harriet V. Hunt ◽  
Matthew C. Lawes ◽  
Mim A. Bower ◽  
John W. Haeger ◽  
Christopher J. Howe
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Vitis Vinifera ◽  
Chloroplast Dna ◽  
Pinot Noir ◽  
Nucleotide Polymorphism ◽  
Wine Grapes ◽  
Wine Production ◽  
Single Nucleotide ◽  
Maternal Parent

A number of widely grown varieties of Vitis vinifera ssp. sativa , the grape used for wine production, are known to have resulted from crosses between Pinot noir and Gouais blanc, although it is not known which was the maternal parent in these crosses. We have analysed microsatellites and a single nucleotide polymorphism (SNP) in chloroplast DNA from these two varieties and twelve progeny strains, including Chardonnay, Gamay noir and Aligoté. The results demonstrate that Gouais blanc was the maternal parent for nine of these strains, including Chardonnay, Gamay noir and Aligoté. This is a striking conclusion, as Gouais is generally considered a highly inferior variety, and its cultivation was banned for many years in parts of Europe.

scholarly journals A multi-tool recipe to identify regions of protein-DNA binding and their influence on associated gene expression

F1000Research ◽  
2017 ◽  
Vol 6 ◽  
pp. 784
Author(s):  
Daniel E. Carlin ◽  
Kassi Kosnicki ◽  
Sara Garamszegi ◽  
Trey Ideker ◽  
Helga Thorvaldsdóttir ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcription Factor ◽  
Transcription Factors ◽  
User Interface ◽  
Dna Binding ◽  
Data Integration ◽  
Differential Expression ◽  
Regulation Of Transcription ◽  
Rna Seq ◽  
Functional Regulation

One commonly performed bioinformatics task is to infer functional regulation of transcription factors by observing differential expression under a knockout, and integrating DNA binding information of that transcription factor.   However, until now, this this task has required dedicated bioinformatics support to perform the necessary data integration. GenomeSpace provides a protocol, or “recipe”, and a user interface with inter-operating software tools to identifying protein occupancies along the genome from a ChIP-seq experiment and associated differentially regulated genes from an RNA-Seq experiment. By integrating RNA-Seq and ChIP-seq analyses, a user is easily able to associate differing expression phenotypes with changing epigenetic landscapes.

scholarly journals Aberrant expression of USF2 in refractory rheumatoid arthritis and its regulation of proinflammatory cytokines in Th17 cells

2020 ◽  
Vol 117 (48) ◽  
pp. 30639-30648
Author(s):  
Dan Hu ◽  
Emily C. Tjon ◽  
Karin M. Andersson ◽  
Gabriela M. Molica ◽  
Minh C. Pham ◽  
...  
Keyword(s):  
Rheumatoid Arthritis ◽  
Gene Expression ◽  
T Cells ◽  
Transcription Factor ◽  
Proinflammatory Cytokines ◽  
Th17 Cells ◽  
Gene Set Enrichment Analysis ◽  
Aberrant Expression ◽  
Signature Genes ◽  
The Impact

IL-17–producing Th17 cells are implicated in the pathogenesis of rheumatoid arthritis (RA) and TNF-α, a proinflammatory cytokine in the rheumatoid joint, facilitates Th17 differentiation. Anti-TNF therapy ameliorates disease in many patients with rheumatoid arthritis (RA). However, a significant proportion of patients do not respond to this therapy. The impact of anti-TNF therapy on Th17 responses in RA is not well understood. We conducted high-throughput gene expression analysis of Th17-enriched CCR6+CXCR3−CD45RA−CD4+T (CCR6+T) cells isolated from anti-TNF–treated RA patients classified as responders or nonresponders to therapy. CCR6+T cells from responders and nonresponders had distinct gene expression profiles. Proinflammatory signaling was elevated in the CCR6+T cells of nonresponders, and pathogenic Th17 signature genes were up-regulated in these cells. Gene set enrichment analysis on these signature genes identified transcription factor USF2 as their upstream regulator, which was also increased in nonresponders. Importantly, short hairpin RNA targetingUSF2in pathogenic Th17 cells led to reduced expression of proinflammatory cytokines IL-17A, IFN-γ, IL-22, and granulocyte-macrophage colony-stimulating factor (GM-CSF) as well as transcription factor T-bet. Together, our results revealed inadequate suppression of Th17 responses by anti-TNF in nonresponders, and direct targeting of the USF2-signaling pathway may be a potential therapeutic approach in the anti-TNF refractory RA.

Subnuclear compartmentalization of sequence-specific transcription factors and regulation of eukaryotic gene expression

2005 ◽  
Vol 83 (4) ◽  
pp. 535-547 ◽  
Author(s):  
Gareth N Corry ◽  
D Alan Underhill
Keyword(s):  
Gene Expression ◽  
Transcription Factor ◽  
Transcription Factors ◽  
Transcriptional Activation ◽  
Current Knowledge ◽  
Nuclear Architecture ◽  
Subnuclear Localization ◽  
Modular Structures

To date, the majority of the research regarding eukaryotic transcription factors has focused on characterizing their function primarily through in vitro methods. These studies have revealed that transcription factors are essentially modular structures, containing separate regions that participate in such activities as DNA binding, protein–protein interaction, and transcriptional activation or repression. To fully comprehend the behavior of a given transcription factor, however, these domains must be analyzed in the context of the entire protein, and in certain cases the context of a multiprotein complex. Furthermore, it must be appreciated that transcription factors function in the nucleus, where they must contend with a variety of factors, including the nuclear architecture, chromatin domains, chromosome territories, and cell-cycle-associated processes. Recent examinations of transcription factors in the nucleus have clarified the behavior of these proteins in vivo and have increased our understanding of how gene expression is regulated in eukaryotes. Here, we review the current knowledge regarding sequence-specific transcription factor compartmentalization within the nucleus and discuss its impact on the regulation of such processes as activation or repression of gene expression and interaction with coregulatory factors.Key words: transcription, subnuclear localization, chromatin, gene expression, nuclear architecture.

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