scholarly journals Pollen Transcriptome and Proteome: Molecular and Functional Analysis

2010 ◽  
Vol 2 (1) ◽  
pp. 29-57 ◽  
Author(s):  
Katarzyna Rafinska ◽  
Krzysztof Zienkiewicz ◽  
Elzbieta Bednarska
Keyword(s):  
Gene Expression ◽  
Functional Analysis ◽  
Structural Organization ◽  
Current Knowledge ◽  
Male Gametophyte ◽  
Plant Cells ◽  
Pollen Grain ◽  
Rapid Progress ◽  
Genetic Studies ◽  
Simple Extraction

SummaryThe pollen grain, because of its unique structural organization, is an extremely useful experimental model in cytological, molecular as well as in genetic studies. Due to the ease of pollen grain isolation, their sorting as well as simple extraction of their DNA, RNA and proteins, male gametophyte cells of angiosperms are presently one of the most intensively studied plant cells. Important and rapid progress in the development of experimental tools for genome exploration caused a significant increase in the number of reports concerning different aspects of gene expression during microsporogenesis and microgametogenesis in angiosperm plants. In this review we present the current knowledge of the pollen transcriptome and proteome during different stages of male gametophyte development, especially in Arabidopsis thaliana. Most of the results presented here were obtained in experiments carried out using microarrays, which were designed on the basis of the known sequence of the Arabidopsis genome.

scholarly journals A CRISPR/dCas9 toolkit for functional analysis of maize genes

Plant Methods ◽  
2020 ◽  
Vol 16 (1) ◽  
Author(s):  
Irene N. Gentzel ◽  
Chan Ho Park ◽  
Maria Bellizzi ◽  
Guiqing Xiao ◽  
Kiran R. Gadhave ◽  
...  
Keyword(s):  
Gene Expression ◽  
Functional Analysis ◽  
Functional Genomics ◽  
Protoplast Isolation ◽  
Genetic Studies ◽  
Transfection Method ◽  
Important Trait ◽  
Maize Gene

Abstract Background The Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas9 system has become a powerful tool for functional genomics in plants. The RNA-guided nuclease can be used to not only generate precise genomic mutations, but also to manipulate gene expression when present as a deactivated protein (dCas9). Results In this study, we describe a vector toolkit for analyzing dCas9-mediated activation (CRISPRa) or inactivation (CRISPRi) of gene expression in maize protoplasts. An improved maize protoplast isolation and transfection method is presented, as well as a description of dCas9 vectors to enhance or repress maize gene expression. Conclusions We anticipate that this maize protoplast toolkit will streamline the analysis of gRNA candidates and facilitate genetic studies of important trait genes in this transformation-recalcitrant plant.

scholarly journals A CRISPR/dCas9 toolkit for functional analysis of maize genes

2020 ◽  
Author(s):  
Irene Gentzel ◽  
Chan Ho Park ◽  
Maria Bellizzi ◽  
Guiqing Xiao ◽  
Kiran Gadharve ◽  
...  
Keyword(s):  
Gene Expression ◽  
Functional Analysis ◽  
Protoplast Isolation ◽  
Genetic Studies ◽  
Guide Rnas ◽  
Transfection Method ◽  
Positive Sense ◽  
Important Trait ◽  
Whole Plants ◽  
Maize Gene

Abstract Background: The C lustered R egularly I nterspaced S hort P alindromic R epeats (CRISPR)/Cas9 system has become a powerful tool for functional genomics in plants. The RNA-guided nuclease can be used to not only generate precise genomic mutations, but also to manipulate gene expression when present as a deactivated protein (dCas9). Results: In this study, we describe a vector toolkit for analyzing dCas9-mediated activation (CRISPRa) or inactivation (CRISPRi) of gene expression in maize protoplasts. An improved maize protoplast isolation and transfection method is presented, as well as a description of dCas9 vectors to enhance or repress maize gene expression. Additionally, we describe the utility of Foxtail Mosaic Virus (FoMV), a positive-sense RNA monocot virus, as a vector for delivering guide RNAs (gRNAs) to maize protoplasts in addition to whole plants. Conclusions: We anticipate that this maize protoplast toolkit will streamline the analysis of gRNA candidates and facilitate genetic studies of important trait genes in this transformation-recalcitrant plant.

scholarly journals A CRISPR/dCas9 toolkit for functional analysis of maize genes

2020 ◽  
Author(s):  
Irene Gentzel ◽  
Chan Ho Park ◽  
Maria Bellizzi ◽  
Guiqing Xiao ◽  
Kiran Gadharve ◽  
...  
Keyword(s):  
Gene Expression ◽  
Functional Analysis ◽  
Functional Genomics ◽  
Protoplast Isolation ◽  
Genetic Studies ◽  
Transfection Method ◽  
Important Trait ◽  
Maize Gene

Abstract Background: The Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas9 system has become a powerful tool for functional genomics in plants. The RNA-guided nuclease can be used to not only generate precise genomic mutations, but also to manipulate gene expression when present as a deactivated protein (dCas9). Results: In this study, we describe a vector toolkit for analyzing dCas9-mediated activation (CRISPRa) or inactivation (CRISPRi) of gene expression in maize protoplasts. An improved maize protoplast isolation and transfection method is presented, as well as a description of dCas9 vectors to enhance or repress maize gene expression. Conclusions: We anticipate that this maize protoplast toolkit will streamline the analysis of gRNA candidates and facilitate genetic studies of important trait genes in this transformation-recalcitrant plant.

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.

scholarly journals Cell states beyond transcriptomics: Integrating structural organization and gene expression in hiPSC-derived cardiomyocytes

Cell Systems ◽  
2021 ◽  
Author(s):  
Kaytlyn A. Gerbin ◽  
Tanya Grancharova ◽  
Rory M. Donovan-Maiye ◽  
Melissa C. Hendershott ◽  
Helen G. Anderson ◽  
...  
Keyword(s):  
Gene Expression ◽  
Structural Organization

scholarly journals Interplay between cofactors and transcription factors in hematopoiesis and hematological malignancies

2021 ◽  
Vol 6 (1) ◽  
Author(s):  
Zi Wang ◽  
Pan Wang ◽  
Yanan Li ◽  
Hongling Peng ◽  
Yu Zhu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcription Factors ◽  
Hematological Malignancies ◽  
Current Knowledge ◽  
Regulation Of Gene Expression ◽  
Hematologic Disorders ◽  
Cell Lineages ◽  
Stage Of Development ◽  
Transcription Complexes ◽  
Insight Into

AbstractHematopoiesis requires finely tuned regulation of gene expression at each stage of development. The regulation of gene transcription involves not only individual transcription factors (TFs) but also transcription complexes (TCs) composed of transcription factor(s) and multisubunit cofactors. In their normal compositions, TCs orchestrate lineage-specific patterns of gene expression and ensure the production of the correct proportions of individual cell lineages during hematopoiesis. The integration of posttranslational and conformational modifications in the chromatin landscape, nucleosomes, histones and interacting components via the cofactor–TF interplay is critical to optimal TF activity. Mutations or translocations of cofactor genes are expected to alter cofactor–TF interactions, which may be causative for the pathogenesis of various hematologic disorders. Blocking TF oncogenic activity in hematologic disorders through targeting cofactors in aberrant complexes has been an exciting therapeutic strategy. In this review, we summarize the current knowledge regarding the models and functions of cofactor–TF interplay in physiological hematopoiesis and highlight their implications in the etiology of hematological malignancies. This review presents a deep insight into the physiological and pathological implications of transcription machinery in the blood system.

scholarly journals Viral-Mediated mRNA Degradation for Pathogenesis

Biomedicines ◽  
2018 ◽  
Vol 6 (4) ◽  
pp. 111
Author(s):  
Shujuan Du ◽  
Xiaoqing Liu ◽  
Qiliang Cai
Keyword(s):  
Gene Expression ◽  
Current Knowledge ◽  
Immune Surveillance ◽  
Viral Gene Expression ◽  
Mrna Degradation ◽  
Vital Role ◽  
Viral Gene ◽  
Antiviral Immune Response ◽  
Successful Infection ◽  
The Stability

Cellular RNA decay machinery plays a vital role in regulating gene expression by altering the stability of mRNAs in response to external stresses, including viral infection. In the primary infection, viruses often conquer the host cell’s antiviral immune response by controlling the inherently cellular mRNA degradation machinery to facilitate viral gene expression and establish a successful infection. This review summarizes the current knowledge about the diverse strategies of viral-mediated regulatory RNA shutoff for pathogenesis, and particularly sheds a light on the mechanisms that viruses evolve to elude immune surveillance during infection.

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