Differential expression of genes during legume seed development

1986 ◽  
Vol 314 (1166) ◽  
pp. 367-384 ◽  
Keyword(s):  
Gene Expression ◽  
Seed Development ◽  
Seed Protein ◽  
Practical Significance ◽  
Specific Expression ◽  
Control Of Gene Expression ◽  
Developing Seeds ◽  
Expression Of Genes ◽  
Seed Protein Genes ◽  
Developmental Programme

The accumulation of certain proteins specific to those tissues in the developing seeds of legumes represents a system of academic and practical significance in the study of differential gene expression. Besides the simple distinction between ‘seed-specific’ and ‘non-seed-specific’ expression of genes, further controls are present in determining the level of expression of a particular gene, and the variations in its expression with cell type, developmental stage and environmental perturbation. There are also genetic factors that lead to variations in the expression of homologous genes between lines or species. Gene expression can be assayed at the levels of synthesis of specific proteins, level of mRNA species, and transcription of specific genes, and the results of all these assays lead to a broad correlation between events at the level of the gene and protein deposition in the developing seed. This correlation is strong at earlier stages of seed development, but is weaker at later stages. Evidence is presented that control of gene expression occurs both at transcription and by post-transcriptional processes. Seed protein genes have conserved sequences in their 5' flanking regions that are specific to gene families, and these are suggested to be involved in transcriptional control of the expression of these genes. Although such sequences are unlikely to be solely responsible for transcription control, there is no strong evidence for changes in DNA methylation or in chromatin conformation being causally related to expression of seed protein genes. Control of gene expression in developing seeds is considered in terms of a genetically determined, conserved developmental programme, the aim of which is to produce a viable embryo. This programme will allow considerable plasticity in gene expression within constraints prescribed by seed viability. Although it may be possible to understand the immediate controls of seed protein gene expression, present systems are not adequate to study the genes that control the developmental programme. More fundamental investigations will be assisted by mutants that possess altered seed development patterns.

Regulation of plant gene expression

1986 ◽  
Vol 314 (1166) ◽  
pp. 343-353 ◽  
Keyword(s):  
Gene Expression ◽  
Gene Transfer ◽  
Dna Sequences ◽  
Seed Protein ◽  
Higher Plants ◽  
Soybean Seed ◽  
Specific Expression ◽  
Sequence Composition ◽  
Organ Systems ◽  
Seed Protein Genes

Differential gene expression is required to establish and maintain specific developmental states in higher plants. For example, an anther has at least 11000 diverse mRNAs that are absent from the polysomes of other organ systems, and the root has at least 7000 organ-specific mRNAs. Both transcriptional and post-transcriptional processes regulate the sequence composition and prevalence distribution of each developmental-specific mRNA set. Soybean seed protein genes represent an excellent example of a highly regulated gene set. These genes are temporally and spatially regulated during embryogenesis, and are either inactive or expressed at low levels in mature plant organ systems. Gene transfer experiments indicate that soybean seed protein genes retain their developmental-specific expression programme in transformed tobacco plants. In addition, large polygenic clusters can be transferred from soybean to tobacco, and the expression pattern of each gene within the cluster is maintained in the foreign cell environment. Although the DNA sequences and cellular factors required to control seed protein gene expression are not yet known, gene transfer studies and emerging DNA binding protein technology should facilitate their identification in the near future.

scholarly journals Transcriptome changes reveal the genetic mechanisms of the reproductive plasticity of workers in lower termites

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Chenxu Ye ◽  
Humaira Rasheed ◽  
Yuehua Ran ◽  
Xiaojuan Yang ◽  
Lianxi Xing ◽  
...  
Keyword(s):  
Gene Expression ◽  
Signal Transduction ◽  
Molecular Mechanisms ◽  
Environmental Changes ◽  
Mapk Pathway ◽  
Specific Expression ◽  
Expression Of Genes ◽  
Genetic Mechanisms ◽  
Ecological Success ◽  
Reproductive Plasticity

Abstract Background The reproductive plasticity of termite workers provides colonies with tremendous flexibility to respond to environmental changes, which is the basis for evolutionary and ecological success. Although it is known that all colony members share the same genetic background and that differences in castes are caused by differences in gene expression, the pattern of the specific expression of genes involved in the differentiation of workers into reproductives remains unclear. In this study, the isolated workers of Reticulitermes labralis developed into reproductives, and then comparative transcriptomes were used for the first time to reveal the molecular mechanisms underlying the reproductive plasticity of workers. Results We identified 38,070 differentially expressed genes and found a pattern of gene expression involved in the differentiation of the workers into reproductives. 12, 543 genes were specifically upregulated in the isolated workers. Twenty-five signal transduction pathways classified into environmental information processing were related to the differentiation of workers into reproductives. Ras functions as a signalling switch regulates the reproductive plasticity of workers. The catalase gene which is related to longevity was up-regulated in reproductives. Conclusion We demonstrate that workers leaving the natal colony can induce the expression of stage-specific genes in the workers, which leads to the differentiation of workers into reproductives and suggests that the signal transduction along the Ras-MAPK pathway crucially controls the reproductive plasticity of the workers. This study also provides an important model for revealing the molecular mechanism of longevity changes.

Cell biology of transcription and pre-mRNA splicing: nuclear architecture meets nuclear function

2000 ◽  
Vol 113 (11) ◽  
pp. 1841-1849 ◽  
Author(s):  
T. Misteli
Keyword(s):  
Gene Expression ◽  
Cell Nucleus ◽  
Cell Biology ◽  
Nuclear Architecture ◽  
Molecular Techniques ◽  
Mrna Splicing ◽  
Cellular Organization ◽  
Control Of Gene Expression ◽  
Expression Of Genes

Gene expression is a fundamental cellular process. The basic mechanisms involved in expression of genes have been characterized at the molecular level. A major challenge is now to uncover how transcription, RNA processing and RNA export are organized within the cell nucleus, how these processes are coordinated with each other and how nuclear architecture influences gene expression and regulation. A significant contribution has come from cell biological approaches, which combine molecular techniques with microscopy methods. These studies have revealed that the mammalian cell nucleus is a complex but highly organized organelle, which contains numerous subcompartments. I discuss here how two essential nuclear processes - transcription and pre-mRNA splicing - are spatially organized and coordinated in vivo, and how this organization might contribute to the control of gene expression. The dynamic nature of nuclear proteins and compartments indicates a high degree of plasticity in the cellular organization of nuclear functions. The cellular organization of transcription and splicing suggest that the morphology of nuclear compartments is largely determined by the activities of the nucleus.

scholarly journals Genomic dissection of the cytokine-controlled STAT5 signaling network in liver

2008 ◽  
Vol 34 (2) ◽  
pp. 135-143 ◽  
Author(s):  
Atsushi Hosui ◽  
Lothar Hennighausen
Keyword(s):  
Gene Expression ◽  
Gene Expression Profiling ◽  
Expression Profiling ◽  
Target Genes ◽  
Global Gene Expression ◽  
Specific Expression ◽  
Partial Explanation ◽  
Downstream Target ◽  
Expression Of Genes ◽  
Global Gene Expression Profiling

Growth hormone (GH) controls the physiology and pathophysiology of the liver, and its signals are conducted by two members of the family of signal transducers and activators of transcription, STAT5A and STAT5B. Mice in which the Stat5a/b locus has been inactivated specifically in hepatocytes display GH resistance, the sex-specific expression of genes associated with liver metabolism and the cytochrome P-450 system is lost, and they develop hepatosteatosis. Several groups have shown by global gene expression profiling that a cadre of STAT5A/B target genes identify genetic cascades induced by GH and other cytokines. Evidence is accumulating that in the absence of STAT5A/B GH aberrantly activates STAT1 and STAT3 and their downstream target genes and thereby offers a partial explanation of some of the physiological alterations observed in Stat5a/b-null mice and human patients. We hypothesize that phenotypic changes observed in the absence of STAT5A/B are due to two distinct molecular consequences: first, the failure of STAT5A/B target genes to be activated by GH and second, the rerouting of GH signaling to other members of the STAT family. Rerouting of GH signaling to STAT1 and STAT3 might partially compensate for the loss of STAT5A/B, but it certainly activates biological programs distinct from STAT5A/B. Here we discuss the extent to which studies on global gene expression profiling have fostered a better understanding of the biology behind cytokine-STAT5A/B networks in hepatocytes. We also explore whether this wealth of information on gene activity can be used to further understand the roles of cytokines in liver disease.

scholarly journals A Floxed exon (Flexon) approach to Cre-mediated conditional gene expression

2021 ◽  
Author(s):  
Justin M Shaffer ◽  
Iva Greenwald
Keyword(s):  
Gene Expression ◽  
Specific Protein ◽  
Specific Gene ◽  
Coding Region ◽  
Specific Expression ◽  
Control Of Gene Expression ◽  
Tissue Specific ◽  
Nonsense Mediated Decay ◽  
Conditional Gene Expression ◽  
Stop Cassette

Conditional gene expression allows for genes to be manipulated and lineages to be marked during development. In the established "lox-stop-lox" approach, Cre-mediated tissue-specific gene expression is achieved by excising the stop cassette, a lox-flanked translational stop that is inserted into the 5' untranslated region of a gene to halt its expression. Although lox-stop-lox has been successfully used in many experimental systems, the design of traditional stop cassettes also has common issues and limitations. Here, we describe the Floxed exon (Flexon), a stop cassette within an artificial exon that can be inserted flexibly into the coding region of any gene to cause premature termination of translation and nonsense-mediated decay of the mRNA. We demonstrate its efficacy in C. elegans by showing that, when promoters that cause weak and/or transient cell-specific expression are used to drive Cre in combination with a gfp(flexon) transgene, strong and sustained expression is obtained in specific lineages. We also describe several potential additional applications for using Flexon for developmental studies, including more precise control of gene expression using intersectional methods, tissue-specific protein degradation or RNAi, and generation of genetic mosaics. The Flexon approach should be feasible in any system where any site-specific recombination-based method may be applied.

scholarly journals Floxed exon (Flexon): A flexibly positioned stop cassette for recombinase-mediated conditional gene expression

2022 ◽  
Vol 119 (3) ◽  
pp. e2117451119
Author(s):  
Justin M. Shaffer ◽  
Iva Greenwald
Keyword(s):  
Gene Expression ◽  
Fluorescent Protein ◽  
Specific Protein ◽  
Specific Expression ◽  
Control Of Gene Expression ◽  
Site Specific ◽  
Tissue Specific ◽  
Endogenous Gene ◽  
Conditional Gene Expression ◽  
Stop Cassette

Conditional gene expression is a powerful tool for genetic analysis of biological phenomena. In the widely used “lox-stop-lox” approach, insertion of a stop cassette consisting of a series of stop codons and polyadenylation signals flanked by lox sites into the 5′ untranslated region (UTR) of a gene prevents expression until the cassette is excised by tissue-specific expression of Cre recombinase. Although lox-stop-lox and similar approaches using other site-specific recombinases have been successfully used in many experimental systems, this design has certain limitations. Here, we describe the Floxed exon (Flexon) approach, which uses a stop cassette composed of an artificial exon flanked by artificial introns, designed to cause premature termination of translation and nonsense-mediated decay of the mRNA and allowing for flexible placement into a gene. We demonstrate its efficacy in Caenorhabditis elegans by showing that, when promoters that cause weak and/or transient cell-specific expression are used to drive Cre in combination with a gfp(flexon) transgene, strong and sustained expression of green fluorescent protein (GFP) is obtained in specific lineages. We also demonstrate its efficacy in an endogenous gene context: we inserted a flexon into the Argonaute gene rde-1 to abrogate RNA interference (RNAi), and restored RNAi tissue specifically by expression of Cre. Finally, we describe several potential additional applications of the Flexon approach, including more precise control of gene expression using intersectional methods, tissue-specific protein degradation, and generation of genetic mosaics. The Flexon approach should be feasible in any system where a site-specific recombination-based method may be applied.

scholarly journals Intronic enhancers regulate the expression of genes involved in tissue-specific functions and homeostasis

2020 ◽  
Author(s):  
Beatrice Borsari ◽  
Pablo Villegas-Mirón ◽  
Hafid Laayouni ◽  
Alba Segarra-Casas ◽  
Jaume Bertranpetit ◽  
...  
Keyword(s):  
Gene Expression ◽  
Embryonic Stem ◽  
Gene Expression Pattern ◽  
Specific Gene ◽  
Control Of Gene Expression ◽  
Tissue Specific ◽  
Tissue Specific Gene ◽  
Specific Gene Expression ◽  
Expression Of Genes ◽  
Genomic Location

AbstractTissue function and homeostasis reflect the gene expression signature by which the combination of ubiquitous and tissue-specific genes contribute to the tissue maintenance and stimuli-responsive function. Enhancers are central to control this tissue-specific gene expression pattern. Here, we explore the correlation between the genomic location of enhancers and their role in tissue-specific gene expression. We found that enhancers showing tissue-specific activity are highly enriched in intronic regions and regulate the expression of genes involved in tissue-specific functions, while housekeeping genes are more often controlled by intergenic enhancers. Notably, an intergenic-to-intronic active enhancers continuum is observed in the transition from developmental to adult stages: the most differentiated tissues present higher rates of intronic enhancers, while the lowest rates are observed in embryonic stem cells. Altogether, our results suggest that the genomic location of active enhancers is key for the tissue-specific control of gene expression.

scholarly journals Transcriptome changes reveal the genetic mechanisms of the reproductive plasticity of workers in lower termites

2019 ◽  
Author(s):  
Chenxu Ye ◽  
Humaira Rasheed ◽  
Yuehua Ran ◽  
Xiaojuan Yang ◽  
Lianxi Xing ◽  
...  
Keyword(s):  
Gene Expression ◽  
Signal Transduction ◽  
Molecular Mechanisms ◽  
Environmental Changes ◽  
Mapk Pathway ◽  
Specific Expression ◽  
Expression Of Genes ◽  
Genetic Mechanisms ◽  
Ecological Success ◽  
Reproductive Plasticity

Abstract Background: The reproductive plasticity of termite workers provides colonies with tremendous flexibility to respond to environmental changes, which is the basis for evolutionary and ecological success. Although it is known that all colony members share the same genetic background and that differences in castes are caused by differences in gene expression, the pattern of the specific expression of genes involved in the differentiation of workers into reproductives remains unclear. In this study, the transition of the female workers into neotenic reproductives (NRs) was induced by a groups of isolated workers (IWs) of Reticulitermes labralis, and then comparative transcriptomes were used for the first time to reveal the molecular mechanisms underlying the reproductive plasticity of workers. Results: We identified 38,070 differentially expressed genes and found profile 5 to be the pattern of gene expression involved in the differentiation of the workers into reproductives. 12,543 genes were specifically upregulated in the IWs. Twenty-five signal transduction pathways classified into environmental information processing were related to the differentiation of workers into NRs. Ras functions as a signalling switch regulated the reproductive plasticity of workers.The catalase gene which is related to longevity was up-regulated in NRs. Conclusion: We demonstrate that workers leaving the natal colony can induce the expression of stage-specific genes in the workers, which leads to the differentiation of workers into queens and suggests that the signal transduction along the Ras-MAPK pathway crucially controls the reproductive plasticity of the workers. This study also provides an important model for revealing the molecular mechanism of longevity changes.

scholarly journals Sexually dimorphic control of gene expression in sensory neurons regulates decision-making behavior in C. elegans

eLife ◽  
2017 ◽  
Vol 6 ◽  
Author(s):  
Zoë A Hilbert ◽  
Dennis H Kim
Keyword(s):  
Gene Expression ◽  
Decision Making ◽  
Sensory Neurons ◽  
Regulation Of Gene Expression ◽  
Sensory Information ◽  
Specific Expression ◽  
Control Of Gene Expression ◽  
Neuron Pair ◽  
C Elegans ◽  
Male Specific

Animal behavior is directed by the integration of sensory information from internal states and the environment. Neuroendocrine regulation of diverse behaviors of Caenorhabditis elegans is under the control of the DAF-7/TGF-β ligand that is secreted from sensory neurons. Here, we show that C. elegans males exhibit an altered, male-specific expression pattern of daf-7 in the ASJ sensory neuron pair with the onset of reproductive maturity, which functions to promote male-specific mate-searching behavior. Molecular genetic analysis of the switch-like regulation of daf-7 expression in the ASJ neuron pair reveals a hierarchy of regulation among multiple inputs—sex, age, nutritional status, and microbial environment—which function in the modulation of behavior. Our results suggest that regulation of gene expression in sensory neurons can function in the integration of a wide array of sensory information and facilitate decision-making behaviors in C. elegans.

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