Information about Synexpression
Synexpression is a type of non-random eukaryotic gene organization. Genes in a synexpression group may not be physically linked, but they are involved in the same process and they are coordinately expressed. It is expected that genes that function in the same process be regulated coordinately. Synexpression groups in particular represent genes that are simultaneously up- or down-regulated, often because their gene products are required in stoichiometric amounts or are protein-complex subunits. [1] It is likely that these gene groups share common cis- and trans-acting control elements to achieve coordinate expression.
Synexpression groups are determined mainly by analysis of expression profiles compiled by the use of DNA microarrays. [1] The use of this technology helps researchers monitor changes in expression patterns for large numbers of genes in a given experiment. Analysis of DNA microarray expression profiles has led to the discovery of a number of genes that are tightly co-regulated.[1]
One simplified example of a synexpression group is the genes cdc6, cdc3, cdc46, and swi4 in yeast, which are all co-expressed early in the G-1 stage of the cell cycle.[1],[5] These genes share one common cis-regulatory element, called ECB, which serves as a binding site for the MCM1 trans-acting protein. Although these genes are not spatially clustered, co-regulation seems to be achieved via this common cis and trans control mechanism. Most synexpression groups are more complicated than the ECB group in yeast, involving a myriad of cis and trans control elements. [1], [5]
The identification of synexpression groups has had an impact on the way some scientists view evolutionary change in higher eukaryotes. [1] Since groups of genes involved in the same biological process often share one or more common control elements, it has been suggested that the differential expression of these synexpression groups in different tissues of organisms can contribute to co-evolution tissues, organs, and appendages. [1] Today it is commonly believed that it is not primarily the gene products themselves that evolve, but that it is the control networks for groups of genes that contribute most to the evolution of higher eukaryotes.[1]
Developmental processes provide an example of how changes in synexpression control networks could have a significant impact on an organism’s capacity to evolve and adapt effectively. In animals, it is often beneficial for appendages to co-evolve, and it has been observed that fore-and hind-limbs share expression of Hox genes early in metazoan development.[1] Thus, changes in the regulatory patterns of these genes would effect the development of both the fore- and hind-limbs, facilitating co-evolution.
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Synexpression groups are determined mainly by analysis of expression profiles compiled by the use of DNA microarrays. [1] The use of this technology helps researchers monitor changes in expression patterns for large numbers of genes in a given experiment. Analysis of DNA microarray expression profiles has led to the discovery of a number of genes that are tightly co-regulated.[1]
One simplified example of a synexpression group is the genes cdc6, cdc3, cdc46, and swi4 in yeast, which are all co-expressed early in the G-1 stage of the cell cycle.[1],[5] These genes share one common cis-regulatory element, called ECB, which serves as a binding site for the MCM1 trans-acting protein. Although these genes are not spatially clustered, co-regulation seems to be achieved via this common cis and trans control mechanism. Most synexpression groups are more complicated than the ECB group in yeast, involving a myriad of cis and trans control elements. [1], [5]
The identification of synexpression groups has had an impact on the way some scientists view evolutionary change in higher eukaryotes. [1] Since groups of genes involved in the same biological process often share one or more common control elements, it has been suggested that the differential expression of these synexpression groups in different tissues of organisms can contribute to co-evolution tissues, organs, and appendages. [1] Today it is commonly believed that it is not primarily the gene products themselves that evolve, but that it is the control networks for groups of genes that contribute most to the evolution of higher eukaryotes.[1]
Developmental processes provide an example of how changes in synexpression control networks could have a significant impact on an organism’s capacity to evolve and adapt effectively. In animals, it is often beneficial for appendages to co-evolve, and it has been observed that fore-and hind-limbs share expression of Hox genes early in metazoan development.[1] Thus, changes in the regulatory patterns of these genes would effect the development of both the fore- and hind-limbs, facilitating co-evolution.
See also
References
1. ^ Niehrs, C. and Pollet, Nicolas. Synexpression groups in eukaryotes. Nature 1999 December 2; 402: 483 - 487.
2. ^ Niehrs, C. and Pollet, Nicolas. Synexpression groups in eukaryotes. Nature 1999 December 2; 402: 483 - 487.
3. ^ Niehrs, C. and Pollet, Nicolas. Synexpression groups in eukaryotes. Nature 1999 December 2; 402: 483 - 487.
4. ^ Niehrs, C. and Pollet, Nicolas. Synexpression groups in eukaryotes. Nature 1999 December 2; 402: 483 - 487.
5. ^ Mai, B. et al. Characterization of the ECB binding complex responsible for the M/G1-specific Transcription of CLN3 and SW14. Molecular and Cell Biology 2002 Jan; 430-441.
6. ^ Niehrs, C. and Pollet, Nicolas. Synexpression groups in eukaryotes. Nature 1999 December 2; 402: 483 - 487.
7. ^ Mai, B. et al. Characterization of the ECB binding complex responsible for the M/G1-specific Transcription of CLN3 and SW14. Molecular and Cell Biology 2002 Jan; 430-441.
8. ^ Niehrs, C. and Pollet, Nicolas. Synexpression groups in eukaryotes. Nature 1999 December 2; 402: 483 - 487.
9. ^ Niehrs, C. and Pollet, Nicolas. Synexpression groups in eukaryotes. Nature 1999 December 2; 402: 483 - 487.
10. ^ Niehrs, C. and Pollet, Nicolas. Synexpression groups in eukaryotes. Nature 1999 December 2; 402: 483 - 487.
11. ^ Niehrs, C. and Pollet, Nicolas. Synexpression groups in eukaryotes. Nature 1999 December 2; 402: 483 - 487.
2. ^ Niehrs, C. and Pollet, Nicolas. Synexpression groups in eukaryotes. Nature 1999 December 2; 402: 483 - 487.
3. ^ Niehrs, C. and Pollet, Nicolas. Synexpression groups in eukaryotes. Nature 1999 December 2; 402: 483 - 487.
4. ^ Niehrs, C. and Pollet, Nicolas. Synexpression groups in eukaryotes. Nature 1999 December 2; 402: 483 - 487.
5. ^ Mai, B. et al. Characterization of the ECB binding complex responsible for the M/G1-specific Transcription of CLN3 and SW14. Molecular and Cell Biology 2002 Jan; 430-441.
6. ^ Niehrs, C. and Pollet, Nicolas. Synexpression groups in eukaryotes. Nature 1999 December 2; 402: 483 - 487.
7. ^ Mai, B. et al. Characterization of the ECB binding complex responsible for the M/G1-specific Transcription of CLN3 and SW14. Molecular and Cell Biology 2002 Jan; 430-441.
8. ^ Niehrs, C. and Pollet, Nicolas. Synexpression groups in eukaryotes. Nature 1999 December 2; 402: 483 - 487.
9. ^ Niehrs, C. and Pollet, Nicolas. Synexpression groups in eukaryotes. Nature 1999 December 2; 402: 483 - 487.
10. ^ Niehrs, C. and Pollet, Nicolas. Synexpression groups in eukaryotes. Nature 1999 December 2; 402: 483 - 487.
11. ^ Niehrs, C. and Pollet, Nicolas. Synexpression groups in eukaryotes. Nature 1999 December 2; 402: 483 - 487.
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For a non-technical introduction to the topic, see .
A gene is a locatable region of genomic sequence, corresponding to a unit of inheritance, which is associated with regulatory regions, transcribed regions and/or other functional sequence regions...... Click the link for more information.
Stoichiometry (sometimes called reaction stoichiometry to distinguish it from composition stoichiometry) is the calculation of quantitative (measurable) relationships of the reactants and products in chemical reactions (chemical equations).
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Proteins are large organic compounds made of amino acids arranged in a linear chain and joined together by peptide bonds between the carboxyl and amino groups of adjacent amino acid residues.
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DNA microarray (also commonly known as gene or genome chip, DNA chip, or gene array) is a collection of microscopic DNA spots, commonly representing single genes, arrayed on a solid surface by covalent attachment to chemically suitable matrices.
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Ascomycota (sac fungi)
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- Saccharomycotina (true yeasts)
- Taphrinomycotina
- Schizosaccharomycetes (fission yeasts)
- Urediniomycetes
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A homeobox is a DNA sequence found within genes that are involved in the regulation of development (morphogenesis) of animals, fungi and plants. Genes that have a homeobox are called homeobox genes and form the homeobox gene family.
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A gene regulatory network (also called a GRN or genetic regulatory network) is a collection of DNA segments in a cell which interact with each other (indirectly through their RNA and protein expression products) and with other substances in the cell, thereby
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