Synexpression
Encyclopedia
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. 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. 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.
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., 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.,
The identification of synexpression groups has had an impact on the way some scientists view evolutionary change in higher eukaryotes. 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. 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.
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. Thus, changes in the regulatory patterns of these genes would effect the development of both the fore- and hind-limbs, facilitating co-evolution.
Gene
A gene is a molecular unit of heredity of a living organism. It is a name given to some stretches of DNA and RNA that code for a type of protein or for an RNA chain that has a function in the organism. Living beings depend on genes, as they specify all proteins and functional RNA chains...
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
Protein
Proteins are biochemical compounds consisting of one or more polypeptides typically folded into a globular or fibrous form, facilitating a biological function. A polypeptide is a single linear polymer chain of amino acids bonded together by peptide bonds between the carboxyl and amino groups of...
-complex subunits. 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. 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.
One simplified example of a synexpression group is the genes cdc6, cdc3, cdc46, and swi4 in yeast
Yeast
Yeasts are eukaryotic micro-organisms classified in the kingdom Fungi, with 1,500 species currently described estimated to be only 1% of all fungal species. Most reproduce asexually by mitosis, and many do so by an asymmetric division process called budding...
, which are all co-expressed early in the G-1 stage
G1 phase
The G1 phase is a period in the cell cycle during interphase, before the S phase. For many cells, this phase is the major period of cell growth during its lifespan. During this stage new organelles are being synthesized, so the cell requires both structural proteins and enzymes, resulting in great...
of the cell cycle., 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.,
The identification of synexpression groups has had an impact on the way some scientists view evolutionary change in higher eukaryotes. 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. 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.
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. Thus, changes in the regulatory patterns of these genes would effect the development of both the fore- and hind-limbs, facilitating co-evolution.