Co-Regulated Genes and Gene Clusters

Abstract

There are many co-regulated genes in eukaryotic cells. The coordinated activation or repression of such genes occurs at specific stages of differentiation, or under the influence of external stimuli. As a rule, co-regulated genes are dispersed in the genome. However, there are also gene clusters, which contain paralogous genes that encode proteins with similar functions. In this aspect, they differ significantly from bacterial operons containing functionally linked genes that are not paralogs. In this review, we discuss the reasons for the existence of gene clusters in vertebrate cells and propose that clustering is necessary to ensure the possibility of selective activation of one of several similar genes.

The genomes of chicory, endive, great burdock and yacon provide insights into Asteraceae palaeo‐polyploidization history and plant inulin production

“…The locus of genes involved in a functional pathway also has an important influence on the regulation of expression (Razin et al, 2021). Interestingly, we found that the inulin synthesis genes 1‐SST and 1‐FFT were located near each other on the genome for all the four studied species (Figure 5e), and the inulin breakdown genes 1‐FEH I and 1‐FEH II were located near each other for all the studied species except yacon (Figure 5f).…”

Enhancer Function in the 3D Genome

“…However, this mechanism cannot explain the selective activation of certain promoters in clusters of paralogous genes since the promoters of all genes in a cluster contain binding sites for the same transcription factors. Here, again, various strategies are implemented to ensure selective gene activation [ 137 ]. In globin gene clusters, promoters of various genes compete for contact with upstream enhancers (Locus Control Region, LCR); promoters located closer to the LCR along the DNA are preferentially activated [ 138 ].…”

A Kaleidoscope of Keratin Gene Expression and the Mosaic of Its Regulatory Mechanisms

“…Genes encoding keratins, as well as globins, protocadherins, immunoglobulins, olfactory receptors, KRAB-ZNF TFs, and ribonucleases of the A superfamily, are grouped into relatively compact genomic domains. These loci possess certain common properties, such as preferentially unidirectional transcription, activation, and repression of individual genes in different biological conditions and cell types, and the presence of complex regulatory elements [ 7 ]. Clustered localization implies tight control of the regulatory system within a domain: activation and repression on the principle of “all or nothing” is impossible, and thus “simple solutions” such as changes in the spectrum of expressed TFs are not applicable.…”

“…Clustered localization is a conserved feature of keratin genes in terrestrial vertebrates [ 6 ] and suggests the presence of mechanisms for the coordinated keratin gene expression within clusters and on different chromosomes. In higher eukaryotes, gathering paralogous genes into a common cluster usually reflects the necessity to choose one or several of these genes to be expressed whereas keeping the other genes silent [ 7 ]. As shown in studies of several multigenic loci, i.e., protocadherin, immunoglobulin, Hox, and globin gene clusters, reconfiguration of spatial regulatory landscape within gene loci is required for the proper regulation of gene activity during differentiation and development [ 8 , 9 , 10 , 11 ].…”