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1. An optimized Tet-On system for conditional control of gene expression in sea urchins

   https://doi.org/10.1242/dev.201373  

   Khor, Jian Ming; Ettensohn, Charles A. (January 2023, Development)

   ABSTRACT Sea urchins and other echinoderms are important experimental models for studying developmental processes. The lack of approaches for conditional gene perturbation, however, has made it challenging to investigate the late developmental functions of genes that have essential roles during early embryogenesis and genes that have diverse functions in multiple tissues. The doxycycline-controlled Tet-On system is a widely used molecular tool for temporally and spatially regulated transgene expression. Here, we optimized the Tet-On system to conditionally induce gene expression in sea urchin embryos. Using this approach, we explored the roles the MAPK signaling plays in skeletogenesis by expressing genes that perturb the pathway specifically in primary mesenchyme cells during later stages of development. We demonstrated the wide utility of the Tet-On system by applying it to a second sea urchin species and in cell types other than the primary mesenchyme cells. Our work provides a robust and flexible platform for the spatiotemporal regulation of gene expression in sea urchins, which will considerably enhance the utility of this prominent model system. 

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2. Gene Gangs of the Chloroviruses: Conserved Clusters of Collinear Monocistronic Genes

   https://doi.org/10.3390/V10100576  

   Seitzer, Phillip; Jeanniard, Adrien; Ma, Fangrui; Van Etten, James; Facciotti, Marc; Dunigan, David (October 2018, Viruses)

   Chloroviruses (family Phycodnaviridae) are dsDNA viruses found throughout the world’s inland waters. The open reading frames in the genomes of 41 sequenced chloroviruses (330 ± 40 kbp each) representing three virus types were analyzed for evidence of evolutionarily conserved local genomic “contexts”, the organization of biological information into units of a scale larger than a gene. Despite a general loss of synteny between virus types, we informatically detected a highly conserved genomic context defined by groups of three or more genes that we have termed “gene gangs”. Unlike previously described local genomic contexts, the definition of gene gangs requires only that member genes be consistently co-localized and are not constrained by strand, regulatory sites, or intervening sequences (and therefore represent a new type of conserved structural genomic element). An analysis of functional annotations and transcriptomic data suggests that some of the gene gangs may organize genes involved in specific biochemical processes, but that this organization does not involve their coordinated expression. 

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3. Profiling conserved transcription factor binding motifs in Phaseolus vulgaris through comparative genomics

   https://doi.org/10.1186/s12864-025-11309-2  

   Kondratova, Liudmyla; Vallejos, C Eduardo; Conesa, Ana (December 2025, BMC Genomics)

   Abstract Common bean (Phaseolus vulgaris), a staple food in Latin America and Africa, serves as a vital source of energy, protein, and essential minerals for millions of people. However, genomics knowledge that breeders could leverage for improvement of this crop is scarce. We have developed and validated a comparative genomics approach to predict conserved transcription factor binding sites (TFBS) in common bean and studied gene regulatory networks. We analyzed promoter regions and identified TFBS for 12,631 bean genes with an average of 6 conserved motifs per gene. Moreover, we discovered a statistically significant relationship between the number of conserved motifs and amount of available experimental evidence of gene regulation. Notably, ERF, MYB, and bHLH transcription factor families dominated conserved motifs, with implications for starch biosynthesis regulation. Furthermore, we provide gene regulatory data as a resource that can be interrogated for the regulatory landscape of any set of genes. Our results underscore the significance of TFBS conservation in legumes and aligns with the notion that core genes often exhibit a more conserved regulatory makeup. The study demonstrates the effectiveness of a comparative genomics approach for addressing genome information gaps in non-model organisms and provides valuable insights into the regulatory networks governing starch biosynthesis genes that can support crop improvement programs. 

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4. The Evolutionary History of a DNA Methylase Reveals Frequent Horizontal Transfer and Within-Gene Recombination

   https://doi.org/10.3390/genes14020288  

   Gosselin, Sophia P.; Arsenault, Danielle R.; Jennings, Catherine A.; Gogarten, Johann Peter (February 2023, Genes)

   Inteins, often referred to as protein introns, are highly mobile genetic elements that invade conserved genes throughout the tree of life. Inteins have been found to invade a wide variety of key genes within actinophages. While in the process of conducting a survey of these inteins in actinophages, we discovered that one protein family of methylases contained a putative intein, and two other unique insertion elements. These methylases are known to occur commonly in phages as orphan methylases (possibly as a form of resistance to restriction–modification systems). We found that the methylase family is not conserved within phage clusters and has a disparate distribution across divergent phage groups. We determined that two of the three insertion elements have a patchy distribution within the methylase protein family. Additionally, we found that the third insertion element is likely a second homing endonuclease, and that all three elements (the intein, the homing endonuclease, and what we refer to as the ShiLan domain) have different insertion sites that are conserved in the methylase gene family. Furthermore, we find strong evidence that both the intein and ShiLan domain are partaking in long-distance horizontal gene transfer events between divergent methylases in disparate phage hosts within the already dispersed methylase distribution. The reticulate evolutionary history of methylases and their insertion elements reveals high rates of gene transfer and within-gene recombination in actinophages. 

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5. Characterizing Gene Copy Number of Heat Shock Protein Gene Families in the Emerald Rockcod, Trematomus bernacchii

   https://doi.org/10.3390/genes11080867  

   Tercero, Anthony D; Place, Sean P (August 2020, Genes)

   The suborder Notothenioidae is comprised of Antarctic fishes, several of which have lost their ability to rapidly upregulate heat shock proteins in response to thermal stress, instead adopting a pattern of expression resembling constitutive genes. Given the cold-denaturing effect that sub-zero waters have on proteins, evolution in the Southern Ocean has likely selected for increased expression of molecular chaperones. These selective pressures may have also enabled retention of gene duplicates, bolstering quantitative output of cytosolic heat shock proteins (HSPs). Given that newly duplicated genes are under more relaxed selection, it is plausible that gene duplication enabled altered regulation of such highly conserved genes. To test for evidence of gene duplication, copy number of various isoforms within major heat shock gene families were characterized via qPCR and compared between the Antarctic notothen, Trematomus bernacchii, which lost the inducible heat shock response, and the non-Antarctic notothen, Notothenia angustata, which maintains an inducible heat shock response. The results indicate duplication of isoforms within the hsp70 and hsp40 super families have occurred in the genome of T. bernacchii. The findings suggest gene duplications may have been critical in maintaining protein folding efficiency in the sub-zero waters and provided an evolutionary mechanism of alternative regulation of these conserved gene families. 

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