DSpace Collection:http://hdl.handle.net/20.500.12164/532024-03-26T07:16:40Z2024-03-26T07:16:40ZAdjacent gene pairing plays a role in the coordinated expression of ribosome biogenesis genes MPP10 and YJR003C in Saccharomyces cerevisiaeArnone, James T.McAlear, Michael A.http://hdl.handle.net/20.500.12164/1492021-03-09T18:58:24Z2011-01-01T00:00:00ZTitle: Adjacent gene pairing plays a role in the coordinated expression of ribosome biogenesis genes MPP10 and YJR003C in Saccharomyces cerevisiae
Authors: Arnone, James T.; McAlear, Michael A.
Abstract: The rRNA and ribosome biogenesis (RRB) regulon from Saccharomyces cerevisiae contains some 200 genes, the expression of which is tightly regulated under changing cellular conditions. RRB gene promoters are enriched for the RRPE and PAC consensus motifs, and a significant fraction of RRB genes are found as adjacent gene pairs. A genetic analysis of the MPP10 promoter revealed that both the RRPE and PAC motifs are important for coordinated expression of MPP10 following heat shock, osmotic stress, and glucose replen-ishment. The association of the RRPE binding factor Stb3 with the MPP10 promoter was found to increase after glucose replenishment and to decrease following heat shock. Similarly, bulk histone H3 clearing and histone H4K12 acetylation levels at the MPP10 promoter were found to increase or decrease following glucose replenishment or heat shock, respectively. Interestingly, substitutions in the PAC and RRPE sequences at the MPP10 promoter were also found to impact the regulated expression of the adjacent RRB gene YJR003, whose promoter lies in the opposite orientation and some 3.8 kb away. Furthermore, the regulated expression of YJR003C could be disrupted by inserting a reporter cassette that increased its distance from MPP10. Given that a high incidence of gene pairing was also found within the ribosomal protein (RP) and RRB regulons across different yeast species, our results indicate that immediately adjacent positioning of genes can be functionally significant for their coregulated expression.2011-01-01T00:00:00ZDissecting the cis and trans elements that regulate adjacent-gene coregulation in Saccharomyces cerevisiaeArnone, James T.Arace, Jeffrey R.Soorneedi, Anand R.Citino, Teryn T.Kamitaki, Tadashi L.McAlear, Michael A.http://hdl.handle.net/20.500.12164/1482021-03-09T18:57:44Z2014-01-01T00:00:00ZTitle: Dissecting the cis and trans elements that regulate adjacent-gene coregulation in Saccharomyces cerevisiae
Authors: Arnone, James T.; Arace, Jeffrey R.; Soorneedi, Anand R.; Citino, Teryn T.; Kamitaki, Tadashi L.; McAlear, Michael A.
Abstract: The relative positions that genes occupy on their respective chromosomes can play a critical role in determining how they are regulated at the transcriptional level. For example, a significant fraction of the genes from a variety of coregulated gene sets, including the ribosomal protein (RP) and the rRNA and ribosome biogenesis (RRB) regulons, exist as immediate, adjacent gene pairs. These gene pairs occur in all possible divergent, tandem, and convergent orientations. Adjacent-gene pairing in these regulons is associated with a tighter transcriptional coregulation than is observed for nonpaired genes of the same regulons. In order to define the cis and trans factors that regulate adjacent-gene coregulation (AGC), we conducted a mutational analysis of the convergently oriented RRB gene pair MPP10-YJR003C. We observed that coupled corepression of the gene pair under heat shock was abrogated when the two genes were separated by an actively expressed RNA polymerase (Pol) II transcription unit (the LEU2 gene) but not when the inserted LEU2 gene was repressed. In contrast, the insertion of an RNA Pol III-transcribed tRNA (Thr) gene did not disrupt the coregulated repression of MPP10 and YJR003C. A targeted screen of mutants defective in regulating chromosome architecture revealed that the Spt20, Snf2, and Chd1 proteins were required for coupling the repression of YJR003C to that of MPP10. Nucleosome occupancy assays performed across the MPP10 and YJR003C promoter regions revealed that the mechanism of corepression of the gene pair was not related to the repositioning of nucleosomes across the respective gene promoters.2014-01-01T00:00:00ZRibosome Biogenesis: Streamlining the Genome for the Efficient Production of this Biological Nanomolecular MachineArnone, James T.http://hdl.handle.net/20.500.12164/1462020-11-14T21:36:55Z2018-01-01T00:00:00ZTitle: Ribosome Biogenesis: Streamlining the Genome for the Efficient Production of this Biological Nanomolecular Machine
Authors: Arnone, James T.
Abstract: One of the most complex nanomolecular machines found within the cell is the ribosome. Integral to translation, the ribosome is conserved on a functional level across all domains of life. The eukaryotic ribosome is comprised of approximately 80 Ribosomal Proteins (RPs) and four rRNAs that are highly processed, folded, and assembled by more than 200 processing and assembly factors (termed rRNA and ribosome biogenesis factors). The cell requires roughly stoichiometric levels of each of these components to meet cellular demand for protein synthesis, to maintain fidelity of this process, and to ensure that faithful translation occurs. Ribosome biogenesis is an energetically consumptive process, and there are many mechanisms the cell employs in order to properly balance expression of the requisite components. The failure to properly regulate this process results in cellular dysfunction, in higher eukaryotes it can lead to disease such as various cancers. This commentary will discuss recent developments in the understanding of the role that spatial positioning – the linear arrangement of genes along the chromosome throughout the genome – plays in the regulation of ribosome biogenesis, focusing on lessons learned from the budding yeast, Saccharomyces cerevisiae, and their implications in higher eukaryotic organisms.2018-01-01T00:00:00ZSystematic identification, characterization, and conservation of adjacent-gene coregulation in the budding yeast Saccharomyces cerevisiaeEldabagh, Reem S.Mejia, Nelson G.Barrett, Rachel L.Monzo, Christopher R.So, Matthew K.Foley, Jonathan J., IVArnone, James T.http://hdl.handle.net/20.500.12164/1292020-12-28T18:16:19Z2018-01-01T00:00:00ZTitle: Systematic identification, characterization, and conservation of adjacent-gene coregulation in the budding yeast Saccharomyces cerevisiae
Authors: Eldabagh, Reem S.; Mejia, Nelson G.; Barrett, Rachel L.; Monzo, Christopher R.; So, Matthew K.; Foley, Jonathan J., IV; Arnone, James T.
Abstract: It is essential that cells orchestrate gene expression for the specific niche that they occupy, and this often requires coordination of the expression of large sets of genes. There are multiple regulatory systems that exist for modulation of gene expression, including the adjacent-gene coregulation of the rRNA and ribosome biogenesis and ribosomal protein families. Both gene families exhibit a nonrandom genomic distribution, often clustered directly adjacent to another member of the same family, which results in a tighter transcriptional coordination among adjacent paired genes than that of the unpaired genes within each regulon and can result in a shared promoter that coordinates expression of the pairs. This nonrandom genomic distribution has been seen in a few functionally related gene families, and many of these functional pairings are conserved across divergent fungal lineages. To date, the significance of these observations has not been extended in a systematic way to characterize how prevalent the role of adjacent-gene coregulation is in transcriptional regulation. In the present study, we systematically analyzed the transcriptional coherence of the functional pairs compared to the singletons within all gene families defined by the Gene Ontology Slim designation, using Saccharomyces cerevisiae as a model system, finding that clusters exhibit a tighter transcriptional correlation under specific contexts. We found that the longer a functional pairing is conserved the tighter its response to broad stress and nutritional responses, that roughly 25% of gene families exhibit a nonrandom genomic distribution, and that many of these clusters are conserved. This suggests that adjacent-gene coregulation is a widespread, yet underappreciated, transcriptional mechanism.2018-01-01T00:00:00Z