Dissecting the cis and trans elements that regulate adjacent-gene coregulation in Saccharomyces cerevisiae.
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.
Department of Molecular Biology and Biochemistry, Wesleyan University, Middletown, Connecticut, USA.
James T
JT
Arnone
Department of Molecular Biology and Biochemistry, Wesleyan University, Middletown, Connecticut, USA.
Jeffrey R
JR
Arace
Department of Molecular Biology and Biochemistry, Wesleyan University, Middletown, Connecticut, USA.
Anand R
AR
Soorneedi
Department of Molecular Biology and Biochemistry, Wesleyan University, Middletown, Connecticut, USA.
Teryn T
TT
Citino
Department of Molecular Biology and Biochemistry, Wesleyan University, Middletown, Connecticut, USA.
Tadashi L
TL
Kamitaki
Department of Molecular Biology and Biochemistry, Wesleyan University, Middletown, Connecticut, USA mmcalear@wesleyan.edu.
Michael A
MA
McAlear
D050539:3-Isopropylmalate Dehydrogenase / Q000235:genetics / Q000378:metabolism; D000251:Adenosine Triphosphatases / Q000235:genetics / Q000378:metabolism; D004268:DNA-Binding Proteins / Q000235:genetics / Q000378:metabolism; D015966:Gene Expression Regulation, Fungal; D018869:Heat-Shock Response; D009707:Nucleosomes / Q000235:genetics / Q000378:metabolism; D010750:Phosphoproteins / Q000235:genetics* / Q000378:metabolism; D011401:Promoter Regions, Genetic; D012319:RNA Polymerase II / Q000235:genetics / Q000378:metabolism; D018085:Regulon; D012261:Ribonucleoproteins / Q000235:genetics* / Q000378:metabolism; D012441:Saccharomyces cerevisiae / Q000235:genetics* / Q000378:metabolism; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics* / Q000378:metabolism; D015534:Trans-Activators / Q000235:genetics / Q000378:metabolism; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism; D014158:Transcription, Genetic
C489847:CHD1 protein, S cerevisiae; D004268:DNA-Binding Proteins; C111098:MPP10 protein, S cerevisiae; D009707:Nucleosomes; D010750:Phosphoproteins; D012261:Ribonucleoproteins; C099690:SPT20 protein, S cerevisiae; D029701:Saccharomyces cerevisiae Proteins; D015534:Trans-Activators; D014157:Transcription Factors; D050539:3-Isopropylmalate Dehydrogenase; C524993:LEU2 protein, S cerevisiae; D012319:RNA Polymerase II; D000251:Adenosine Triphosphatases; C499333:SNF2 protein, S cerevisiae