DNA microarray approaches to understanding the regulation and evolution of gene expression networks

DNA microarray technology allows biological and medical research to shift from investigation of individual functions of a few related genes to the whole genome level. This creates opportunities for discovery of complex and coordinated transcriptional networks in biological systems. The aim of this thesis has been to study gene regulation and evolution using yeast responses to environmental cues as a model system.

We first developed and validated a fission yeast cDNA microarray for genome-wide expression analysis (Paper I). It is the first commercially available fission yeast microarray, which presents a useful resouce for yeast researchers and provides information required to contruct the array from scratch. Next, we characterised the gene regulatory networks involved in the pheromone response (Paper II) and investigate the role of Gcn5 transcription co-regulator, a histone acetyltransferase (HAT), in re-programming gene expression during the salt stress response in fission yeast (Paper III).

We further investigated evolutionary conservation and divergence of Gcn5 in gene regulation by comparing its role in the evolutionarily distantly related yeast species. The parallel study of the fission yeast and budding yeast showed that Gcn5 has a conserved physiological role in salt stress responses, but it regulates diverged sets of stress response genes potentially via distinct mechanisms (paper IV).

Finally, we investigated interactions between different HATs and between HATs and HDACs (histone deacetylases). Phenotypic studies and gene expression profiling revealed that Gcn5 has overlapping functions with another HAT, Mst2, in the stress response and DNA damage repair (Paper V). We found that the HDAC Clr3 acts antagonistically to Gcn5 in transcriptional elongation and stress responses (Paper VI).

List of scientific papers

I. Xue Y, Haas SA, Brino L, Gusnanto A, Reimers M, Talibi D, Vingron M, Ekwall K, Wright AP (2004). A DNA microarray for fission yeast: minimal changes in global gene expression after temperature shift. Yeast. 21(1): 25-39
https://pubmed.ncbi.nlm.nih.gov/14745780

II. Xue-Franzén Y, Kjaerulff S, Holmberg C, Wright A, Nielsen O (2006). Genomewide identification of pheromone-targeted transcription in fission yeast. BMC Genomics. 7: 303
https://pubmed.ncbi.nlm.nih.gov/17137508

III. Johnsson A, Xue-Franzén Y, Lundin M, Wright AP (2006). Stress-specific role of fission yeast Gcn5 histone acetyltransferase in programming a subset of stress response genes. Eukaryot Cell. 5(8): 1337-46
https://pubmed.ncbi.nlm.nih.gov/16896217

IV. Xue-Franzén Y, Johnsson A , Brodin D*, Henriksson J, Bürglin TR, Wright APH (2009). Genome-wide characterisation of the Gcn5 histone acetyltransferase in budding yeast during stress adaptation reveals evolutionarily conserved and diverged roles. [Submitted]

V. Nugent R, Johnsson A, Fleharty B, Gogol M, Xue-Franzén Y, Seidel C, Wright APH, Forsburg SL (2009). Expression profiling of S. pombe acetyltransferase mutants identifies redundant pathways of gene regulation. [Submitted]

VI. Johnsson A, Durand-Dubief M, Xue-Franzén Y, Rönnerblad M, Ekwall K, Wright A (2009). HAT-HDAC interplay modulates global histone H3K14 acetylation in gene-coding regions during stress. EMBO Rep. 10(9): 1009-14. Epub 2009 Jul 24
https://pubmed.ncbi.nlm.nih.gov/19633696