Genome-wide expression analysis of transcription regulatory complexes

Transcription regulation is important for nearly all cellular processes. To understand how transcription is regulated by different regulatory complexes, DNA microarray expression analysis is used to determine the genome-wide changes in mRNA levels upon deletion of individual factors that belong to different transcription regulatory complexes. We analyzed the expression changes in 165 chromatin factor deletion mutants, encompassing 32 regulatory complexes. The mRNA expression patterns are very specific, with 80% of the mutants showing differential expression from wildtype. The data is assembled into a network of chromatin interaction pathways. The network is function-based, has a branched, interconnected topology and lacks strict one-to-one relationships between complexes. Chromatin pathways are not separate entities for different gene sets, but share many components. The study evaluates which interactions are important for which genes and predicts additional interactions, for example between Paf1C and Set3C, as well as a role for Mediator in subtelomeric silencing. The results indicate the presence of gene-dependent effects that go beyond context-dependent binding of chromatin factors and provide a framework for understanding how specificity is achieved through regulating chromatin. The expression changes of chromatin factor mutations are also compared to a recently published survey of genomic binding locations. Surprisingly, a large disconnect between chromatin factor binding and expression effects upon deletion is observed. Several possible explanations are presented. Since the specificity of the expression signatures cannot be explained by specific patterns of chromatin factor binding, we propose that other gene-specific properties determine which genes are dependent on which chromatin factors for expression. By examining mRNA expression changes in individual deletion mutants, one can learn about the cellular roles that the factors are involved. This is already exemplified for the chromatin complexes where new roles are proposed and confirmed for the coregulatory complexes Mediator and Paf1. Two further examples are presented where examination of the changes in the expression signatures improves our understanding of regulatory complexes. We show that the evolutionary conserved EKC/KEOPS complex, previously implicated in telomere maintenance and transcription regulation, functions in N6-threonylcarbamoyl adenosine modification of tRNAs, resulting in regulation of gene expression through translational control of a gene-specific transcription factor. Also, we provide evidence that CTDK-1 is involved in Nrd1-dependent termination of small, non-coding RNAs. Expression analysis of individual factors can thus be a powerful method to discover new functions