<p>Gene expression is a complex process by which genetic information flow from genes to proteins. Factors regulating gene expression are diverse ranging from sequence elements on DNA, to various types of RNA, to proteins. These factors are categorized into two main categories, <em>cis</em>-acting elements and <em>trans</em>-acting elements. <em>PHO84</em> is a budding yeast gene that was previously reported to be regulated by its cognate antisense transcripts both in <em>cis</em> and in <em>trans</em>. The antisense transcripts of <em>PHO84</em> are a group of long non-coding RNAs (lncRNAs). In my project, I performed RNA-seq and TT-seq analysis to investigate the global correlation of sense/antisense pairs, which showed that the model of sense/antisense negative correlation is not always true for <em>PHO84</em> locus as well as others. I conducted a series of gene expression analysis experiments to decipher the mechanisms regulating <em>PHO84</em> gene, which showed that the 3’ untranslated region (3’UTR) of <em>PHO84</em> plays a regulatory role in the sense expression, an activity not linked to the antisense transcript levels. I also performed a genetic screen to identify <em>trans</em>-acting protein factors that promote the 3’UTR-dependent regulation at <em>PHO84</em> locus.</p> <p>Taken together, I provided insights on both <em>cis</em>- and <em>trans</em>-acting elements controlling the expression of the model gene <em>PHO84</em>. Such information can be taken further and be applied to other higher organisms, with possible implication in the identification of key players in human diseases arising from gene expression dysregulation. </p>