title: Unsupervised detection of regulatory gene expression information in different genomic regions enables gene expression ranking.
abstract: BACKGROUND
  The regulation of all gene expression steps (e.g., Transcription, RNA processing, Translation, and mRNA Degradation) is known to be primarily encoded in different parts of genes and in genomic regions in proximity to genes (e.g., promoters, untranslated regions, coding regions, introns, etc.). However, the entire gene expression codes and the genomic regions where they are encoded are still unknown.
  
  
  RESULTS
  Here, we employ an unsupervised approach to estimate the concentration of gene expression codes in different non-coding parts of genes and transcripts, such as introns and untranslated regions, focusing on three model organisms (Escherichia coli, Saccharomyces cerevisiae, and Schizosaccharomyces pombe). Our analyses support the conjecture that regions adjacent to the beginning and end of ORFs and the beginning and end of introns tend to include higher concentration of gene expression information relatively to regions further away. In addition, we report the exact regions with elevated concentration of gene expression codes. Furthermore, we demonstrate that the concentration of these codes in different genetic regions is correlated with the expression levels of the corresponding genes, and with splicing efficiency measurements and meiotic stage gene expression measurements in S. cerevisiae.
  
  
  CONCLUSIONS
  We suggest that these discoveries improve our understanding of gene expression regulation and evolution; they can also be used for developing improved models of genome/gene evolution and for engineering gene expression in various biotechnological and synthetic biology applications.
authors.affiliation: Department of Biomedical Engineering, Tel Aviv University, P.O. Box 39040, Tel Aviv, 6997801, Israel.
authors.forename: Zohar
authors.initials: Z
authors.lastname: Zafrir
authors.affiliation: Department of Biomedical Engineering, Tel Aviv University, P.O. Box 39040, Tel Aviv, 6997801, Israel. tamirtul@post.tau.ac.il.|Sagol School of Neuroscience, Tel Aviv University, P.O. Box 39040, Tel Aviv, 6997801, Israel. tamirtul@post.tau.ac.il.
authors.forename: Tamir
authors.initials: T
authors.lastname: Tuller
mesh_terms: D000465:Algorithms; D004926:Escherichia coli / Q000235:genetics*; D005786:Gene Expression Regulation; D007438:Introns; D016366:Open Reading Frames / Q000235:genetics; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D012441:Saccharomyces cerevisiae / Q000235:genetics*; D012568:Schizosaccharomyces / Q000235:genetics*; D020506:Untranslated Regions
chemical_list: D012333:RNA, Messenger; D020506:Untranslated Regions
keywords: Gene expression; Intron evolution; Transcript evolution