title: Measurements of the impact of 3' end sequences on gene expression reveal wide range and sequence dependent effects.
abstract: A full understanding of gene regulation requires an understanding of the contributions that the various regulatory regions have on gene expression. Although it is well established that sequences downstream of the main promoter can affect expression, our understanding of the scale of this effect and how it is encoded in the DNA is limited. Here, to measure the effect of native S. cerevisiae 3' end sequences on expression, we constructed a library of 85 fluorescent reporter strains that differ only in their 3' end region. Notably, despite being driven by the same strong promoter, our library spans a continuous twelve-fold range of expression values. These measurements correlate with endogenous mRNA levels, suggesting that the 3' end contributes to constitutive differences in mRNA levels. We used deep sequencing to map the 3'UTR ends of our strains and show that determination of polyadenylation sites is intrinsic to the local 3' end sequence. Polyadenylation mapping was followed by sequence analysis, we found that increased A/T content upstream of the main polyadenylation site correlates with higher expression, both in the library and genome-wide, suggesting that native genes differ by the encoded efficiency of 3' end processing. Finally, we use single cells fluorescence measurements, in different promoter activation levels, to show that 3' end sequences modulate protein expression dynamics differently than promoters, by predominantly affecting the size of protein production bursts as opposed to the frequency at which these bursts occur. Altogether, our results lead to a more complete understanding of gene regulation by demonstrating that 3' end regions have a unique and sequence dependent effect on gene expression.
authors.affiliation: Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel.
authors.forename: Ophir
authors.initials: O
authors.lastname: Shalem
authors.forename: Lucas
authors.initials: L
authors.lastname: Carey
authors.forename: Danny
authors.initials: D
authors.lastname: Zeevi
authors.forename: Eilon
authors.initials: E
authors.lastname: Sharon
authors.forename: Leeat
authors.initials: L
authors.lastname: Keren
authors.forename: Adina
authors.initials: A
authors.lastname: Weinberger
authors.forename: Orna
authors.initials: O
authors.lastname: Dahan
authors.forename: Yitzhak
authors.initials: Y
authors.lastname: Pilpel
authors.forename: Eran
authors.initials: E
authors.lastname: Segal
mesh_terms: D020413:3' Untranslated Regions; D001482:Base Composition; D019295:Computational Biology; D015966:Gene Expression Regulation, Fungal; D005800:Genes, Fungal; D017930:Genes, Reporter; D011061:Poly A / Q000235:genetics / Q000378:metabolism; D011401:Promoter Regions, Genetic; D012333:RNA, Messenger / Q000235:genetics* / Q000378:metabolism*; D012441:Saccharomyces cerevisiae / Q000235:genetics / Q000378:metabolism
chemical_list: D020413:3' Untranslated Regions; D012333:RNA, Messenger; D011061:Poly A