Measurements of the impact of 3' end sequences on gene expression reveal wide range and sequence dependent effects.

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...

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Autores principales:	Ophir Shalem, Lucas Carey, Danny Zeevi, Eilon Sharon, Leeat Keren, Adina Weinberger, Orna Dahan, Yitzhak Pilpel, Eran Segal
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2013
Materias:	Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/cd7d16c8cac74f149b293de92017aa43
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spelling	oai:doaj.org-article:cd7d16c8cac74f149b293de92017aa432021-11-18T05:52:23ZMeasurements of the impact of 3' end sequences on gene expression reveal wide range and sequence dependent effects.1553-734X1553-735810.1371/journal.pcbi.1002934https://doaj.org/article/cd7d16c8cac74f149b293de92017aa432013-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23505350/?tool=EBIhttps://doaj.org/toc/1553-734Xhttps://doaj.org/toc/1553-7358A 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.Ophir ShalemLucas CareyDanny ZeeviEilon SharonLeeat KerenAdina WeinbergerOrna DahanYitzhak PilpelEran SegalPublic Library of Science (PLoS)articleBiology (General)QH301-705.5ENPLoS Computational Biology, Vol 9, Iss 3, p e1002934 (2013)
institution	DOAJ
collection	DOAJ
language	EN
topic	Biology (General) QH301-705.5
spellingShingle	Biology (General) QH301-705.5 Ophir Shalem Lucas Carey Danny Zeevi Eilon Sharon Leeat Keren Adina Weinberger Orna Dahan Yitzhak Pilpel Eran Segal Measurements of the impact of 3' end sequences on gene expression reveal wide range and sequence dependent effects.
description	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.
format	article
author	Ophir Shalem Lucas Carey Danny Zeevi Eilon Sharon Leeat Keren Adina Weinberger Orna Dahan Yitzhak Pilpel Eran Segal
author_facet	Ophir Shalem Lucas Carey Danny Zeevi Eilon Sharon Leeat Keren Adina Weinberger Orna Dahan Yitzhak Pilpel Eran Segal
author_sort	Ophir Shalem
title	Measurements of the impact of 3' end sequences on gene expression reveal wide range and sequence dependent effects.
title_short	Measurements of the impact of 3' end sequences on gene expression reveal wide range and sequence dependent effects.
title_full	Measurements of the impact of 3' end sequences on gene expression reveal wide range and sequence dependent effects.
title_fullStr	Measurements of the impact of 3' end sequences on gene expression reveal wide range and sequence dependent effects.
title_full_unstemmed	Measurements of the impact of 3' end sequences on gene expression reveal wide range and sequence dependent effects.
title_sort	measurements of the impact of 3' end sequences on gene expression reveal wide range and sequence dependent effects.
publisher	Public Library of Science (PLoS)
publishDate	2013
url	https://doaj.org/article/cd7d16c8cac74f149b293de92017aa43
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Measurements of the impact of 3' end sequences on gene expression reveal wide range and sequence dependent effects.

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