Design of synthetic yeast promoters via tuning of nucleosome architecture

Kathleen A. Curran; Nathan C. Crook; Ashty S. Karim; Akash Gupta; Allison M. Wagman; Hal S. Alper

doi:10.1038/ncomms5002

Design of synthetic yeast promoters via tuning of nucleosome architecture

Kathleen A. Curran, Nathan C. Crook, Ashty S. Karim, Akash Gupta, Allison M. Wagman, Hal S. Alper^*

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

82 Scopus citations

Abstract

Model-based design of biological parts is a critical goal of synthetic biology, especially for eukaryotes. Here we demonstrate thatnucleosome architecture can have a role in defining yeast promoter activity and utilize a computationally-guided approach that can enable both the redesign of endogenous promoter sequences and the de novodesign of synthetic promoters. Initially, we use our approach to reprogram native promoters for increased expression and evaluate their performance in various genetic contexts. Increases in expression ranging from 1.5- to nearly 6-fold in a plasmid-based system and up to 16-fold in a genomic context were obtained. Next, we demonstrate that, in a single design cycle, it is possible to create functional, purely synthetic yeast promoters that achieve substantial expression levels (within the top sixth percentile among native yeast promoters). In doing so, this work establishes a unique DNA-level specification of promoter activity and demonstrates predictive design of synthetic parts.

Original language	English (US)
Article number	4002
Journal	Nature communications
Volume	5
DOIs	https://doi.org/10.1038/ncomms5002
State	Published - May 27 2014
Externally published	Yes

ASJC Scopus subject areas

Chemistry(all)
Biochemistry, Genetics and Molecular Biology(all)
Physics and Astronomy(all)

Access to Document

10.1038/ncomms5002

Fingerprint Dive into the research topics of 'Design of synthetic yeast promoters via tuning of nucleosome architecture'. Together they form a unique fingerprint.

Cite this

@article{cab2fcdc34f34faaa11eb37675f082f5,

title = "Design of synthetic yeast promoters via tuning of nucleosome architecture",

abstract = "Model-based design of biological parts is a critical goal of synthetic biology, especially for eukaryotes. Here we demonstrate thatnucleosome architecture can have a role in defining yeast promoter activity and utilize a computationally-guided approach that can enable both the redesign of endogenous promoter sequences and the de novodesign of synthetic promoters. Initially, we use our approach to reprogram native promoters for increased expression and evaluate their performance in various genetic contexts. Increases in expression ranging from 1.5- to nearly 6-fold in a plasmid-based system and up to 16-fold in a genomic context were obtained. Next, we demonstrate that, in a single design cycle, it is possible to create functional, purely synthetic yeast promoters that achieve substantial expression levels (within the top sixth percentile among native yeast promoters). In doing so, this work establishes a unique DNA-level specification of promoter activity and demonstrates predictive design of synthetic parts.",

author = "Curran, {Kathleen A.} and Crook, {Nathan C.} and Karim, {Ashty S.} and Akash Gupta and Wagman, {Allison M.} and Alper, {Hal S.}",

note = "Funding Information: This work was funded by National Science Foundation Graduate Research Fellowships to K.A.C. and N.C.C. and by the National Institutes of Health (grant number R01GM090221). The content is solely the responsibility of the authors and does not necessarily reflect the official views of the National Institute of General Medical Sciences or the National Institutes of Health. Dr Vishwanath Iyer and Dia Bagchi graciously provided the protocol and helpful advice for the micrococcal nuclease assay. Copyright: Copyright 2014 Elsevier B.V., All rights reserved.",

year = "2014",

month = may,

day = "27",

doi = "10.1038/ncomms5002",

language = "English (US)",

volume = "5",

journal = "Nature Communications",

issn = "2041-1723",

publisher = "Nature Publishing Group",

}

TY - JOUR

T1 - Design of synthetic yeast promoters via tuning of nucleosome architecture

AU - Curran, Kathleen A.

AU - Crook, Nathan C.

AU - Karim, Ashty S.

AU - Gupta, Akash

AU - Wagman, Allison M.

AU - Alper, Hal S.

N1 - Funding Information: This work was funded by National Science Foundation Graduate Research Fellowships to K.A.C. and N.C.C. and by the National Institutes of Health (grant number R01GM090221). The content is solely the responsibility of the authors and does not necessarily reflect the official views of the National Institute of General Medical Sciences or the National Institutes of Health. Dr Vishwanath Iyer and Dia Bagchi graciously provided the protocol and helpful advice for the micrococcal nuclease assay. Copyright: Copyright 2014 Elsevier B.V., All rights reserved.

PY - 2014/5/27

Y1 - 2014/5/27

N2 - Model-based design of biological parts is a critical goal of synthetic biology, especially for eukaryotes. Here we demonstrate thatnucleosome architecture can have a role in defining yeast promoter activity and utilize a computationally-guided approach that can enable both the redesign of endogenous promoter sequences and the de novodesign of synthetic promoters. Initially, we use our approach to reprogram native promoters for increased expression and evaluate their performance in various genetic contexts. Increases in expression ranging from 1.5- to nearly 6-fold in a plasmid-based system and up to 16-fold in a genomic context were obtained. Next, we demonstrate that, in a single design cycle, it is possible to create functional, purely synthetic yeast promoters that achieve substantial expression levels (within the top sixth percentile among native yeast promoters). In doing so, this work establishes a unique DNA-level specification of promoter activity and demonstrates predictive design of synthetic parts.

AB - Model-based design of biological parts is a critical goal of synthetic biology, especially for eukaryotes. Here we demonstrate thatnucleosome architecture can have a role in defining yeast promoter activity and utilize a computationally-guided approach that can enable both the redesign of endogenous promoter sequences and the de novodesign of synthetic promoters. Initially, we use our approach to reprogram native promoters for increased expression and evaluate their performance in various genetic contexts. Increases in expression ranging from 1.5- to nearly 6-fold in a plasmid-based system and up to 16-fold in a genomic context were obtained. Next, we demonstrate that, in a single design cycle, it is possible to create functional, purely synthetic yeast promoters that achieve substantial expression levels (within the top sixth percentile among native yeast promoters). In doing so, this work establishes a unique DNA-level specification of promoter activity and demonstrates predictive design of synthetic parts.

UR - http://www.scopus.com/inward/record.url?scp=84901388705&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84901388705&partnerID=8YFLogxK

U2 - 10.1038/ncomms5002

DO - 10.1038/ncomms5002

M3 - Article

C2 - 24862902

AN - SCOPUS:84901388705

VL - 5

JO - Nature Communications

JF - Nature Communications

SN - 2041-1723

M1 - 4002

ER -

Design of synthetic yeast promoters via tuning of nucleosome architecture

Abstract

ASJC Scopus subject areas

Access to Document

Other files and links

Cite this