Total synthesis of a functional designer eukaryotic chromosome

Narayana Annaluru; Héloïse Muller; Leslie A. Mitchell; Sivaprakash Ramalingam; Giovanni Stracquadanio; Sarah M. Richardson; Jessica S. Dymond; Zheng Kuang; Lisa Z. Scheifele; Eric M. Cooper; Yizhi Cai; Karen Zeller; Neta Agmon; Jeffrey S. Han; Michalis Hadjithomas; Jennifer Tullman; Katrina Caravelli; Kimberly Cirelli; Zheyuan Guo; Viktoriya London; Apurva Yeluru; Sindurathy Murugan; Karthikeyan Kandavelou; Nicolas Agier; Gilles Fischer; Kun Yang; J. Andrew Martin; Murat Bilgel; Pavlo Bohutski; Kristin M. Boulier; Brian J. Capaldo; Joy Chang; Kristie Charoen; Woo Jin Choi; Peter Deng; James E. DiCarlo; Judy Doong; Jessilyn Dunn; Jason I. Feinberg; Christopher Fernandez; Charlotte E. Floria; David Gladowski; Pasha Hadidi; Isabel Ishizuka; Javaneh Jabbari; Calvin Y.L. Lau; Pablo A. Lee; Sean Li; Denise Lin; Matthias E. Linder; Jonathan Ling; Jaime Liu; Jonathan Liu; Mariya London; Ma Henry; Jessica Mao; Jessica E. McDade; Alexandra McMillan; Aaron M. Moore; Won Chan Oh; Yu Ouyang; Ruchi Patel; Marina Paul; Laura C. Paulsen; Judy Qiu; Alex Rhee; Matthew G. Rubashkin; Ina Y. Soh; Nathaniel E. Sotuyo; Venkatesh Srinivas; Allison Suarez; Andy Wong; Remus Wong; Wei Rose Xie; Yijie Xu; Allen T. Yu; Romain Koszul; Joel S. Bader; Jef D. Boeke; Srinivasan Chandrasegaran

doi:10.1126/science.1249252

Total synthesis of a functional designer eukaryotic chromosome

Narayana Annaluru, Héloïse Muller, Leslie A. Mitchell, Sivaprakash Ramalingam, Giovanni Stracquadanio, Sarah M. Richardson, Jessica S. Dymond, Zheng Kuang, Lisa Z. Scheifele, Eric M. Cooper, Yizhi Cai, Karen Zeller, Neta Agmon, Jeffrey S. Han, Michalis Hadjithomas, Jennifer Tullman, Katrina Caravelli, Kimberly Cirelli, Zheyuan Guo, Viktoriya LondonApurva Yeluru, Sindurathy Murugan, Karthikeyan Kandavelou, Nicolas Agier, Gilles Fischer, Kun Yang, J. Andrew Martin, Murat Bilgel, Pavlo Bohutski, Kristin M. Boulier, Brian J. Capaldo, Joy Chang, Kristie Charoen, Woo Jin Choi, Peter Deng, James E. DiCarlo, Judy Doong, Jessilyn Dunn, Jason I. Feinberg, Christopher Fernandez, Charlotte E. Floria, David Gladowski, Pasha Hadidi, Isabel Ishizuka, Javaneh Jabbari, Calvin Y.L. Lau, Pablo A. Lee, Sean Li, Denise Lin, Matthias E. Linder, Jonathan Ling, Jaime Liu, Jonathan Liu, Mariya London, Ma Henry, Jessica Mao, Jessica E. McDade, Alexandra McMillan, Aaron M. Moore, Won Chan Oh, Yu Ouyang, Ruchi Patel, Marina Paul, Laura C. Paulsen, Judy Qiu, Alex Rhee, Matthew G. Rubashkin, Ina Y. Soh, Nathaniel E. Sotuyo, Venkatesh Srinivas, Allison Suarez, Andy Wong, Remus Wong, Wei Rose Xie, Yijie Xu, Allen T. Yu, Romain Koszul, Joel S. Bader, Jef D. Boeke, Srinivasan Chandrasegaran

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

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Abstract

Rapid advances in DNA synthesis techniques have made it possible to engineer viruses, biochemical pathways and assemble bacterial genomes. Here, we report the synthesis of a functional 272,871-base pair designer eukaryotic chromosome, synIII, which is based on the 316,617-base pair native Saccharomyces cerevisiae chromosome III. Changes to synIII include TAG/TAA stop-codon replacements, deletion of subtelomeric regions, introns, transfer RNAs, transposons, and silent mating loci as well as insertion of loxPsym sites to enable genome scrambling. SynIII is functional in S. cerevisiae. Scrambling of the chromosome in a heterozygous diploid reveals a large increase in a-mater derivatives resulting from loss of the MATα allele on synIII. The complete design and synthesis of synIII establishes S. cerevisiae as the basis for designer eukaryotic genome biology.

Original language	English (US)
Pages (from-to)	55-58
Number of pages	4
Journal	Science
Volume	344
Issue number	6179
DOIs	https://doi.org/10.1126/science.1249252
State	Published - 2014

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Annaluru, N., Muller, H., Mitchell, L. A., Ramalingam, S., Stracquadanio, G., Richardson, S. M., Dymond, J. S., Kuang, Z., Scheifele, L. Z., Cooper, E. M., Cai, Y., Zeller, K., Agmon, N., Han, J. S., Hadjithomas, M., Tullman, J., Caravelli, K., Cirelli, K., Guo, Z., ... Chandrasegaran, S. (2014). Total synthesis of a functional designer eukaryotic chromosome. Science, 344(6179), 55-58. https://doi.org/10.1126/science.1249252

Annaluru, N, Muller, H, Mitchell, LA, Ramalingam, S, Stracquadanio, G, Richardson, SM, Dymond, JS, Kuang, Z, Scheifele, LZ, Cooper, EM, Cai, Y, Zeller, K, Agmon, N, Han, JS, Hadjithomas, M, Tullman, J, Caravelli, K, Cirelli, K, Guo, Z, London, V, Yeluru, A, Murugan, S, Kandavelou, K, Agier, N, Fischer, G, Yang, K, Martin, JA, Bilgel, M, Bohutski, P, Boulier, KM, Capaldo, BJ, Chang, J, Charoen, K, Choi, WJ, Deng, P, DiCarlo, JE, Doong, J, Dunn, J, Feinberg, JI, Fernandez, C, Floria, CE, Gladowski, D, Hadidi, P, Ishizuka, I, Jabbari, J, Lau, CYL, Lee, PA, Li, S, Lin, D, Linder, ME, Ling, J, Liu, J, Liu, J, London, M, Henry, M, Mao, J, McDade, JE, McMillan, A, Moore, AM, Oh, WC, Ouyang, Y, Patel, R, Paul, M, Paulsen, LC, Qiu, J, Rhee, A, Rubashkin, MG, Soh, IY, Sotuyo, NE, Srinivas, V, Suarez, A, Wong, A, Wong, R, Xie, WR, Xu, Y, Yu, AT, Koszul, R, Bader, JS , Boeke, JD & Chandrasegaran, S 2014, 'Total synthesis of a functional designer eukaryotic chromosome', Science, vol. 344, no. 6179, pp. 55-58. https://doi.org/10.1126/science.1249252

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title = "Total synthesis of a functional designer eukaryotic chromosome",

abstract = "Rapid advances in DNA synthesis techniques have made it possible to engineer viruses, biochemical pathways and assemble bacterial genomes. Here, we report the synthesis of a functional 272,871-base pair designer eukaryotic chromosome, synIII, which is based on the 316,617-base pair native Saccharomyces cerevisiae chromosome III. Changes to synIII include TAG/TAA stop-codon replacements, deletion of subtelomeric regions, introns, transfer RNAs, transposons, and silent mating loci as well as insertion of loxPsym sites to enable genome scrambling. SynIII is functional in S. cerevisiae. Scrambling of the chromosome in a heterozygous diploid reveals a large increase in a-mater derivatives resulting from loss of the MATα allele on synIII. The complete design and synthesis of synIII establishes S. cerevisiae as the basis for designer eukaryotic genome biology.",

author = "Narayana Annaluru and H{\'e}lo{\"i}se Muller and Mitchell, {Leslie A.} and Sivaprakash Ramalingam and Giovanni Stracquadanio and Richardson, {Sarah M.} and Dymond, {Jessica S.} and Zheng Kuang and Scheifele, {Lisa Z.} and Cooper, {Eric M.} and Yizhi Cai and Karen Zeller and Neta Agmon and Han, {Jeffrey S.} and Michalis Hadjithomas and Jennifer Tullman and Katrina Caravelli and Kimberly Cirelli and Zheyuan Guo and Viktoriya London and Apurva Yeluru and Sindurathy Murugan and Karthikeyan Kandavelou and Nicolas Agier and Gilles Fischer and Kun Yang and Martin, {J. Andrew} and Murat Bilgel and Pavlo Bohutski and Boulier, {Kristin M.} and Capaldo, {Brian J.} and Joy Chang and Kristie Charoen and Choi, {Woo Jin} and Peter Deng and DiCarlo, {James E.} and Judy Doong and Jessilyn Dunn and Feinberg, {Jason I.} and Christopher Fernandez and Floria, {Charlotte E.} and David Gladowski and Pasha Hadidi and Isabel Ishizuka and Javaneh Jabbari and Lau, {Calvin Y.L.} and Lee, {Pablo A.} and Sean Li and Denise Lin and Linder, {Matthias E.} and Jonathan Ling and Jaime Liu and Jonathan Liu and Mariya London and Ma Henry and Jessica Mao and McDade, {Jessica E.} and Alexandra McMillan and Moore, {Aaron M.} and Oh, {Won Chan} and Yu Ouyang and Ruchi Patel and Marina Paul and Paulsen, {Laura C.} and Judy Qiu and Alex Rhee and Rubashkin, {Matthew G.} and Soh, {Ina Y.} and Sotuyo, {Nathaniel E.} and Venkatesh Srinivas and Allison Suarez and Andy Wong and Remus Wong and Xie, {Wei Rose} and Yijie Xu and Yu, {Allen T.} and Romain Koszul and Bader, {Joel S.} and Boeke, {Jef D.} and Srinivasan Chandrasegaran",

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doi = "10.1126/science.1249252",

language = "English (US)",

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pages = "55--58",

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AU - Annaluru, Narayana

AU - Muller, Héloïse

AU - Mitchell, Leslie A.

AU - Ramalingam, Sivaprakash

AU - Stracquadanio, Giovanni

AU - Richardson, Sarah M.

AU - Dymond, Jessica S.

AU - Kuang, Zheng

AU - Scheifele, Lisa Z.

AU - Cooper, Eric M.

AU - Cai, Yizhi

AU - Zeller, Karen

AU - Agmon, Neta

AU - Han, Jeffrey S.

AU - Hadjithomas, Michalis

AU - Tullman, Jennifer

AU - Caravelli, Katrina

AU - Cirelli, Kimberly

AU - Guo, Zheyuan

AU - London, Viktoriya

AU - Yeluru, Apurva

AU - Murugan, Sindurathy

AU - Kandavelou, Karthikeyan

AU - Agier, Nicolas

AU - Fischer, Gilles

AU - Yang, Kun

AU - Martin, J. Andrew

AU - Bilgel, Murat

AU - Bohutski, Pavlo

AU - Boulier, Kristin M.

AU - Capaldo, Brian J.

AU - Chang, Joy

AU - Charoen, Kristie

AU - Choi, Woo Jin

AU - Deng, Peter

AU - DiCarlo, James E.

AU - Doong, Judy

AU - Dunn, Jessilyn

AU - Feinberg, Jason I.

AU - Fernandez, Christopher

AU - Floria, Charlotte E.

AU - Gladowski, David

AU - Hadidi, Pasha

AU - Ishizuka, Isabel

AU - Jabbari, Javaneh

AU - Lau, Calvin Y.L.

AU - Lee, Pablo A.

AU - Li, Sean

AU - Lin, Denise

AU - Linder, Matthias E.

AU - Ling, Jonathan

AU - Liu, Jaime

AU - Liu, Jonathan

AU - London, Mariya

AU - Henry, Ma

AU - Mao, Jessica

AU - McDade, Jessica E.

AU - McMillan, Alexandra

AU - Moore, Aaron M.

AU - Oh, Won Chan

AU - Ouyang, Yu

AU - Patel, Ruchi

AU - Paul, Marina

AU - Paulsen, Laura C.

AU - Qiu, Judy

AU - Rhee, Alex

AU - Rubashkin, Matthew G.

AU - Soh, Ina Y.

AU - Sotuyo, Nathaniel E.

AU - Srinivas, Venkatesh

AU - Suarez, Allison

AU - Wong, Andy

AU - Wong, Remus

AU - Xie, Wei Rose

AU - Xu, Yijie

AU - Yu, Allen T.

AU - Koszul, Romain

AU - Bader, Joel S.

AU - Boeke, Jef D.

AU - Chandrasegaran, Srinivasan

PY - 2014

Y1 - 2014

N2 - Rapid advances in DNA synthesis techniques have made it possible to engineer viruses, biochemical pathways and assemble bacterial genomes. Here, we report the synthesis of a functional 272,871-base pair designer eukaryotic chromosome, synIII, which is based on the 316,617-base pair native Saccharomyces cerevisiae chromosome III. Changes to synIII include TAG/TAA stop-codon replacements, deletion of subtelomeric regions, introns, transfer RNAs, transposons, and silent mating loci as well as insertion of loxPsym sites to enable genome scrambling. SynIII is functional in S. cerevisiae. Scrambling of the chromosome in a heterozygous diploid reveals a large increase in a-mater derivatives resulting from loss of the MATα allele on synIII. The complete design and synthesis of synIII establishes S. cerevisiae as the basis for designer eukaryotic genome biology.

AB - Rapid advances in DNA synthesis techniques have made it possible to engineer viruses, biochemical pathways and assemble bacterial genomes. Here, we report the synthesis of a functional 272,871-base pair designer eukaryotic chromosome, synIII, which is based on the 316,617-base pair native Saccharomyces cerevisiae chromosome III. Changes to synIII include TAG/TAA stop-codon replacements, deletion of subtelomeric regions, introns, transfer RNAs, transposons, and silent mating loci as well as insertion of loxPsym sites to enable genome scrambling. SynIII is functional in S. cerevisiae. Scrambling of the chromosome in a heterozygous diploid reveals a large increase in a-mater derivatives resulting from loss of the MATα allele on synIII. The complete design and synthesis of synIII establishes S. cerevisiae as the basis for designer eukaryotic genome biology.

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DO - 10.1126/science.1249252

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SP - 55

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JO - Science

JF - Science

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ER -

Total synthesis of a functional designer eukaryotic chromosome

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