Comparative functional genomics of the fission yeasts

Nicholas Rhind; Zehua Chen; Moran Yassour; Dawn A. Thompson; Brian J. Haas; Naomi Habib; Ilan Wapinski; Sushmita Roy; Michael F. Lin; David I. Heiman; Sarah K. Young; Kanji Furuya; Yabin Guo; Alison Pidoux; Huei Mei Chen; Barbara Robbertse; Jonathan M. Goldberg; Keita Aoki; Elizabeth H. Bayne; Aaron M. Berlin; Christopher A. Desjardins; Edward Dobbs; Livio Dukaj; Lin Fan; Michael G. FitzGerald; Courtney French; Sharvari Gujja; Klavs Hansen; Dan Keifenheim; Joshua Z. Levin; Rebecca A. Mosher; Carolin A. Müller; Jenna Pfiffner; Margaret Priest; Carsten Russ; Agata Smialowska; Peter Swoboda; Sean M. Sykes; Matthew Vaughn; Sonya Vengrova; Ryan Yoder; Qiandong Zeng; Robin Allshire; David Baulcombe; Bruce W. Birren; William Brown; Karl Ekwall; Manolis Kellis; Janet Leatherwood; Henry Levin; Hanah Margalit; Rob Martienssen; Conrad A. Nieduszynski; Joseph W. Spatafora; Nir Friedman; Jacob Z. Dalgaard; Peter Baumann; Hironori Niki; Aviv Regev; Chad Nusbaum

doi:10.1126/science.1203357

Comparative functional genomics of the fission yeasts

Nicholas Rhind, Zehua Chen, Moran Yassour, Dawn A. Thompson, Brian J. Haas, Naomi Habib, Ilan Wapinski, Sushmita Roy, Michael F. Lin, David I. Heiman, Sarah K. Young, Kanji Furuya, Yabin Guo, Alison Pidoux, Huei Mei Chen, Barbara Robbertse, Jonathan M. Goldberg, Keita Aoki, Elizabeth H. Bayne, Aaron M. BerlinChristopher A. Desjardins, Edward Dobbs, Livio Dukaj, Lin Fan, Michael G. FitzGerald, Courtney French, Sharvari Gujja, Klavs Hansen, Dan Keifenheim, Joshua Z. Levin, Rebecca A. Mosher, Carolin A. Müller, Jenna Pfiffner, Margaret Priest, Carsten Russ, Agata Smialowska, Peter Swoboda, Sean M. Sykes, Matthew Vaughn, Sonya Vengrova, Ryan Yoder, Qiandong Zeng, Robin Allshire, David Baulcombe, Bruce W. Birren, William Brown, Karl Ekwall, Manolis Kellis, Janet Leatherwood, Henry Levin, Hanah Margalit, Rob Martienssen, Conrad A. Nieduszynski, Joseph W. Spatafora, Nir Friedman, Jacob Z. Dalgaard, Peter Baumann, Hironori Niki, Aviv Regev, Chad Nusbaum

Genetics, Cell Biology and Development (TMED)

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

378 Scopus citations

Abstract

The fission yeast clade - comprising Schizosaccharomyces pombe, S. octosporus, S. cryophilus, and S. japonicus - occupies the basal branch of Ascomycete fungi and is an important model of eukaryote biology. A comparative annotation of these genomes identified a near extinction of transposons and the associated innovation of transposon-free centromeres. Expression analysis established that meiotic genes are subject to antisense transcription during vegetative growth, which suggests a mechanism for their tight regulation. In addition, trans-acting regulators control new genes within the context of expanded functional modules for meiosis and stress response. Differences in gene content and regulation also explain why, unlike the budding yeast of Saccharomycotina, fission yeasts cannot use ethanol as a primary carbon source. These analyses elucidate the genome structure and gene regulation of fission yeast and provide tools for investigation across the Schizosaccharomyces clade.

Original language	English (US)
Pages (from-to)	930-936
Number of pages	7
Journal	Science
Volume	332
Issue number	6032
DOIs	https://doi.org/10.1126/science.1203357
State	Published - May 20 2011

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Rhind, N., Chen, Z., Yassour, M., Thompson, D. A., Haas, B. J., Habib, N., Wapinski, I., Roy, S., Lin, M. F., Heiman, D. I., Young, S. K., Furuya, K., Guo, Y., Pidoux, A., Chen, H. M., Robbertse, B., Goldberg, J. M., Aoki, K., Bayne, E. H., ... Nusbaum, C. (2011). Comparative functional genomics of the fission yeasts. Science, 332(6032), 930-936. https://doi.org/10.1126/science.1203357

Rhind, N, Chen, Z, Yassour, M, Thompson, DA, Haas, BJ, Habib, N, Wapinski, I, Roy, S, Lin, MF, Heiman, DI, Young, SK, Furuya, K, Guo, Y, Pidoux, A, Chen, HM, Robbertse, B, Goldberg, JM, Aoki, K, Bayne, EH, Berlin, AM, Desjardins, CA, Dobbs, E, Dukaj, L, Fan, L, FitzGerald, MG, French, C, Gujja, S, Hansen, K, Keifenheim, D, Levin, JZ, Mosher, RA, Müller, CA, Pfiffner, J, Priest, M, Russ, C, Smialowska, A, Swoboda, P, Sykes, SM, Vaughn, M, Vengrova, S, Yoder, R, Zeng, Q, Allshire, R, Baulcombe, D, Birren, BW, Brown, W, Ekwall, K, Kellis, M, Leatherwood, J, Levin, H, Margalit, H, Martienssen, R, Nieduszynski, CA, Spatafora, JW, Friedman, N, Dalgaard, JZ, Baumann, P, Niki, H, Regev, A & Nusbaum, C 2011, 'Comparative functional genomics of the fission yeasts', Science, vol. 332, no. 6032, pp. 930-936. https://doi.org/10.1126/science.1203357

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title = "Comparative functional genomics of the fission yeasts",

abstract = "The fission yeast clade - comprising Schizosaccharomyces pombe, S. octosporus, S. cryophilus, and S. japonicus - occupies the basal branch of Ascomycete fungi and is an important model of eukaryote biology. A comparative annotation of these genomes identified a near extinction of transposons and the associated innovation of transposon-free centromeres. Expression analysis established that meiotic genes are subject to antisense transcription during vegetative growth, which suggests a mechanism for their tight regulation. In addition, trans-acting regulators control new genes within the context of expanded functional modules for meiosis and stress response. Differences in gene content and regulation also explain why, unlike the budding yeast of Saccharomycotina, fission yeasts cannot use ethanol as a primary carbon source. These analyses elucidate the genome structure and gene regulation of fission yeast and provide tools for investigation across the Schizosaccharomyces clade.",

author = "Nicholas Rhind and Zehua Chen and Moran Yassour and Thompson, {Dawn A.} and Haas, {Brian J.} and Naomi Habib and Ilan Wapinski and Sushmita Roy and Lin, {Michael F.} and Heiman, {David I.} and Young, {Sarah K.} and Kanji Furuya and Yabin Guo and Alison Pidoux and Chen, {Huei Mei} and Barbara Robbertse and Goldberg, {Jonathan M.} and Keita Aoki and Bayne, {Elizabeth H.} and Berlin, {Aaron M.} and Desjardins, {Christopher A.} and Edward Dobbs and Livio Dukaj and Lin Fan and FitzGerald, {Michael G.} and Courtney French and Sharvari Gujja and Klavs Hansen and Dan Keifenheim and Levin, {Joshua Z.} and Mosher, {Rebecca A.} and M{\"u}ller, {Carolin A.} and Jenna Pfiffner and Margaret Priest and Carsten Russ and Agata Smialowska and Peter Swoboda and Sykes, {Sean M.} and Matthew Vaughn and Sonya Vengrova and Ryan Yoder and Qiandong Zeng and Robin Allshire and David Baulcombe and Birren, {Bruce W.} and William Brown and Karl Ekwall and Manolis Kellis and Janet Leatherwood and Henry Levin and Hanah Margalit and Rob Martienssen and Nieduszynski, {Conrad A.} and Spatafora, {Joseph W.} and Nir Friedman and Dalgaard, {Jacob Z.} and Peter Baumann and Hironori Niki and Aviv Regev and Chad Nusbaum",

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AU - Yassour, Moran

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AU - Wapinski, Ilan

AU - Roy, Sushmita

AU - Lin, Michael F.

AU - Heiman, David I.

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AU - Furuya, Kanji

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AU - Desjardins, Christopher A.

AU - Dobbs, Edward

AU - Dukaj, Livio

AU - Fan, Lin

AU - FitzGerald, Michael G.

AU - French, Courtney

AU - Gujja, Sharvari

AU - Hansen, Klavs

AU - Keifenheim, Dan

AU - Levin, Joshua Z.

AU - Mosher, Rebecca A.

AU - Müller, Carolin A.

AU - Pfiffner, Jenna

AU - Priest, Margaret

AU - Russ, Carsten

AU - Smialowska, Agata

AU - Swoboda, Peter

AU - Sykes, Sean M.

AU - Vaughn, Matthew

AU - Vengrova, Sonya

AU - Yoder, Ryan

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AU - Spatafora, Joseph W.

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Comparative functional genomics of the fission yeasts

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