3D organization of synthetic and scrambled chromosomes

Guillaume Mercy, Julien Mozziconacci, Vittore F. Scolari, Kun Yang, Guanghou Zhao, Agnès Thierry, Yisha Luo, Leslie A. Mitchell, Michael Shen, Yue Shen, Roy Walker, Weimin Zhang, Yi Wu, Ze Xiong Xie, Zhouqing Luo, Yizhi Cai, Junbiao Dai, Huanming Yang, Ying Jin Yuan, Jef D. Boeke & 3 others Joel S. Bader, Héloïse Muller, Romain Koszul

Research output: Research - peer-reviewArticle

Abstract

Although the design of the synthetic yeast genome Sc2.0 is highly conservative with respect to gene content, the deletion of several classes of repeated sequences and the introduction of thousands of designer changes may affect genome organization and potentially alter cellular functions. We report here the Hi-C-determined three-dimensional (3D) conformations of Sc2.0 chromosomes. The absence of repeats leads to a smoother contact pattern and more precisely tractable chromosome conformations, and the large-scale genomic organization is globally unaffected by the presence of synthetic chromosome(s). Two exceptions are synIII, which lacks the silent mating-type cassettes, and synXII, specifically when the ribosomal DNA is moved to another chromosome. We also exploit the contact maps to detect rearrangements induced in SCRaMbLE (synthetic chromosome rearrangement and modification by loxP-mediated evolution) strains.

LanguageEnglish (US)
Article numbereaaf4597
JournalScience
Volume355
Issue number6329
DOIs
StatePublished - Mar 10 2017
Externally publishedYes

Fingerprint

Chromosomes
Genome
Gene Deletion
Ribosomal DNA
Yeasts

ASJC Scopus subject areas

  • Medicine(all)
  • General

Cite this

Mercy, G., Mozziconacci, J., Scolari, V. F., Yang, K., Zhao, G., Thierry, A., ... Koszul, R. (2017). 3D organization of synthetic and scrambled chromosomes. Science, 355(6329), [eaaf4597]. DOI: 10.1126/science.aaf4597

3D organization of synthetic and scrambled chromosomes. / Mercy, Guillaume; Mozziconacci, Julien; Scolari, Vittore F.; Yang, Kun; Zhao, Guanghou; Thierry, Agnès; Luo, Yisha; Mitchell, Leslie A.; Shen, Michael; Shen, Yue; Walker, Roy; Zhang, Weimin; Wu, Yi; Xie, Ze Xiong; Luo, Zhouqing; Cai, Yizhi; Dai, Junbiao; Yang, Huanming; Yuan, Ying Jin; Boeke, Jef D.; Bader, Joel S.; Muller, Héloïse; Koszul, Romain.

In: Science, Vol. 355, No. 6329, eaaf4597, 10.03.2017.

Research output: Research - peer-reviewArticle

Mercy, G, Mozziconacci, J, Scolari, VF, Yang, K, Zhao, G, Thierry, A, Luo, Y, Mitchell, LA, Shen, M, Shen, Y, Walker, R, Zhang, W, Wu, Y, Xie, ZX, Luo, Z, Cai, Y, Dai, J, Yang, H, Yuan, YJ, Boeke, JD, Bader, JS, Muller, H & Koszul, R 2017, '3D organization of synthetic and scrambled chromosomes' Science, vol 355, no. 6329, eaaf4597. DOI: 10.1126/science.aaf4597
Mercy G, Mozziconacci J, Scolari VF, Yang K, Zhao G, Thierry A et al. 3D organization of synthetic and scrambled chromosomes. Science. 2017 Mar 10;355(6329). eaaf4597. Available from, DOI: 10.1126/science.aaf4597
Mercy, Guillaume ; Mozziconacci, Julien ; Scolari, Vittore F. ; Yang, Kun ; Zhao, Guanghou ; Thierry, Agnès ; Luo, Yisha ; Mitchell, Leslie A. ; Shen, Michael ; Shen, Yue ; Walker, Roy ; Zhang, Weimin ; Wu, Yi ; Xie, Ze Xiong ; Luo, Zhouqing ; Cai, Yizhi ; Dai, Junbiao ; Yang, Huanming ; Yuan, Ying Jin ; Boeke, Jef D. ; Bader, Joel S. ; Muller, Héloïse ; Koszul, Romain. / 3D organization of synthetic and scrambled chromosomes. In: Science. 2017 ; Vol. 355, No. 6329.
@article{fd665426ac4541e48ab73a114dcacc49,
title = "3D organization of synthetic and scrambled chromosomes",
abstract = "Although the design of the synthetic yeast genome Sc2.0 is highly conservative with respect to gene content, the deletion of several classes of repeated sequences and the introduction of thousands of designer changes may affect genome organization and potentially alter cellular functions. We report here the Hi-C-determined three-dimensional (3D) conformations of Sc2.0 chromosomes. The absence of repeats leads to a smoother contact pattern and more precisely tractable chromosome conformations, and the large-scale genomic organization is globally unaffected by the presence of synthetic chromosome(s). Two exceptions are synIII, which lacks the silent mating-type cassettes, and synXII, specifically when the ribosomal DNA is moved to another chromosome. We also exploit the contact maps to detect rearrangements induced in SCRaMbLE (synthetic chromosome rearrangement and modification by loxP-mediated evolution) strains.",
author = "Guillaume Mercy and Julien Mozziconacci and Scolari, {Vittore F.} and Kun Yang and Guanghou Zhao and Agnès Thierry and Yisha Luo and Mitchell, {Leslie A.} and Michael Shen and Yue Shen and Roy Walker and Weimin Zhang and Yi Wu and Xie, {Ze Xiong} and Zhouqing Luo and Yizhi Cai and Junbiao Dai and Huanming Yang and Yuan, {Ying Jin} and Boeke, {Jef D.} and Bader, {Joel S.} and Héloïse Muller and Romain Koszul",
year = "2017",
month = "3",
doi = "10.1126/science.aaf4597",
volume = "355",
journal = "Science",
issn = "0036-8075",
publisher = "American Association for the Advancement of Science",
number = "6329",

}

TY - JOUR

T1 - 3D organization of synthetic and scrambled chromosomes

AU - Mercy,Guillaume

AU - Mozziconacci,Julien

AU - Scolari,Vittore F.

AU - Yang,Kun

AU - Zhao,Guanghou

AU - Thierry,Agnès

AU - Luo,Yisha

AU - Mitchell,Leslie A.

AU - Shen,Michael

AU - Shen,Yue

AU - Walker,Roy

AU - Zhang,Weimin

AU - Wu,Yi

AU - Xie,Ze Xiong

AU - Luo,Zhouqing

AU - Cai,Yizhi

AU - Dai,Junbiao

AU - Yang,Huanming

AU - Yuan,Ying Jin

AU - Boeke,Jef D.

AU - Bader,Joel S.

AU - Muller,Héloïse

AU - Koszul,Romain

PY - 2017/3/10

Y1 - 2017/3/10

N2 - Although the design of the synthetic yeast genome Sc2.0 is highly conservative with respect to gene content, the deletion of several classes of repeated sequences and the introduction of thousands of designer changes may affect genome organization and potentially alter cellular functions. We report here the Hi-C-determined three-dimensional (3D) conformations of Sc2.0 chromosomes. The absence of repeats leads to a smoother contact pattern and more precisely tractable chromosome conformations, and the large-scale genomic organization is globally unaffected by the presence of synthetic chromosome(s). Two exceptions are synIII, which lacks the silent mating-type cassettes, and synXII, specifically when the ribosomal DNA is moved to another chromosome. We also exploit the contact maps to detect rearrangements induced in SCRaMbLE (synthetic chromosome rearrangement and modification by loxP-mediated evolution) strains.

AB - Although the design of the synthetic yeast genome Sc2.0 is highly conservative with respect to gene content, the deletion of several classes of repeated sequences and the introduction of thousands of designer changes may affect genome organization and potentially alter cellular functions. We report here the Hi-C-determined three-dimensional (3D) conformations of Sc2.0 chromosomes. The absence of repeats leads to a smoother contact pattern and more precisely tractable chromosome conformations, and the large-scale genomic organization is globally unaffected by the presence of synthetic chromosome(s). Two exceptions are synIII, which lacks the silent mating-type cassettes, and synXII, specifically when the ribosomal DNA is moved to another chromosome. We also exploit the contact maps to detect rearrangements induced in SCRaMbLE (synthetic chromosome rearrangement and modification by loxP-mediated evolution) strains.

UR - http://www.scopus.com/inward/record.url?scp=85014855889&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85014855889&partnerID=8YFLogxK

U2 - 10.1126/science.aaf4597

DO - 10.1126/science.aaf4597

M3 - Article

VL - 355

JO - Science

T2 - Science

JF - Science

SN - 0036-8075

IS - 6329

M1 - eaaf4597

ER -