3D organization of synthetic and scrambled chromosomes

Science

Volumn 355, Issue 6329, 2017, Pages

  Mercy, Guillaume ^a,b,c   Mozziconacci, Julien ^d   Scolari, Vittore F ^a,b   Yang, Kun ^e   Zhao, Guanghou ^f   Thierry, Agnès ^a,b   Luo, Yisha ^g   Mitchell, Leslie A ^h   Shen, Michael ^h   Shen, Yue ^g,i,j   Walker, Roy ^g   Zhang, Weimin ^f   Wu, Yi ^k   Xie, Ze Xiong ^k   Luo, Zhouqing ^f   Cai, Yizhi ^g   Dai, Junbiao ^f   Yang, Huanming ^i,l   Yuan, Ying Jin ^k   Boeke, Jef D ^h   Bader, Joel S ^e   Muller, Héloïse ^a,b,m   Koszul, Romain ^a,b   more..

^a INSTITUT PASTEUR   (France)

^b CNRS   (France)

^c SORBONNE UNIVERSITÉ   (France)

^d UNIVERSITÉ PIERRE ET MARIE CURIE   (France)

^e Johns Hopkins University   (United States)

^f TSINGHUA UNIVERSITY   (China)

^g UNIVERSITY OF EDINBURGH   (United Kingdom)

^h NEW YORK UNIVERSITY MEDICAL CENTER   (United States)

ⁱ BGI SHENZHEN   (China)

^j BGI Qingdao ^*  (China)

^k TIANJIN UNIVERSITY   (China)

^l James D Watson Institute of Genome Sciences   (China)

^m INSTITUT CURIE   (France)

more..

Author keywords

[No Author keywords available]

Indexed keywords

TRANSFER RNA; RIBOSOME DNA;

CHROMOSOME; DNA; GENE; GENE EXPRESSION; GENOME; THREE-DIMENSIONAL MODELING; YEAST;

ARTICLE; BUDDING YEAST; CELL NUCLEUS MEMBRANE; CELL POPULATION; CENTROMERE; CHROMOSOME; CHROMOSOME REARRANGEMENT; CHROMOSOME STRUCTURE; CONFORMATION; DNA METABOLISM; MATING TYPE; NONHUMAN; NUCLEOLUS; PRIORITY JOURNAL; SACCHAROMYCES CEREVISIAE; SPINDLE POLE BODY; TRANSPOSON; CELL NUCLEUS; CHEMISTRY; FUNGAL GENOME; GENE DELETION; GENETICS; NUCLEOTIDE REPEAT; SYNTHETIC BIOLOGY; TELOMERE; ULTRASTRUCTURE; YEAST ARTIFICIAL CHROMOSOME;

CELL NUCLEUS; CENTROMERE; CHROMOSOMES, ARTIFICIAL, YEAST; DNA, RIBOSOMAL; GENOME, FUNGAL; NUCLEIC ACID CONFORMATION; REPETITIVE SEQUENCES, NUCLEIC ACID; SACCHAROMYCES CEREVISIAE; SEQUENCE DELETION; SYNTHETIC BIOLOGY; TELOMERE;

EID: 85014855889     PISSN: 00368075     EISSN: 10959203     Source Type: Journal    
DOI: 10.1126/science.aaf4597     Document Type: Article

References (42)

1. P. M. Sharp, A. T. Lloyd, Regional base composition variation along yeast chromosome III: Evolution of chromosome primary structure. Nucleic Acids Res. 21, 179-183 (1993). doi: 10.1093/nar/21.2.179; pmid:8441625
2. K. R. Bradnam, C. Seoighe, P. M. Sharp, K. H. Wolfe, G+C content variation along and among Saccharomyces cerevisiae chromosomes. Mol. Biol. Evol. 16, 666-675 (1999). doi: 10.1093/oxfordjournals.molbev.a026149; pmid: 10335660
3. B. A. Cohen, R. D. Mitra, J. D. Hughes, G. M. Church, A computational analysis of whole-genome expression data reveals chromosomal domains of gene expression. Nat. Genet. 26, 183-186 (2000). doi: 10.1038/79896; pmid: 11017073
4. E. J. Louis, A. V. Vershinin, Chromosome ends: Different sequences may provide conserved functions. BioEssays 27, 685-697 (2005).
5. S. M. Burgess, N. Kleckner, Collisions between yeast chromosomal loci in vivo are governed by three layers of organization. Genes Dev. 13, 1871-1883 (1999). doi: 10.1101/gad.13.14.1871; pmid: 10421638
6. V. Guacci, E. Hogan, D. Koshland, Centromere position in budding yeast: Evidence for anaphase A. Mol. Biol. Cell 8, 957-972 (1997). doi: 10.1091/mbc.8.6.957; pmid: 9201708
7. P. Therizols, T. Duong, B. Dujon, C. Zimmer, E. Fabre, Chromosome arm length and nuclear constraints determine the dynamic relationship of yeast subtelomeres. Proc. Natl. Acad. Sci. U.S.A. 107, 2025-2030 (2010). doi: 10.1073/pnas.0914187107; pmid: 20080699
8. A. Taddei, S. M. Gasser, Structure and function in the budding yeast nucleus. Genetics 192, 107-129 (2012). doi: 10.1534/genetics.112.140608; pmid: 22964839
9. C. Rabl, On cell division. Morphol. Jahrb. 10, 214-330 (1985).
10. M. Thompson, R. A. Haeusler, P. D. Good, D. R. Engelke, Nucleolar clustering of dispersed tRNA genes. Science 302, 1399-1401 (2003). doi: 10.1126/science.1089814; pmid: 14631041
11. R. A. Haeusler, D. R. Engelke, Genome organization in three dimensions: Thinking outside the line. Cell Cycle 3, 273-275 (2004). doi: 10.4161/cc.3.3.732; pmid: 14726665
12. H. Schober et al., Controlled exchange of chromosomal arms reveals principles driving telomere interactions in yeast. Genome Res. 18, 261-271 (2008). doi: 10.1101/gr.6687808; pmid: 18096749
13. S. M. Richardson et al., Design of a synthetic yeast genome. Science 355, 1040-1044 (2017).
14. J. S. Dymond et al., Synthetic chromosome arms function in yeast and generate phenotypic diversity by design. Nature 477, 471-476 (2011). doi: 10.1038/nature10403; pmid: 21918511
15. J. Dymond, J. Boeke, The Saccharomyces cerevisiae SCRaMbLE system and genome minimization. Bioeng. Bugs 3, 168-171 (2012). pmid: 22572789
16. Y. Shen et al., SCRaMbLE generates designed combinatorial stochastic diversity in synthetic chromosomes. Genome Res. 26, 36-49 (2016). doi: 10.1101/gr.193433.115; pmid: 26566658
17. Y. Shen et al., Deep functional analysis of synII, a 770-kilobase synthetic yeast chromosome. Science 355, eaaf4791 (2017).
18. N. Annaluru et al., Total synthesis of a functional designer eukaryotic chromosome. Science 344, 55-58 (2014). doi: 10.1126/science.1249252; pmid: 24674868
19. Z.-X. Xie et al., "Perfect" designer chromosome V and behavior of a ring derivative. Science 355, eaaf4704 (2017).
20. L. A. Mitchell et al., Synthesis, debugging, and effects of synthetic chromosome consolidation: synVI and beyond. Science 355, eaaf4831 (2017).
21. Y. Wu et al., Bug mapping and fitness testing of chemically synthesized chromosome X. Science 355, eaaf4706 (2017).
22. W. Zhang et al., Engineering the ribosomal DNA in a megabase synthetic chromosome. Science 355, eaaf3981 (2017).
23. J. Dekker, K. Rippe, M. Dekker, N. Kleckner, Capturing chromosome conformation. Science 295, 1306-1311 (2002). doi: 10.1126/science.1067799; pmid: 11847345
24. E. Lieberman-Aiden et al., Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326, 289-293 (2009). doi: 10.1126/science.1181369; pmid: 19815776
25. Z. Duan et al., A three-dimensional model of the yeast genome. Nature 465, 363-367 (2010). doi: 10.1038/nature08973; pmid: 20436457
26. H. Marie-Nelly et al., Filling annotation gaps in yeast genomes using genome-wide contact maps. Bioinformatics 30, 2105-2113 (2014). doi: 10.1093/bioinformatics/btu162; pmid: 24711652
27. A. Lesne, J. Riposo, P. Roger, A. Cournac, J. Mozziconacci, 3D genome reconstruction from chromosomal contacts. Nat. Methods 11, 1141-1143 (2014). doi: 10.1038/nmeth.3104; pmid: 25240436
28. A. Cournac, M. Marbouty, J. Mozziconacci, R. Koszul, Generation and analysis of chromosomal contact maps of yeast species. Methods Mol. Biol. 1361, 227-245 (2016). doi: 10.1007/978-1-4939-3079-1-13; pmid: 26483025
29. A. Miele, K. Bystricky, J. Dekker, Yeast silent mating type loci form heterochromatic clusters through silencer protein-dependent long-range interactions. PLOS Genet. 5, e1000478 (2009). doi: 10.1371/journal.pgen.1000478; pmid: 19424429
30. J.-M. Belton et al., The conformation of yeast chromosome III is mating type dependent and controlled by the recombination enhancer. Cell Rep. 13, 1855-1867 (2015). doi: 10.1016/j.celrep.2015.10.063; pmid:26655901
31. K. Bystricky, T. Laroche, G. van Houwe, M. Blaszczyk, S. M. Gasser, Chromosome looping in yeast. J. Cell Biol. 168, 375-387 (2005). doi: 10.1083/jcb.200409091; pmid: 15684028
32. M. Oakes et al., Mutational analysis of the structure and localization of the nucleolus in the yeast Saccharomyces cerevisiae. J. Cell Biol. 143, 23-34 (1998). doi: 10.1083/jcb.143.1.23; pmid: 9763418
33. E. R. Hildebrandt, N. R. Cozzarelli, Comparison of recombination in vitro and in E. coli cells: Measure of the effective concentration of DNA in vivo. Cell 81, 331-340 (1995). doi: 10.1016/0092-8674(95)90386-0; pmid: 7736586
34. H. Marie-Nelly et al., High-quality genome (re)assembly using chromosomal contact data. Nat. Commun. 5, 5695 (2014). doi: 10.1038/ncomms6695; pmid: 25517223
35. N. Kaplan, J. Dekker, High-throughput genome scaffolding from in vivo DNA interaction frequency. Nat. Biotechnol. 31, 1143-1147 (2013). doi: 10.1038/nbt.2768; pmid: 24270850
36. J.-F. Flot, H. Marie-Nelly, R. Koszul, Contact genomics: Scaffolding and phasing (meta)genomes using chromosome 3D physical signatures. FEBS Lett. 589, 2966-2974 (2015). doi: 10.1016/j.febslet.2015.04.034; pmid:25935414
37. J. N. Burton et al., Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions. Nat. Biotechnol. 31, 1119-1125 (2013). doi: 10.1038/nbt.2727; pmid: 24185095
38. M. Guidi et al., Spatial reorganization of telomeres in long-lived quiescent cells. Genome Biol. 16, 206 (2015). doi: 10.1186/s13059-015-0766-2; pmid: 26399229
39. B. Langmead, S. L. Salzberg, Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357-359 (2012). doi: 10.1038/nmeth.1923; pmid: 22388286
40. A. Cournac, H. Marie-Nelly, M. Marbouty, R. Koszul, J. Mozziconacci, Normalization of a chromosomal contact map. BMC Genomics 13, 436(2012).doi:10.1186/1471-2164-13-436; pmid:22935139
41. W. Humphrey, A. Dalke, K. Schulten, VMD: Visual molecular dynamics. J. Mol. Graph. 14, 33-38 (1996). doi: 10.1016/0263-7855(96)00018-5; pmid:8744570
42. P. Rice, I. Longden, A. Bleasby, EMBOSS: The European Molecular Biology Open Software Suite. Trends Genet. 16, 276-277 (2000). doi: 10.1016/S0168-9525(00)02024-2; pmid: 10827456