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Items: 43

1.

Characterizing meiotic chromosomes' structure and pairing using a designer sequence optimized for Hi-C.

Muller H, Scolari VF, Agier N, Piazza A, Thierry A, Mercy G, Descorps-Declere S, Lazar-Stefanita L, Espeli O, Llorente B, Fischer G, Mozziconacci J, Koszul R.

Mol Syst Biol. 2018 Jul 16;14(7):e8293. doi: 10.15252/msb.20188293.

2.

Correction to: Proximity ligation scaffolding and comparison of two Trichoderma reesei strains genomes.

Jourdier E, Baudry L, Poggi-Parodi D, Vicq Y, Koszul R, Margeot A, Marbouty M, Bidard F.

Biotechnol Biofuels. 2018 Jun 13;11:163. doi: 10.1186/s13068-018-1161-5. eCollection 2018.

3.

A Proximity Ligation-Based Method for Quantitative Measurement of D-Loop Extension in S. cerevisiae.

Piazza A, Koszul R, Heyer WD.

Methods Enzymol. 2018;601:27-44. doi: 10.1016/bs.mie.2017.11.024. Epub 2018 Feb 24.

4.

Multiscale Structuring of the E. coli Chromosome by Nucleoid-Associated and Condensin Proteins.

Lioy VS, Cournac A, Marbouty M, Duigou S, Mozziconacci J, Espéli O, Boccard F, Koszul R.

Cell. 2018 Feb 8;172(4):771-783.e18. doi: 10.1016/j.cell.2017.12.027. Epub 2018 Jan 18.

PMID:
29358050
5.

Generation and Analysis of Chromosomal Contact Maps of Bacteria.

Marbouty M, Koszul R.

Methods Mol Biol. 2017;1624:75-84. doi: 10.1007/978-1-4939-7098-8_7.

PMID:
28842877
6.

Cohesins and condensins orchestrate the 4D dynamics of yeast chromosomes during the cell cycle.

Lazar-Stefanita L, Scolari VF, Mercy G, Muller H, Guérin TM, Thierry A, Mozziconacci J, Koszul R.

EMBO J. 2017 Sep 15;36(18):2684-2697. doi: 10.15252/embj.201797342. Epub 2017 Jul 20.

7.

Proximity ligation scaffolding and comparison of two Trichoderma reesei strains genomes.

Jourdier E, Baudry L, Poggi-Parodi D, Vicq Y, Koszul R, Margeot A, Marbouty M, Bidard F.

Biotechnol Biofuels. 2017 Jun 12;10:151. doi: 10.1186/s13068-017-0837-6. eCollection 2017. Erratum in: Biotechnol Biofuels. 2018 Jun 13;11:163.

8.

Deep functional analysis of synII, a 770-kilobase synthetic yeast chromosome.

Shen Y, Wang Y, Chen T, Gao F, Gong J, Abramczyk D, Walker R, Zhao H, Chen S, Liu W, Luo Y, Müller CA, Paul-Dubois-Taine A, Alver B, Stracquadanio G, Mitchell LA, Luo Z, Fan Y, Zhou B, Wen B, Tan F, Wang Y, Zi J, Xie Z, Li B, Yang K, Richardson SM, Jiang H, French CE, Nieduszynski CA, Koszul R, Marston AL, Yuan Y, Wang J, Bader JS, Dai J, Boeke JD, Xu X, Cai Y, Yang H.

Science. 2017 Mar 10;355(6329). pii: eaaf4791. doi: 10.1126/science.aaf4791.

9.

3D organization of synthetic and scrambled chromosomes.

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.

Science. 2017 Mar 10;355(6329). pii: eaaf4597. doi: 10.1126/science.aaf4597.

10.

Scaffolding bacterial genomes and probing host-virus interactions in gut microbiome by proximity ligation (chromosome capture) assay.

Marbouty M, Baudry L, Cournac A, Koszul R.

Sci Adv. 2017 Feb 17;3(2):e1602105. doi: 10.1126/sciadv.1602105. eCollection 2017 Feb.

11.

Beyond the bounds of evolution: Synthetic chromosomes… How and what for?

Koszul R.

C R Biol. 2016 Jul-Aug;339(7-8):324-8. doi: 10.1016/j.crvi.2016.05.007. Epub 2016 Jun 8. Review.

12.

A checkpoint control orchestrates the replication of the two chromosomes of Vibrio cholerae.

Val ME, Marbouty M, de Lemos Martins F, Kennedy SP, Kemble H, Bland MJ, Possoz C, Koszul R, Skovgaard O, Mazel D.

Sci Adv. 2016 Apr 22;2(4):e1501914. doi: 10.1126/sciadv.1501914. eCollection 2016 Apr.

13.

Evidence for a dual role of actin in regulating chromosome organization and dynamics in yeast.

Spichal M, Brion A, Herbert S, Cournac A, Marbouty M, Zimmer C, Koszul R, Fabre E.

J Cell Sci. 2016 Feb 15;129(4):681-92. doi: 10.1242/jcs.175745. Epub 2016 Jan 13.

14.

The 3D folding of metazoan genomes correlates with the association of similar repetitive elements.

Cournac A, Koszul R, Mozziconacci J.

Nucleic Acids Res. 2016 Jan 8;44(1):245-55. doi: 10.1093/nar/gkv1292. Epub 2015 Nov 24.

15.

Metagenome Analysis Exploiting High-Throughput Chromosome Conformation Capture (3C) Data.

Marbouty M, Koszul R.

Trends Genet. 2015 Dec;31(12):673-682. doi: 10.1016/j.tig.2015.10.003. Epub 2015 Nov 19. Review.

16.

Generation and Analysis of Chromosomal Contact Maps of Yeast Species.

Cournac A, Marbouty M, Mozziconacci J, Koszul R.

Methods Mol Biol. 2016;1361:227-45. doi: 10.1007/978-1-4939-3079-1_13.

17.

Spatial reorganization of telomeres in long-lived quiescent cells.

Guidi M, Ruault M, Marbouty M, Loïodice I, Cournac A, Billaudeau C, Hocher A, Mozziconacci J, Koszul R, Taddei A.

Genome Biol. 2015 Sep 23;16:206. doi: 10.1186/s13059-015-0766-2.

18.

Genome-wide replication landscape of Candida glabrata.

Descorps-Declère S, Saguez C, Cournac A, Marbouty M, Rolland T, Ma L, Bouchier C, Moszer I, Dujon B, Koszul R, Richard GF.

BMC Biol. 2015 Sep 2;13:69. doi: 10.1186/s12915-015-0177-6.

19.

Condensin- and Replication-Mediated Bacterial Chromosome Folding and Origin Condensation Revealed by Hi-C and Super-resolution Imaging.

Marbouty M, Le Gall A, Cattoni DI, Cournac A, Koh A, Fiche JB, Mozziconacci J, Murray H, Koszul R, Nollmann M.

Mol Cell. 2015 Aug 20;59(4):588-602. doi: 10.1016/j.molcel.2015.07.020.

20.

Filling the gap: Micro-C accesses the nucleosomal fiber at 100-1000 bp resolution.

Mozziconacci J, Koszul R.

Genome Biol. 2015 Aug 21;16:169. doi: 10.1186/s13059-015-0744-8.

21.

Contact genomics: scaffolding and phasing (meta)genomes using chromosome 3D physical signatures.

Flot JF, Marie-Nelly H, Koszul R.

FEBS Lett. 2015 Oct 7;589(20 Pt A):2966-74. doi: 10.1016/j.febslet.2015.04.034. Epub 2015 Apr 29. Review.

22.

High-quality genome (re)assembly using chromosomal contact data.

Marie-Nelly H, Marbouty M, Cournac A, Flot JF, Liti G, Parodi DP, Syan S, Guillén N, Margeot A, Zimmer C, Koszul R.

Nat Commun. 2014 Dec 17;5:5695. doi: 10.1038/ncomms6695.

23.

Metagenomic chromosome conformation capture (meta3C) unveils the diversity of chromosome organization in microorganisms.

Marbouty M, Cournac A, Flot JF, Marie-Nelly H, Mozziconacci J, Koszul R.

Elife. 2014 Dec 17;3:e03318. doi: 10.7554/eLife.03318.

24.

Gateway to genetic exchange? DNA double-strand breaks in the bdelloid rotifer Adineta vaga submitted to desiccation.

Hespeels B, Knapen M, Hanot-Mambres D, Heuskin AC, Pineux F, LUCAS S, Koszul R, Van Doninck K.

J Evol Biol. 2014 Jul;27(7):1334-45.

25.

Filling annotation gaps in yeast genomes using genome-wide contact maps.

Marie-Nelly H, Marbouty M, Cournac A, Liti G, Fischer G, Zimmer C, Koszul R.

Bioinformatics. 2014 Aug 1;30(15):2105-13. doi: 10.1093/bioinformatics/btu162. Epub 2014 Apr 7.

26.

Total synthesis of a functional designer eukaryotic chromosome.

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 CY, Lee PA, Li S, Lin D, Linder ME, Ling J, Liu J, Liu J, London M, Ma H, 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.

Science. 2014 Apr 4;344(6179):55-8. doi: 10.1126/science.1249252. Epub 2014 Mar 27. Erratum in: Science. 2014 May 23;344(6186):816.

27.

Purification of G1 daughter cells from different Saccharomycetes species through an optimized centrifugal elutriation procedure.

Marbouty M, Ermont C, Dujon B, Richard GF, Koszul R.

Yeast. 2014 May;31(5):159-66. doi: 10.1002/yea.3005. Epub 2014 Mar 26.

28.

Genomic evidence for ameiotic evolution in the bdelloid rotifer Adineta vaga.

Flot JF, Hespeels B, Li X, Noel B, Arkhipova I, Danchin EG, Hejnol A, Henrissat B, Koszul R, Aury JM, Barbe V, Barthélémy RM, Bast J, Bazykin GA, Chabrol O, Couloux A, Da Rocha M, Da Silva C, Gladyshev E, Gouret P, Hallatschek O, Hecox-Lea B, Labadie K, Lejeune B, Piskurek O, Poulain J, Rodriguez F, Ryan JF, Vakhrusheva OA, Wajnberg E, Wirth B, Yushenova I, Kellis M, Kondrashov AS, Mark Welch DB, Pontarotti P, Weissenbach J, Wincker P, Jaillon O, Van Doninck K.

Nature. 2013 Aug 22;500(7463):453-7. doi: 10.1038/nature12326. Epub 2013 Jul 21.

29.

A predictive computational model of the dynamic 3D interphase yeast nucleus.

Wong H, Marie-Nelly H, Herbert S, Carrivain P, Blanc H, Koszul R, Fabre E, Zimmer C.

Curr Biol. 2012 Oct 23;22(20):1881-90. doi: 10.1016/j.cub.2012.07.069. Epub 2012 Aug 30.

30.

Normalization of a chromosomal contact map.

Cournac A, Marie-Nelly H, Marbouty M, Koszul R, Mozziconacci J.

BMC Genomics. 2012 Aug 30;13:436. doi: 10.1186/1471-2164-13-436.

31.

The chiasmatype theory. A new interpretation of the maturation divisions. 1909.

Janssens FA, Koszul R, Zickler D.

Genetics. 2012 Jun;191(2):319-46. doi: 10.1534/genetics.112.139725. No abstract available.

32.

The centenary of Janssens's chiasmatype theory.

Koszul R, Meselson M, Van Doninck K, Vandenhaute J, Zickler D.

Genetics. 2012 Jun;191(2):309-17. doi: 10.1534/genetics.112.139733. Erratum in: Genetics. 2012 Oct;192(2):757.

33.

Dynamic chromosome movements during meiosis: a way to eliminate unwanted connections?

Koszul R, Kleckner N.

Trends Cell Biol. 2009 Dec;19(12):716-24. doi: 10.1016/j.tcb.2009.09.007. Epub 2009 Oct 23. Review. Erratum in: Trends Cell Biol. 2010 Feb;20(2):63.

34.

Real-time imaging of meiotic chromosomes in Saccharomyces cerevisiae.

Koszul R, Kameoka S, Weiner BM.

Methods Mol Biol. 2009;558:81-9. doi: 10.1007/978-1-60761-103-5_6. Review.

35.

A prominent role for segmental duplications in modeling eukaryotic genomes.

Koszul R, Fischer G.

C R Biol. 2009 Feb-Mar;332(2-3):254-66. doi: 10.1016/j.crvi.2008.07.005. Epub 2008 Dec 2. Review.

PMID:
19281956
36.

Csm4, in collaboration with Ndj1, mediates telomere-led chromosome dynamics and recombination during yeast meiosis.

Wanat JJ, Kim KP, Koszul R, Zanders S, Weiner B, Kleckner N, Alani E.

PLoS Genet. 2008 Sep 26;4(9):e1000188. doi: 10.1371/journal.pgen.1000188.

37.

Segmental duplications arise from Pol32-dependent repair of broken forks through two alternative replication-based mechanisms.

Payen C, Koszul R, Dujon B, Fischer G.

PLoS Genet. 2008 Sep 5;4(9):e1000175. doi: 10.1371/journal.pgen.1000175.

38.

Meiotic chromosomes move by linkage to dynamic actin cables with transduction of force through the nuclear envelope.

Koszul R, Kim KP, Prentiss M, Kleckner N, Kameoka S.

Cell. 2008 Jun 27;133(7):1188-201. doi: 10.1016/j.cell.2008.04.050.

39.

Stability of large segmental duplications in the yeast genome.

Koszul R, Dujon B, Fischer G.

Genetics. 2006 Apr;172(4):2211-22. Epub 2006 Feb 19.

40.

Large-scale exploration of growth inhibition caused by overexpression of genomic fragments in Saccharomyces cerevisiae.

Boyer J, Badis G, Fairhead C, Talla E, Hantraye F, Fabre E, Fischer G, Hennequin C, Koszul R, Lafontaine I, Ozier-Kalogeropoulos O, Ricchetti M, Richard GF, Thierry A, Dujon B.

Genome Biol. 2004;5(9):R72. Epub 2004 Aug 31.

41.

Genome evolution in yeasts.

Dujon B, Sherman D, Fischer G, Durrens P, Casaregola S, Lafontaine I, De Montigny J, Marck C, Neuvéglise C, Talla E, Goffard N, Frangeul L, Aigle M, Anthouard V, Babour A, Barbe V, Barnay S, Blanchin S, Beckerich JM, Beyne E, Bleykasten C, Boisramé A, Boyer J, Cattolico L, Confanioleri F, De Daruvar A, Despons L, Fabre E, Fairhead C, Ferry-Dumazet H, Groppi A, Hantraye F, Hennequin C, Jauniaux N, Joyet P, Kachouri R, Kerrest A, Koszul R, Lemaire M, Lesur I, Ma L, Muller H, Nicaud JM, Nikolski M, Oztas S, Ozier-Kalogeropoulos O, Pellenz S, Potier S, Richard GF, Straub ML, Suleau A, Swennen D, Tekaia F, Wésolowski-Louvel M, Westhof E, Wirth B, Zeniou-Meyer M, Zivanovic I, Bolotin-Fukuhara M, Thierry A, Bouchier C, Caudron B, Scarpelli C, Gaillardin C, Weissenbach J, Wincker P, Souciet JL.

Nature. 2004 Jul 1;430(6995):35-44.

PMID:
15229592
42.

Eucaryotic genome evolution through the spontaneous duplication of large chromosomal segments.

Koszul R, Caburet S, Dujon B, Fischer G.

EMBO J. 2004 Jan 14;23(1):234-43. Epub 2003 Dec 18.

43.

The complete mitochondrial genome sequence of the pathogenic yeast Candida (Torulopsis) glabrata.

Koszul R, Malpertuy A, Frangeul L, Bouchier C, Wincker P, Thierry A, Duthoy S, Ferris S, Hennequin C, Dujon B.

FEBS Lett. 2003 Jan 16;534(1-3):39-48.

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