Lab presentation
Gene transcription and chromosome replication are subjected to severe topological constraints due to the double helical structure and the enormous length of the DNA molecules. Firstly, while intracellular DNA molecules are closely packaged, they have to be also accessible and untangled to facilitate genome transactions. Apparently, this is achieved throughout periodic coiling and looping of DNA to produce a fractal of topological domains, which can be rearranged into functional compartments and physico-chemical phases. Secondly, as gene transcription and chromosome replication require unwinding the double helix, DNA strands undergo helical tension that needs to be dissipated. Yet, DNA helical tension is also useful to tune up the spatial folding (supercoiling), conformational transitions and molecular interactions of DNA.
Despite the pivotal role of DNA topology, its interplay with the multiplicity of genomic regulators commonly investigated is often overlooked (or mis-understood). However, only by assessing DNA topology, it will be possible to understand truly the nano-mechanics that govern chromosome biology and its dysfunctions. Our research aims thereby to decipher the structural and enzymatic ensembles that determine the 3D path of intracellular DNA strands, and how DNA pulling and twisting forces interplay with chromatin architecture and genomic activities.
Projects
Our experimental research exploits mainly the “topological method”, which relies in the analysis of topology invariants (DNA strand links & knots) to infer how DNA molecules are deformed and manipulated in biological systems.
We use the topological method to disclose the mechanism of the two enzymatic complexes that are essential to organize DNA molecules within chromosomes and are highly conserved throughout evolution:
A ) Type-2A topoisomerases, identified mainly as topo IV and gyrase in bacteria, and topo II in eukaryotic cells.
B ) SMC (Structural Maintenance of Chromosomes) complexes, such as condensin and cohesin in eukaryotic cells.
We aim also to outline the 3D path of intracellular DNA by using topological methods in two research lines:
C ) Characterization of DNA knots. DNA knots are topological invariants that capture (i.e. footprint) the spatial trajectory of DNA. We compare the spectrum and chirality of DNA knots produced in biological ensembles with that obtained by computer simulations to infer the spatial path of DNA molecules.
D ) Genome-wide analysis of constrained and unconstrained DNA supercoils. By examining changes in the DNA linking number of circularized chromosomes and DNA unwinding probability, we infer how DNA is deformed by structural elements and motor activities of chromatin, both locally and genome-wide.
Lab people
Joaquim Roca Bosch
Joaquim Roca is the head of the DNA Topology Lab at the Molecular Biology Institute of Barcelona (IBMB-CSIC). He obtained a MD degree (BSc in Medicine & Surgery) in 1984 from the University of Barcelona, a Ms degree in Molecular Biology in 1985 from the Technology University of Catalonia, and a PhD degree in 1988 from the University of Barcelona. In 1989 he moved to Harvard University to join the Laboratory of James Wang as Postdoctoral Fellow and to work later on as Research Associate. He returned to Barcelona in 1996 as Staff Scientist of the Spanish Research Council (CSIC) to create the DNA Topology Lab at IBMB. Joaquim Roca was Chairman of the Molecular and Cellular Biology Department of IBMB from 2002 to 2006, Deputy Director of the IBMB from 2006 to 2010, and he was promoted to full research Professor in 2008.
Personal web page http://dnatopology.rocabosch.com/
Belen Martinez Garcia
Ofelia Diaz Ingelmo
Alba Ayats Fraile
Past Students
Joana Segura Martinez
Sílvia Dyson Coral
Selected publications
Martínez-García B, Dyson S, Segura J, Ayats A, Cutts E, Gutierrez-Escribano P, Aragón L, Roca J (2022)
Condensin pinches a short negatively supercoiled DNA loop during each round of ATP usage.
EMBO J 19: e111913
Roca J, Mezquita C (1989)
DNA topoisomerase II activity in nonreplicating, transcriptionally inactive, chicken late spermatids.
EMBO J 8: 1855-60
Roca J, Wang JC (1992)
The capture of a DNA double helix by an ATP-dependent protein clamp: a key step in DNA transport by type II DNA topoisomerases.
Cell 71: 833-40
Roca J, Ishida R, Berger JM, Andoh T, Wang JC (1994)
Antitumor bisdioxopiperazines inhibit yeast DNA topoisomerase II by trapping the enzyme in the form of a closed protein clamp.
PNAS 91: 1781-5
Roca J, Wang JC (1994)
DNA transport by a type II DNA topoisomerase: evidence in favor of a two-gate mechanism.
Cell 77: 609-16
Roca J (1995)
The mechanisms of DNA topoisomerases.
TiBS 20: 156-60
Roca J, Berger JM, Harrison SC, Wang JC (1996)
DNA transport by a type II topoisomerase: direct evidence for a two-gate mechanism.
PNAS 93: 4057-62
Arsuaga J, Vazquez M, Trigueros S, Sumners D, Roca J (2002)
Knotting probability of DNA molecules confined in restricted volumes: DNA knotting in phage capsids.
PNAS 99: 5373-7
Arsuaga J, Vazquez M, McGuirk P, Trigueros S, Sumners D, Roca J (2005)
DNA knots reveal a chiral organization of DNA in phage capsids.
PNAS 102: 9165-9
Salceda J, Fernandez X, Roca J (2006)
Topoisomerase II, not topoisomerase I, is the proficient relaxase of nucleosomal DNA.
EMBO J 25: 2575-83
Joshi RS, Pina B, Roca J (2010)
Positional dependence of transcriptional inhibition by DNA torsional stress in yeast chromosomes.
EMBO J 29: 740-8
Fernandez X, Diaz-Ingelmo O, Martinez-Garcia B, Roca J (2014)
Chromatin regulates DNA torsional energy via topoisomerase II-mediated relaxation of positive supercoils.
EMBO J 33: 1492-501
Diaz-Ingelmo O, Martinez-Garcia B, Segura J, Valdes A, Roca J (2015)
DNA Topology and Global Architecture of Point Centromeres.
Cell Rep 13: 667-77
Segura J, Joshi RS, Diaz-Ingelmo O, Valdes A, Dyson S, Martinez-Garcia B, Roca J (2018)
Intracellular nucleosomes constrain a DNA linking number difference of -1.26 that reconciles the Lk paradox.
Nature Com 9: 3989
Dyson S, Segura J, Martinez-Garcia B, Valdes A, Roca J (2021)
Condensin minimizes topoisomerase II-mediated entanglements of DNA in vivo.
EMBO J 40: e105393
All publications
Condensin pinches a short negatively supercoiled DNA loop during each round of ATP usage.
Martínez-García B, Dyson S, Segura J, Ayats A, Cutts E, Gutierrez-Escribano P, Aragón L, Roca J.
EMBO J 19: e111913 (2022)
Condensin minimizes topoisomerase II-mediated entanglements of DNA in vivo.
Dyson S, Segura J, Martinez-Garcia B, Valdes A, Roca J
EMBO J 40: e105393 (2021)
Transcriptional supercoiling boosts topoisomerase II-mediated knotting of intracellular DNA.
Valdés A, Coronel L, Martínez-García B, Segura J, Dyson S, Díaz-Ingelmo O, Micheletti C, Roca J.
Nucleic Acids Res. 2019 Jun 5. pii: gkz491.
Quantitative disclosure of DNA knot chirality by high-resolution 2D-gel electrophoresis.
Valdés A, Martínez-García B, Segura J, Dyson S, Díaz-Ingelmo O, Roca J.
Nucleic Acids Res. 2019 Mar 18;47(5):e29.
Electrophoretic Analysis of the DNA Supercoiling Activity of DNA Gyrase.
Martínez-García B, Valdés A, Segura J, Dyson S, Díaz-Ingelmo O, Roca J.
Methods Mol Biol. 2018;1805:291-300. doi: 10.1007/978-1-4939-8556-2_15.
Segura J, Joshi RS, Díaz-Ingelmo O, Valdés A, Dyson S, Martínez-García B, Roca J.
Nat Commun. 2018 Sep 28;9(1):3989. doi: 10.1038/s41467-018-06547-w.
DNA knots occur in intracellular chromatin
Valdés A, Segura J, Dyson S, Martínez-García B and Roca J
Nucleic Acids Res. 2018 Jan 25;46(2):650-660.
Structure and Chromosomal Organization of Yeast Genes Regulated by Topoisomerase II.
Joshi R.S., Nikolaou C., Roca J.
Int J Mol Sci. 2018 Jan 3;19(1). pii: E134.
Tsochatzidou M, Malliarou M, Papanikolaou N, Roca J, Nikolaou C
Nucleic Acids Res. vol 45, pp. 5818-5828 (2017)
In silico, In vitro and In vivo Imageries of Type II Topoisomerases
Roca J
Phys Life Rev vol 8, pp. 147-149 (2016)
The Effect of Oxidative Stress on Thawed Bulk-Sorted Red Deer Sperm.
Anel-López L, García-Álvarez O, Parrilla I, Del Olmo D, Fernández-Santos MR, Soler AJ, Maroto-Morales A, Ortiz JA, Alkmin DV, Tarantini T, Roca J, Martínez EA, Vazquez JM, Garde JJ.
Reprod Domest Anim. 2016; 51(3):407-14
DNA Topology and Global Architecture of Point Centromeres
Díaz-Ingelmo O, Martínez-García B, Segura J, Valdés A, Roca J.
Cell Rep. 2015 Oct 27;13(4):667-77.
Fernández X, Díaz-Ingelmo O, Martínez-García B, Roca J.
EMBO J. 2014 Jul 1;33(13):1492-501
Topoisomerase II minimizes DNA entanglements by proofreading DNA topology after DNA strand passage.
Martínez-García B, Fernández X, Díaz-Ingelmo O, Rodríguez-Campos A, Manichanh C, Roca J.
Nucleic Acids Res. 2014 Feb;42(3):1821-30.
Topoisomerase II regulates yeast genes with singular chromatin architectures.
Nikolaou C, Bermúdez I, Manichanh C, García-Martinez J, Guigó R, Pérez-Ortín JE, Roca J.
Nucleic Acids Res. 2013 Nov;41(20):9243-56
Martinez-Alborcia MJ, Morrell JM, Gil MA, Barranco I, Maside C, Alkmin DV, Parrilla I, Martinez EA, Roca J.
Anim Reprod Sci. 2013 Aug;140(3-4):173-9
Roca J, Martinez-Alborcia MJ, Gil MA, Parrilla I, Martinez EA.
Fertil Steril. 2013 Sep;100(3):875-81
Anal gas evacuation and colonic microbiota in patients with flatulence: effect of diet.
Manichanh C, Eck A, Varela E, Roca J, Clemente JC, González A, Knights D, Knight R, Estrella S, Hernandez C, Guyonnet D, Accarino A, Santos J, Malagelada JR, Guarner F, Azpiroz F.
Gut. 2014 Mar;63(3):401-8
The nuclear DNA longevity in cryopreserved boar spermatozoa assessed using the Sperm-Sus-Halomax.
Alkmin DV, Martinez-Alborcia MJ, Parrilla I, Vazquez JM, Martinez EA, Roca J.
Theriogenology. 2013 Jun;79(9):1294-300
Narayanan R, Zhu L, Velmurugu Y, Roca J, Kuznetsov SV, Prehna G, Lapidus LJ, Ansari A.
J Am Chem Soc. 2012 Nov 21;134(46):18952-63
Storage conditions of intestinal microbiota matter in metagenomic analysis
Cardona S, Eck A, Cassellas M, Gallart M, Alastrue C, Dore J, Azpiroz F, Roca J, Guarner F, Manichanh C.
BMC Microbiol. 2012 Jul 30;12:158
Gil MA, Maside C, Cuello C, Parrilla I, Vazquez JM, Roca J, Martinez EA.
Mol Reprod Dev. 2012 Sep;79(9):651-63.
Topoisomerase II is required for the production of long Pol II gene transcripts in yeast.
Joshi RS, Piña B, Roca J.
Nucleic Acids Res. 2012 Sep;40(16):7907-15.
Parrilla I, del Olmo D, Sijses L, Martinez-Alborcia MJ, Cuello C, Vazquez JM, Martinez EA, Roca J.
Anim Reprod Sci. 2012 May;132(1-2):66-73
Parrilla I, del Olmo D, Caballero I, Tarantini T, Cuello C, Gil MA, Roca J, Martinez EA, Vazquez JM.
Reprod Domest Anim. 2012 Dec;47(6):965-74
The torsional state of DNA within the chromosome.
Roca J.
Chromosoma, 2011 Aug;120(4):323-34
Transcriptional inhibition by DNA torsional stress.
Roca J.
Transcription, 2011 Mar;2(2):82-85
A method for genome-wide analysis of DNA helical tension by means of psoralen-DNA photobinding.
Bermúdez I, García-Martínez J, Pérez-Ortín JE, Roca J.
Nucleic Acids Res. 2010 Oct;38(19):e182.
Study of the BMPR2 gene in patients with pulmonary arterial hypertension
Portillo K, Santos S, Madrigal I, Blanco I, Paré C, Borderías L, Peinado VI, Roca J, Milà M, Barberà JA.
Arch Bronconeumol. 2010 Mar;46(3):129-34
Positional dependence of transcriptional inhibition by DNA torsional stress in yeast chromosomes
Joshi RS, Piña B, Roca J.
EMBO J. 2010 Feb 17;29(4):740-8.
Two-dimensional agarose gel electrophoresis of DNA topoisomers.
Roca J.
Methods Mol Biol. 2009;582:27-37.
Topoisomerase II: a fitted mechanism for the chromatin landscape.
Roca J.
Nucleic Acids Res. 2009 Feb;37(3):721-30
Sex-sorting sperm by flow cytometry in pigs: issues and perspectives.
Vazquez JM, Parrilla I, Roca J, Gil MA, Cuello C, Vazquez JL, Martínez EA.
Theriogenology. 2009 Jan 1;71(1):80-8
Saravia F, Wallgren M, Johannisson A, Calvete JJ, Sanz L, Peña FJ, Roca J, Rodríguez-Martínez H.
Theriogenology. 2009 Mar 1;71(4):662-75
Chronic endurance exercise induces quadriceps nitrosative stress in patients with severe COPD.
Barreiro E, Rabinovich R, Marin-Corral J, Barberà JA, Gea J, Roca J.
Thorax. 2009 Jan;64(1):13-9.
Improving the efficiency of insemination with sex-sorted spermatozoa.
Vazquez JM, Parrilla I, Gil MA, Cuello C, Caballero I, Vazquez JL, Roca J, Martínez EA.
Reprod Domest Anim. 2008 Oct;43 Suppl 4:1-8
Carranza S, Arnold EN, Geniez P, Roca J, Mateo JA. Mol
Phylogenet Evol. 2008 Mar;46(3):1071-94
Production of highly knotted DNA by means of cosmid circularization inside phage capsids.
Trigueros S, Roca J.
BMC Biotechnol. 2007 Dec 21;7:94.
García EM, Vázquez JM, Parrilla I, Ortega MD, Calvete JJ, Sanz L, Martínez EA, Roca J, Rodríguez-Martínez H.
Int J Androl. 2008 Aug;31(4):408-17.
Fractal dimension and localization of DNA knots.
Ercolini E, Valle F, Adamcik J, Witz G, Metzler R, De Los Rios P, Roca J, Dietler G.
Phys Rev Lett. 2007 Feb 2;98(5):058102.
Differences in SCSA outcome among boars with different sperm freezability.
Hernández M, Roca J, Ballester J, Vázquez JM, Martínez EA, Johannisson A, Saravia F, Rodríguez-Martínez H.
Int J Androl. 2006 Dec;29(6):583-91.
Topoisomerase II, not topoisomerase I, is the proficient relaxase of nucleosomal DNA.
Salceda J, Fernández X, Roca J.
EMBO J. 2006 Jun 7;25(11):2575-83.
Reduced diversity of faecal microbiota in Crohn’s disease revealed by a metagenomic approach.
Manichanh C, Rigottier-Gois L, Bonnaud E, Gloux K, Pelletier E, Frangeul L, Nalin R, Jarrin C, Chardon P, Marteau P, Roca J, Dore J.
Gut. 2006 Feb;55(2):205-11.
DNA knots reveal a chiral organization of DNA in phage capsids.
Arsuaga J, Vazquez M, McGuirk P, Trigueros S, Sumners D, Roca J.
Proc Natl Acad Sci U S A. 2005 Jun 28;102(26):9165-9.
Oxidative stress and airway inflammation in severe exacerbations of COPD.
Drost EM, Skwarski KM, Sauleda J, Soler N, Roca J, Agusti A, MacNee W.
Thorax. 2005 Apr;60(4):293-300.
Ardite E, Barbera JA, Roca J, Fernández-Checa JC.
Am J Pathol. 2004 Sep;165(3):719-28.
Flow cytometry identification of X- and Y-chromosome-bearing goat spermatozoa.
Parrilla I, Vazquez JM, Roca J, Martinez EA.
Reprod Domest Anim. 2004 Feb;39(1):58-60.
Effects of centrifugation before freezing on boar sperm cryosurvival.
Carvajal G, Cuello C, Ruiz M, Vázquez JM, Martínez EA, Roca J.
J Androl. 2004 May-Jun;25(3):389-96.
The path of the DNA along the dimer interface of topoisomerase II.
Roca J.
J Biol Chem. 2004 Jun 11;279(24):25783-8.
Asymmetric removal of supercoils suggests how topoisomerase II simplifies DNA topology.
Trigueros S, Salceda J, Bermúdez I, Fernández X, Roca J.
J Mol Biol. 2004 Jan 16;335(3):723-31.
Parrilla I, Vázquez JM, Oliver-Bonet M, Navarro J, Yelamos J, Roca J, Martínez EA.
Reproduction. 2003 Sep;126(3):317-25
Hanke T, Ramiro MJ, Trigueros S, Roca J, Larraga V.
Nucleic Acids Res. 2003 Aug 15;31(16):4917-28.
Two-dimensional agarose-gel electrophoresis of DNA topoisomers.
Hanai R, Roca J.
Methods Mol Biol. 1999;94:19-27.
Pentón N, Musacchio A, Rivera JM, Roca J, Ponce M, Rodríguez D, Caballero A, Tallo YI, Narciandi RE.
Clin Biochem. 2003 Feb;36(1):41-9
Trigueros S, Roca J.
J Biol Chem. 2002 Oct 4;277(40):37207-11.
Knotting probability of DNA molecules confined in restricted volumes: DNA knotting in phage capsids.
Arsuaga J, Vázquez M, Trigueros S, Sumners D, Roca J.
Proc Natl Acad Sci U S A. 2002 Apr 16;99(8):5373-7
Trigueros S, Roca J.
Genes Cells. 2002 Mar;7(3):249-57
Novel display of knotted DNA molecules by two-dimensional gel electrophoresis.
Trigueros S, Arsuaga J, Vazquez ME, Sumners DW, Roca J
Nucleic Acids Res. 2001 Jul 1;29(13):E67-7
Roca J.
J Mol Biol. 2001 Jan 19;305(3):441-50.
Filter binding assays for topoisomerase-DNA complexes.
Roca J.
Methods Mol Biol. 2001;95:75-80
Circular minichromosomes become highly recombinogenic in topoisomerase-deficient yeast cells.
Trigueros S, Roca J.
J Biol Chem. 2001 Jan 19;276(3):2243-8
Niubò J, Pérez JL, Manito N, García A, Roca J, Martín R.
]. Med Clin (Barc). 1999 Feb 6;112(4):121-4.
DNA transport by a type II topoisomerase: direct evidence for a two-gate mechanism.
Roca J, Berger JM, Harrison SC, Wang JC.
Proc Natl Acad Sci U SA. 1996 Apr 30;93(9):4057-62
Genotype determination of hepatitis C virus from northern India: identification of a new subtype.
Panigrahi AK, Roca J, Acharya SK, Jameel S, Panda SK.
J Med Virol. 1996 Feb;48(2):191-8.
The probabilities of supercoil removal and decatenation by yeast DNA topoisomerase II.
Roca J, Wang JC.
Genes Cells. 1996 Jan;1(1):17-27
The mechanisms of DNA topoisomerases.
Roca J.
Trends Biochem Sci. 1995 Apr;20(4):156-60.
DNA transport by a type II DNA topoisomerase: evidence in favor of a two-gate mechanism.
Roca J, Wang JC.
Cell. 1994 May 20;77(4):609-16
Roca J, Ishida R, Berger JM, Andoh T, Wang JC.
Proc Natl Acad Sci U S A. 1994 Mar 1;91(5):1781-5
Roca J, Berger JM, Wang JC.
J Biol Chem. 1993 Jul 5;268(19):14250-5
Separation of rooster spermatogenic nuclei by means of centrifugal elutriation.
Boix J, Roca J.
Cytometry. 1993;14(4):465-7.
Roca J, Wang JC.
Cell. 1992 Nov 27;71(5):833-40.
A hit-and-run system for targeted genetic manipulations in yeast.
Roca J, Gartenberg MR, Oshima Y, Wang JC.
Nucleic Acids Res. 1992 Sep 11;20(17):4671-2.
Roca J, Mezquita C.
EMBO J. 1989 Jun;8(6):1855-60
Structural organization of sperm chromatin from the fish Carassius auratus.
Muñoz-Guerra S, Azorín F, Casas MT, Marcet X, Maristany MA, Roca J, Subirana JA.
Exp Cell Res. 1982 Jan;137(1):47-53
Project funding
“DNA Topology: Regulation and Biological Implications” (VI)
MINCINN – Ref. PID2019-109482GB-I00 – 350.900 € (2020 – 2024)
Proyecto PID2019-109482GB-I00 financiado por:
Ayuda Extraordinaria Menciones de Excelencia Severo Ochoa 2020
CSIC – Ref. 20202CEX003 – 281.250 € (2020 – 2021)
Ayudas extraordinarias preparación proyectos 2019
CSIC – Ref. 2019AEP174 – 31.478 € (2020 – 2020)
“DNA Topology: Regulation and Biological Implications” (V)
MINECO – Ref. BFU2015-67007-P – 355.740 € (2016 – 2020)
Proyecto BFU2015-67007-P financiado por:
Apoyo a las Unidades de Excelencia Maria de Maeztu
MINECO – Ref. MDM 2014-0435 – 2.000.000 € (2015 – 2019)
“DNA Topology: Regulation and Biological Implications” (IV)
MINECO – Ref. BFU2011-23851 – 310.970 € (2012 – 2015)
“Structural & Applied Genomics” (II)
AGAUR – Ref. 2009 SGR 01222 – 43.680 € (2010 – 2013)
“DNA Topology: Regulation and Biological Implications” (III)
MICINN – Ref. BFU2008-00366/BMC – 239.580 € (2009 – 2011)
“DNA Topology: Regulation and Biological Implications” (II)
MEC – Ref. BFU2005-01311 – 119.000 € (2006 – 2008)
“Structural & Applied Genomics” (I)
DURSI – Ref. 2005 SGR 00601 – 36.000 € (2006 – 2009)
“DNA Topology: Regulation and Biological Implications” (I)
MCyT – Ref. BMC2002-03275 – 93.000 € (2003 – 2005)
“Genomic Stress in Yeast”
MCyT Genomics and Proteomics – 81.000 € (2003 – 2005)
“Biological roles of Eukaryotic DNA Topoisomerases” (II)
DGESIC – Ref PB1998-0487 – 60.100 € (2000 – 2002)
“Biological roles of Eukaryotic DNA Topoisomerases” (I)
DGICYT – Ref PB95-0131 – 60.100 € (1997 – 1999)
Vacancies/Jobs
Interested in joining our group as PhD student or Postdoctoral fellow are welcome to apply at anytime.
Please send your CV and cover letter to: joaquim.roca@ibmb.csic.es
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