Lab Presentation

Our research focuses on the topology of intracellular DNA, its regulation and its biological implications. We investigate the occurrence of DNA supercoils, knots and catenanes across eukaryotic chromosomes; and the molecular mechanisms that generate, stabilize and dissolve them.

DNA torsion
DNA topology

As DNA molecules are extremely long, they are folded into a precise hierarchy of chromatin domains. Yet, most genome transactions require unfolding the chromatin and unwinding the DNA double helix. Consequently, intracellular DNA undergoes tough topological constraints. This problem is solved by the enzymes termed topoisomerases, which transiently break the DNA strands to pass them throughout each other. Numerous antibiotics and anti-cancer drugs work by interfering the activity of topoisomerases. The topological state of DNA closely correlates to genome transactions, such as DNA transcription and chromosome replication. The torsional energy of the DNA double helix determines the probability of duplex unwinding and juxtaposition of distant DNA sites. DNA topology affects the interaction of DNA with structural elements and enzymatic machinery of chromatin. Ultimately, cell fate is defined by epigenomes, by which differential chromatin configurations may determine how DNA twisting forces are generated and dissipated, and when DNA entanglements need to be preserved or dissolved. Faithful understanding of the mechanisms that govern genome biology and cell fate will be possible after uncovering the topology of intracellular DNA, its dynamics and its regulation. To this aim, we study the mechanism and function of DNA topoisomerases, and we develop novel experimental approaches to assess in vivo DNA topology, both at local and genome-wide scale. Main research contributions: · The three-gate mechanism of DNA transport by type-2 topoisomerases · DNA transport preferences and proofreading activity of topoisomerase II · Capture of 3D path of packaged DNA by means of DNA knot analysis. · Response of chromatin structure to DNA torsional stress. · Topoisomerase activity on chromatinized DNA. · Genome-wide analysis of DNA topology by means of psoralen-DNA photo-binding · Distinctive DNA topology at centromeres, telomeres and other chromatin elements. For more details visit my webpage.

Projects

  • GUIDE TOPO II. Study the regulation of the multiple functions of topoisomerase II.
  • DNA TANGLES Study of DNA knots and catenanes to deduce the 3D path of intracellular DNA.
  • TOPOLOMICS Genome-wide analysis of constrained and unconstrained DNA topology.

Lab People

Joaquim Roca Bosch

Joaquim Roca Bosch

Research Professor CSIC

jrbbmc@ibmb.csic.es

Joaquim Roca is the head of the DNA Topology Lab at the Molecular Biology Institute of Barcelona (IBMB-CSIC). He obtained his BSc degree in Medicine and Surgery in 1984 from the University of Barcelona, his Ms in Molecular Biology in 1985 from the Technology University of Catalonia, and his PhD in 1988 from the University of Barcelona. In 1989 he joined the laboratory of Prof. James Wang at Harvard University as Postdoctoral Fellow and, later on, as Research Associate until 1996. At Harvard, he researched on Chromosomal DNA Topology and disclosed the mechanism of Type-2 Topoisomerases. In 1996, he returned to Barcelona as Staff Scientist of the CSIC and created the DNA Topology research group. Joaquim Roca is presently a CSIC Professor. He has been Chairman of the Molecular and Cellular Biology Department from 2002 to 2006 and Deputy Director of the IBMB from 2006 to 2010.

Belen Martinez Garcia

Belen Martinez Garcia

Staff scientist

bmabmc@ibmb.csic.es

Joana Segura Martinez

Joana Segura Martinez

PhD Student

jsmbmc@ibmb.csic.es

Antonio Valdes Gutierrez

Antonio Valdes Gutierrez

PhD Student

avabmc@ibmb.csic.es

Sílvia Dyson Coral

Sílvia Dyson Coral

PhD Student

sdcbmc@ibmb.csic.es

Ricky Joshi

Ricky Joshi

Instructor

rjobmc@ibmb.csic.es

Selected Publications

DNA knots occur in intracellular chromatin Valdés A, Segura J, Dyson S, Martínez-García B and Roca J Nucleic Acids Res. 15 Nov (2017)


DNA topology and global architecture of point centromeres Ofelia Díaz-Ingelmo, Belén Martínez-García, Joana Segura, Antonio Valdés, and Joaquim Roca. Cell Reports, 2015; 13: 667–677.


Chromatin regulates DNA torsional energy via topoisomerase II-mediated relaxation of positive supercoils. Xavier Fernández, Ofelia Díaz-Ingelmo, Belén Martínez-García & Joaquim Roca. EMBO Journal, 2014; 33: 1492–1501.


Positional dependence of transcriptional inhibition by DNA torsional stress in yeast chromosomes. Joshi, R.S., Pina, B., and Roca, J. EMBO Journal, 2010; 29, 740-748.


Topoisomerase II, not topoisomerase I, is the proficient relaxase of nucleosomal DNA. Salceda, J., Fernandez, X., and Roca, J. EMBO Journal, 2006; 25, 2575-2583.


DNA knots reveal a chiral organization of DNA in phage capsids. Arsuaga, J., Vazquez, M., McGuirk, P., Trigueros, S., Sumners, D., and Roca, J. Proc Natl Acad Sci U S A, 2005; 102, 9165-9169.


Knotting probability of DNA molecules confined in restricted volumes: DNA knotting in phage capsids Arsuaga, J., Vazquez, M., Trigueros, S., Sumners, D., and Roca, J. Proc Natl Acad Sci U S A, 2002; 99, 5373-5377.


DNA transport by a type II DNA topoisomerase: evidence in favor of a two-gate mechanism. Roca, J., and Wang, J.C. Cell, 1994; 77, 609-616.


Antitumor bisdioxopiperazines inhibit yeast DNA topoisomerase II by trapping the enzyme in the form of a closed protein clamp. Roca, J., Ishida, R., Berger, J.M., Andoh, T., and Wang, J.C. (1994). Proc Natl Acad Sci U S A, 1994; 91, 1781-1785.


The capture of a DNA double helix by an ATP-dependent protein clamp: a key step in DNA transport by type II DNA topoisomerases. Roca, J., and Wang, J.C. Cell, 1992; 71, 833-840.


DNA topoisomerase II activity in nonreplicating, transcriptionally inactive, chicken late spermatids Roca, J., and Mezquita, C. EMBO Journal, 1989; 8, 1855-1860.


All Publications

DNA knots occur in intracellular chromatin

Valdés A, Segura J, Dyson S, Martínez-García B and Roca J

Nucleic Acids Res. 15 Nov (2017)


Genome urbanization: clusters of topologically co-regulated genes delineate functional compartments in the genome of Saccharomyces cerevisiae.

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.


Chromatin regulates DNA torsional energy via topoisomerase II-mediated relaxation of positive supercoils.

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


Suitability and effectiveness of single layer centrifugation using Androcoll-P in the cryopreservation protocol for boar spermatozoa.

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


Dead spermatozoa in raw semen samples impair in vitro fertilization outcomes of frozen-thawed spermatozoa.

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


Exploring the energy landscape of nucleic acid hairpins using laser temperature-jump and microfluidic mixing.

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


Effects of Hoechst 33342 staining and ultraviolet irradiation on mitochondrial distribution and DNA copy number in porcine oocytes and preimplantation embryos.

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.


Differences in the ability of spermatozoa from individual boar ejaculates to withstand different semen-processing techniques.

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


The effect of glycerol concentrations on the post-thaw in vitro characteristics of cryopreserved sex-sorted boar spermatozoa.

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


Exposure to the seminal plasma of different portions of the boar ejaculate modulates the survival of spermatozoa cryopreserved in MiniFlatPacks.

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


Radiation, multiple dispersal and parallelism in the skinks, Chalcides and Sphenops (Squamata: Scincidae), with comments on Scincus and Scincopus and the age of the Sahara Desert.

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.


Localization and expression of spermadhesin PSP-I/PSP-II subunits in the reproductive organs of the boar.

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.


Glutathione depletion impairs myogenic differentiation of murine skeletal muscle C2C12 cells through sustained NF-kappaB activation.

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.


Fluorescence in situ hybridization in diluted and flow cytometrically sorted boar spermatozoa using specific DNA direct probes labeled by nick translation.

Parrilla I, Vázquez JM, Oliver-Bonet M, Navarro J, Yelamos J, Roca J, Martínez EA.

Reproduction. 2003 Sep;126(3):317-25


Cloning, functional analysis and post-transcriptional regulation of a type II DNA topoisomerase from Leishmania infantum. A new potential target for anti-parasite drugs.

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.


Antigenicity of a recombinant NS3 protein representative of ATPase/helicase domain from hepatitis C virus.

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


Failure to relax negative supercoiling of DNA is a primary cause of mitotic hyper-recombination in topoisomerase-deficient yeast cells.

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


A GyrB-GyrA fusion protein expressed in yeast cells is able to remove DNA supercoils but cannot substitute eukaryotic topoisomerase II.

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


Varying levels of positive and negative supercoiling differently affect the efficiency with which topoisomerase II catenates and decatenates DNA.

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


The polymerase chain reaction as a marker of cytomegalovirus infection in heart transplant recipients

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


Antitumor bisdioxopiperazines inhibit yeast DNA topoisomerase II by trapping the enzyme in the form of a closed protein clamp.

Roca J, Ishida R, Berger JM, Andoh T, Wang JC.

Proc Natl Acad Sci U S A. 1994 Mar 1;91(5):1781-5


On the simultaneous binding of eukaryotic DNA topoisomerase II to a pair of double-stranded DNA helices.

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.


The capture of a DNA double helix by an ATP-dependent protein clamp: a key step in DNA transport by type II DNA topoisomerases

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.


DNA topoisomerase II activity in nonreplicating, transcriptionally inactive, chicken late spermatids.

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


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