Genome Integrity and Instability
Research Lines
The research activity of the research group has as its main objective to study the mechanism(s) responsible for the origin and maintenance of the integrity of the mammalian genome.
We achieve our main objective through a multidisciplinary approach, combining computational analysis and whole genome comparisons with cutting-edge experimental technologies in both somatic and meiotic cells.
More specifically, the group is currently working on the following lines of research:
- Investigating the conservation and functionality of the high-structure organization of mammalian genomes, both in the somatic and germline lineages.
- Analysis of the signaling pathway that controls the progression of meiotic recombination in mammalian meiocytes.
- Identification of the role of the DNA damage response machinery in the repair of the "DSB" that occurs during meiotic prophase.
- Study how the DNA damage response mechanism controls oocyte assembly in mammals.
- Identification of unannotated genes in the mammalian genome required for the completion of meiosis.
- Identification of the genetic basis of reproductive isolation and barriers to gene flow in natural mammalian populations.
- Development of a repository of cell lines of endangered mammalian species.
- Implementation of integrative and computational bioinformatics tools for the analysis of the conservation and function of vertebrate genomes.
- Study the impact of COVID-19 on fertility.
Information of interest
This group receives financial support from:
- Ministry of Economy and Competitiveness (MINECO)
- European Union's Fondo Europeo de Desarrollo Regional (FEDER)
- Agency for Management of University and Research Grants (AGAUR)
- Catalan Studies Institute (IEC)
- Human Frontier Science Program (HFSP)
2024
- L. Álvarez-González & A Ruiz-Herrera*. Evolution of 3D Chromatin Folding. Annual Review of Animal Biosciences (in press) DOI: 10.1146/annurev-animal-111523-102233 (IF= 8.7, Q1 Zoology).
- M. Coulée, C. Gobé, M. Blanco, A. de la Iglesia, C. Lapoujade, C. Ialy-Radio, L. Alvarez-Gonzalez, A. Ruiz-Herrera, G. Meurice, P. Fouchet, J. Cocquet, L. El Khattabi. Chromatin Environment-Dependent Effects of DOT1L on Gene Expression in Male Germ Cells. Communication Biology (in press). (IF= 5.2, Q1).
- B. Bista#, L. González-Rodelas#, L. Álvarez-González, Z.Q. Wu, E.E. Montiel, L.S. Lee, D.B. Badenhorst, S. Radhakrishnan, R. Literman, B. Navarro-Rodriguez, J.B. Iverson, A. Ruiz-Herrera*, N. Valenzuela*. De novo genome assemblies of two cryptodiran turtles with ZZ/ZW and XX/XY sex chromosomes provide insights into patterns of genome reshuffling and uncover novel 3D genome folding in amniotes. Genome Research (2024), 34(10):1553-1569. (IF= 6.2, Q1 Genetics and Heredity).
- A. M. Milton, L. Marin-Gual, B. J. Hanrahan, A. Ruiz-Herrera, P. D. Waters. Imprinted X chromosome inactivation in marsupials: the paternal X arrives at the egg with a silent DNA methylation profile. PNAS (2024) 121 (36), e2412185121. (IF= 9.4, Q1 Multidisciplinary Sciences).
- N.C. Lister, A.M. Milton, B.J. Hanrahan, H.R. Patel, K.L. McIntyre, W.B. Horspool. A. M. Livernois, S.A. Waters, L. Kian Wee, A. Ruiz-Herrera, P.D. Waters. Incomplete transcriptional dosage compensation of chicken and platypus sex chromosomes is balanced by post-transcriptional compensation. PNAS (2024) 21(32):e2322360121. (IF= 9.4, Q1 Multidisciplinary Sciences).
- M. Corominas, T. Marquès-Bonet, M. A. Arnedo, M. Bayés, J. Belmonte, H. Escrivà, R. Fernández, T. Gabaldón, T. Garnatje, J. Germain, M. Niell, F. Palero, J. Pons, P. Puigdomènech, The Catalan Initiative for the Earth BioGenome Project (including A. Ruiz-Herrera), V. Arroyo, C. Cuevas-Caballé, J. Ferrer Obiol, I. Gut, M. Gut, O. Hidalgo, G. Izquierdo-Arànega, L. Pérez-Sorribes, E. Righi, M. Riutort, J. Vallès, J. Rozas, T. Alioto, R. Guigó. The Catalan initiative for the Earth BioGenome Project: contributing local data to global biodiversity genomics. NAR Genomics and Bioinformatics (2024) 6, lqae075. https://doi.org/10.1093/nargab/lqae075. (IF= 4.0, Q1 Mathematical & Computational Biology).
- M. Sandoval- Velasco, O. Dudchenko, J. A. Rodríguez, C. Perez Estrada, M.Dehasque, C. Fontsere1, S. S.T. Mak, V.Plotnikov, R. Khan, D.Weisz, V.G. Contessoto, A.B. Oliveira Junior, A. Kalluchi, S. S. Batra, M. S. Shamim, N.C. Durand, B. O’Connell, R. E. Green, B.Shapiro, A.L. Roca, A. Gnirke, I.Garcia-Treviño, R.Coke, J. P. Flanagan, K. Pletch, A. Ruiz-Herrera, E. S. Lander, J. Rowley, J.N. Onichic, L. Dalén, M.A. Marti-Renom, M. T. P. Gilbert, E. Lieberman Aiden. Three-dimensional genome architecture persists in a 52,000-year-old woolly mammoth skin sample. Cell (2024) 187, 3541–3562 (IF= 66.85, D1 Cell Biology Biology).
- C. J. Hogg, R. J. Edwards, K. A. Farquharson, L. W. Silver, P. Brandies, E. Peel, M. Escalona, F. R. Jaya, R. Thavornkanlapachai, K. Batley, T. M. Bradford, J. K. Chang, Z. Chen, N. Deshpande, M. Dziminski, K. M. Ewart, O. W. Griffith, L. Marin-Gual, K. L. Moon, K. J. Travouillon, P. Waters, C. M. Whittington, M. R. Wilkins, K. M. Helgen, N. Lo, S. Y. W. Ho, A. Ruiz Herrera, R. Paltridge, J. A. M. Graves, M. Renfree, B. Shapiro, K. Ottewell, K. Rangers, K. Belov. Extant and extinct bilby genomes combined with Indigenous knowledge improve conservation of a unique Australian marsupial. Nature Ecology and Evolution (2024) 8, 311–1326 (IF= 15.46, D1 Evolutionary Biology).
- C. Marín-Garcia, L. Álvarez-González, S. Casillas, L. Marín-Gual, J. Picón, K. Yam, M. Garcias-Ramis, C. Vara, J. Ventura, A. Ruiz-Herrera*. Multiple Genomic Landscapes of Recombination and Genomic Divergence in Wild Populations of House Mice—The Role of Chromosomal Fusions and Prdm9. Mol Biol Evol (2024) 41(4):msae063 (IF= 10.7, D1 Evolutionary Biology).
- Nikou N., López Panadés M. and Roig I (2024) Histological and cytological techniques to study perinatal mouse ovaries and oocytes. Chapter for Methods in Molecular Biology: Germ Cells Development; 2770:151-170; M. Barchi (Ed.), Springer-Nature, Berlin.
- Leiva Benítez M, Lopez-Panades M, Wang D, Domingo Lopez M, Castillo Corull J, Roig I, Oliva Virgili R, Jodar M (2024) Viruses and Assisted Reproductive Technologies (ART). Chapter for Systems Biology in Reproductive Medicine (in Press).
2023
- Huang Y, Roig I. Genetic control of meiosis surveillance mechanisms in mammals. Frontiers in Cell and Developmental Biology 2023 Feb 23;11:1127440. (IF:6.081; Q1 Developmental Biology).
- S. Alonso-Alonso, A. Esteve-Codina, B. Martin-Mur, L. Álvarez-González, A. Ruiz-Herrera J. Santaló, E. Ibáñez. Blastomeres of 8-cell mouse embryos differ in their ability to generate stem cells and produce lines with different transcriptional signatures. Frontiers in Cell and Developmental Biology (2023) doi: 10.3389/fcell.2023.1274660 (IF= 6.081, Q1 Developmental Biology).
- F. Javier Valero-Regalón, M. Solé, P. López Jiménez, R. de la Fuente, M. Martín-Ruiz, L. Marin-Gual, M. Valerio-de Arana, R. Gómez, M. Renfree, S. Berríos, A. Ruiz-Herrera, R. Fernández-Donoso and J. Page. Divergent dynamics of chromosome synapsis and DNA damage signalling and distribution in marsupial meiosis. Frontiers in Cell and Developmental Biology 11:1147610, 2023. (IF= 6.081, Q1 Developmental Biology).
- P.D. Waters*,#, JAM Graves, S.L. Whiteley, A. Georges*, A. Ruiz-Herrera*,#. The three dimensions of thermolabile sex determination. Bioessays 45 (2), 2200123, 2023 (IF= 4.653, Q1 Biology).
2022
- Sanchez-Donoso I, Ravagni S, Rodríguez-Teijeiro JD, Christmas MJ, Huang Y, Maldonado-Linares A, Puigcerver M, Jiménez-Blasco I, Andrade P, Gonçalves D, Friis G, Roig I, Webster MT, Leonard JA, Vilà C. Massive genome inversion drives coexistence of divergent morphs in common quails. Curr Biol 2022;32(2):462-469.e6. (IF: 10.900; D1).
- L. Álvarez-González, C. Arias-Sardá, L. Marin-Gual, C. Vara, F. Garcia, J. Deakin, M.B. Renfree, T.J. Robinson, Marc A. Martí-Renom, P.D. Waters, M. Farré, A. Ruiz-Herrera*. Principles of 3D chromosome folding and evolutionary genome reshuffling in mammals. Cell Reports 41, 111839, 2022 (IF= 9.995, Q1, Cell Biology). Journal Cover
- L. Marin-Gual#, L. González-Rodelas#, M.G. Ramis, L. Kratochvil, N. Valenzuela, A. Georges, P. D Waters, A. Ruiz-Herrera*. Meiotic chromosome dynamics and double strand break formation in reptiles. Frontiers in Cell and Developmental Biology 10:1009776, 2022. (IF= 6.081, Q1 Developmental Biology).
- L. Álvarez-González#, F. Burden#, D. Doddamani#, R. Malinverni, Emma Leach, C. Marín-García, L. Marin-Gual, A. Gubern, C. Vara, A. Paytuví-Gallart, Marcus Buschbeck, P. Ellis*, M. Farré*, A. Ruiz-Herrera*. 3D chromatin remodeling in the germ line modulates genome evolutionary plasticity. Nature Communications 13 (2608), 2022 (IF= 14.919, Q1 Multidisciplinary Science).
- A. Ruiz-Herrera* and P. D. Waters*. Fragile, unfaithful and persistent Ys: drivers of recombination rates. Heredity, 129, 22–30, 2022. (IF= 3.821, Q2 Genetics and Heredity).
- L. Marin-Gual, L. Rodríguez-Rodelas, G. Pujol, C. Vara, M. Martín-Ruiz, S. Berríos, R. Fernández-Donoso, A. Pask, M. Renfree, J. Page, P. D Waters, A. Ruiz-Herrera*. Strategies for meiotic sex chromosome dynamics and telomeric elongation in Marsupials. PLOS Genet 18(2): e1010040, 2022 (IF= 5.917, Q1 Genetics and Heredity).
- C. Vara, A. Ruiz-Herrera*. Unpacking chromatin remodelling in germ cells. Trends in Genetics, 38(5), pp. 422–425, 2022 (IF= 11. 639, Q1 Genetics and Heredity).
2021
- C. Vara, A. Paytuví-Gallart, Y. Cuartero, L. Álvarez-González, L. Marín-Gual, F. Garcia, B. Florit-Sabater, L. Capilla, R.A. Sanchéz-Guillén, Z. Sarrate, R.A. Cigliano, W. Sanseverino, J.B. Searle, J. Ventura, M. Marti-Renom, F. Le Dily, A. Ruiz-Herrera*. The impact of chromosomal fusions on 3D genome folding and recombination in the germ line. Nature Communications 12 (2981), 2021 (IF= 14.919, Q1 Multidisciplinary Science).
- Ruth KS*, Day FR*, Hussain J*, Martínez-Marchal A*, Aiken CE, Azad A, Thompson DJ, Knoblochova L, Abe H, Tarry-Adkins JL, Gonzalez JM, Fontanillas P, Claringbould A, Bakker OB, Sulem P, Walters RG, Terao C, Turon S, Horikoshi M, Lin K, Onland-Moret NC, Sankar A, Hertz EPT, Timshel PN, Shukla V, Borup R, Olsen KW, Aguilera P, Ferrer-Roda M, Huang Y, Stankovic S, Timmers PRHJ, Ahearn TU, Alizadeh BZ, Naderi E, Andrulis IL, Arnold AM, Aronson KJ, Augustinsson A, Bandinelli S, Barbieri CM, Beaumont RN, Becher H, Beckmann MW, Benonisdottir S, Bergmann S, Bochud M, Boerwinkle E, Bojesen SE, Bolla MK, Boomsma DI, Bowker N, Brody JA, Broer L, Buring JE, Campbell A, Campbell H, Castelao JE, Catamo E, Chanock SJ, Chenevix-Trench G, Ciullo M, Corre T, Couch FJ, Cox A, Crisponi L, Cross SS, Cucca F, Czene K, Smith GD, de Geus EJCN, de Mutsert R, De Vivo I, Demerath EW, Dennis J, Dunning AM, Dwek M, Eriksson M, Esko T, Fasching PA, Faul JD, Ferrucci L, Franceschini N, Frayling TM, Gago-Dominguez M, Mezzavilla M, García-Closas M, Gieger C, Giles GG, Grallert H, Gudbjartsson DF, Gudnason V, Guénel P, Haiman CA, Håkansson N, Hall P, Hayward C, He C, He W, Heiss G, Høffding MK, Hopper JL, Hottenga JJ, Hu F, Hunter D, Ikram MA, Jackson RD, Joaquim MDR, John EM, Joshi PK, Karasik D, Kardia SLR, Kartsonaki C, Karlsson R, Kitahara CM, Kolcic I, Kooperberg C, Kraft P, Kurian AW, Kutalik Z, La Bianca M, LaChance G, Langenberg C, Launer LJ, Laven JSE, Lawlor DA, Le Marchand L, Li J, Lindblom A, Lindstrom S, Lindstrom T, Linet M, Liu Y, Liu S, Luan J, Mägi R, Magnusson PKE, Mangino M, Mannermaa A, Marco B, Marten J, Martin NG, Mbarek H, McKnight B, Medland SE, Meisinger C, Meitinger T, Menni C, Metspalu A, Milani L, Milne RL, Montgomery GW, Mook-Kanamori DO, Mulas A, Mulligan AM, Murray A, Nalls MA, Newman A, Noordam R, Nutile T, Nyholt DR, Olshan AF, Olsson H, Painter JN, Patel AV, Pedersen NL, Perjakova N, Peters A, Peters U, Pharoah PDP, Polasek O, Porcu E, Psaty BM, Rahman I, Rennert G, Rennert HS, Ridker PM, Ring SM, Robino A, Rose LM, Rosendaal FR, Rossouw J, Rudan I, Rueedi R, Ruggiero D, Sala CF, Saloustros E, Sandler DP, Sanna S, Sawyer EJ, Sarnowski C, Schlessinger D, Schmidt MK, Schoemaker MJ, Schraut KE, Scott C, Shekari S, Shrikhande A, Smith AV, Smith BH, Smith JA, Sorice R, Southey MC, Spector TD, Spinelli JJ, Stampfer M, Stöckl D, van Meurs JBJ, Strauch K, Styrkarsdottir U, Swerdlow AJ, Tanaka T, Teras LR, Teumer A, Þorsteinsdottir U, Timpson NJ, Toniolo D, Traglia M, Troester MA, Truong T, Tyrrell J, Uitterlinden AG, Ulivi S, Vachon CM, Vitart V, Völker U, Vollenweider P, Völzke H, Wang Q, Wareham NJ, Weinberg CR, Weir DR, Wilcox AN, van Dijk KW, Willemsen G, Wilson JF, Wolffenbuttel BHR, Wolk A, Wood AR, Zhao W, Zygmunt M; Biobank-based Integrative Omics Study (BIOS) Consortium; eQTLGen Consortium; Biobank Japan Project; China Kadoorie Biobank Collaborative Group; kConFab Investigators; LifeLines Cohort Study; InterAct consortium; 23andMe Research Team, Chen Z, Li L, Franke L, Burgess S, Deelen P, Pers TH, Grøndahl ML, Andersen CY, Pujol A, Lopez-Contreras AJ, Daniel JA, Stefansson K, Chang-Claude J, van der Schouw YT, Lunetta KL, Chasman DI, Easton DF, Visser JA, Ozanne SE, Namekawa SH, Solc P, Murabito JM, Ong KK, Hoffmann ER*, Murray A*, Roig I*, Perry JRB*. Genetic insights into biological mechanisms governing human ovarian ageing. Nature. 2021 Aug;596(7872):393-397. (*co-corresponding authors). (IF: 69.504; D1).
- P.D. Waters, H. R. Patel, A. Ruiz-Herrera, L. Álvarez-González, N. C. Lister, O. Simakov, T. Ezaz, P. Kaur, C. Frere, F. Grützner, A. Georges, J. A. M. Graves. Microchromosomes are building blocks of bird, reptile and mammal chromosomes. Proc Natl Acad Sci U S A, 118(45) e2112494118, 2021. (IF= 11.205, Q1 Multidisciplinary Sciences).
- T.J. Robinson, H. Cernohorska, S. Kubickova, M. Vozdova, P. Musilova, A. Ruiz-Herrera. Chromosomal evolution in Raphicerus antelope suggests divergent X chromosomes may drive speciation through females, rather than males, contrary to Haldane's rule. Scientific Reports, 11, 3152, 2021. (IF= 4.458, Q1 Multidisciplinary Science).
2020
- Hoffmann ER, Roig I. Cas9 in Human Embryos: On Target but No Repair. Cell. 2020;183(6):1464-1466. (IF: 41.584; D1).
- M. Godia, J. Casellas, A. Ruiz-Herrera, J.E. Rodríguez-Gil., A. Castelló, A. Sanchez, A. Clop. Whole genome sequencing identifies Allelic Ratio Distortion in sperm involving genes related to spermatogenesis in a swine model. DNA Research 27 (5), dsaa019, 2020. (IF= 4.009, Q2 Genetics and Heredity).
- P. D. Waters* and A. Ruiz-Herrera*. Meiotic Executioner Genes Protect the Y from Extinction. Trends in Genetics, 36(10):728-738, 2020. (IF= 11. 639, Q1 Genetics and Heredity). Journal Cover
- M. Farré* and A. Ruiz-Herrera*. The Plasticity of Genome Architecture. Genes, 11(12), 1413, 2020 (IF= 4.096, Q2 Genetics and Heredity).
- F. Garcia, L. Biedma, J. Calzada, J. Román, A. Lozano, F. Cortes, J. A. Godoy *, A. Ruiz-Herrera*. Chromosomal differentiation in genetically isolated populations of the marsh-specialist Crocidura suaveolens (Mammalia: Soricidae). Genes, 11, 270, 2020 (IF= 4.096, Q2 Genetics and Heredity).
Interview to Aurora Ruiz-Herrera (2022)
Three generations of female scientists at the IBB, Montserrat García, Aurora Ruiz-Herrera and Laia Marín, tell us about their personal experiences and their opinion on the gender gap.
Elevator Pitch IBB-UAB 2019 by Covadonga Vara
Funding
Additional information
