Ruiz-Herrera’s Lab

Lab Members

Aurora Ruiz-Herrera, PI
Francisca García, PhD
Covadonga Vara, PhD student
Andreu Paytuví, PhD student
Beatriu Florit, MSc student
Marta Pla, research internship

Track record of the group

The research activity of our group is focused on three main areas, (i) comparative genomics, (ii) reproductive biology and (iii) genomic instability, faces of a three-sided pyramid that meet in the main goal of searching for the mechanisms driving genome evolution and architecture in mammals.

Through comparative genomics of both closely and distantly related mammalian species our research group, along with others, has contributed to models that explain genome structure and evolution. Such reconstructions have revealed that the genomic regions implicated in large-scale structural changes, disrupt genomic synteny and are clustered in regions more prone to break and reorganize (Ruiz-Herrera et al. 2006; Ruiz-Herrera and Robinson. 2008; Farré et al. 2011; 2013; 2015; Ullastres et al. 2014; Capilla et al. 2016). Our experience with comparative genomics has contributed to the Great Apes genomic project (Pardo-Martinez et al. 2013), the Lynx genome project (Abascal et al. 2016) as well as in the delineation of evolutionary genomic regions in Primates (Ruiz-Herrera et al. 2006; Farré et al. 2011; Ruiz-Herrera et al. 2012; Aguado et al. 2014), Afrotheria (Ruiz-Herrera and Robinson 2007) and Rodentia (Capilla et al. 2016).

In searching for the origin of mammalian genome architecture, our group has provided insights on the genomic features that characterize unstable regions. These included: (i) the delineation of regions involved in genome reshuffling in several mammalian species using high-throughput genomic data and ‘in silico’ analysis (Farré et al. 2011; 2013; Ruiz-Herrera et al. 2012; Ullastres et al., 2014; Capilla et al. 2016), (ii) the study of the evolutionary mechanisms that are influencing the organization of meiotic chromosomes and recombination in mammals (Garcia-Cruz et al. 2011; Segura et al. 2013; Farré et al. 2013; Reig-Viader et al., 2013; 2014a; 2014b; Capilla et al. 2014; Ullastres et al., 2014; Vozdova et al. 2016; Ruiz-Herrera et al. 2017), and (iii) the analysis the topological distribution and transmission of unstable genomic regions in the germ line (Farré et al. 2013; Ullastres et al., 2014; Capilla et al. 2016).

Given the diversity of factors associated with genome instability, it is most unlikely that the sequence composition of genomes is solely responsible for genome reshuffling and that involves repetitive elements (i.e., turning DNA more susceptible to chromosomal change), functional constrains (i.e., genes related to species-specific phenotypes) and, more importantly, the way in which genomes are folded inside cells and its effect on gene function and regulation (Farré et al. 2011; 2015; Ullastres et al., 2014; Capilla et al. 2014; 2016; Ruiz-Herrera et al. 2017). This view represents a new interpretative hypothesis that has recently been unified by our research group as the ‘Integrative Breakage Model’, which postulates that the permissiveness of some genomic regions to undergo chromosomal breakage and large-scale rearangements could be influenced by chromatin conformation (Farré et al. 2015; Capilla et al. 2016).

For more information see: http://grupsderecerca.uab.cat/evolgenom/

Most relevant publications

  1. Mammalian comparative genomics reveals genetic and epigenetic features associated with genome reshuffling in Rodentia. Capilla L, Sánchez-Guillén RA, Farré M, Paytuví-Gallart A, Malinverni R, Ventura J, Larkin DM, Ruiz-Herrera A. Genome Biol Evol. 2016 Dec 1;8(12):3703-3717. doi: 10.1093/gbe/evw276.
  1. Recombination correlates with synaptonemal complex length and chromatin loop size in bovids-insights into mammalian meiotic chromosomal organization. Ruiz-Herrera A, Vozdova M, Fernández J, Sebestova H, Capilla L, Frohlich J, Vara C, Hernández-Marsal A, Sipek J, Robinson TJ, Rubes J. Chromosoma. 2017 Jan 18. doi: 10.1007/s00412-016-0624-3.
  1. Detailed analysis of inversions predicted between two human genomes: errors, real polymorphisms, and their origin and population distribution. Vicente-Salvador D, Puig M, Gayà-Vidal M, Pacheco S, Giner-Delgado C, Noguera I, Izquierdo D, Martínez-Fundichely A, Ruiz-Herrera A, Estivill X, Aguado C, Lucas-Lledó JI, Cáceres M. Hum Mol Genet. 2017 Feb 1;26(3):567-581. doi: 10.1093/hmg/ddw415.
  1. Extreme genomic erosion after recurrent demographic bottlenecks in the highly endangered Iberian lynx. Abascal F, Corvelo A, Cruz F, Villanueva-Cañas JL, Vlasova A, Marcet-Houben M, Martínez-Cruz B, Cheng JY, Prieto P, Quesada V, Quilez J, Li G, García F, Rubio-Camarillo M, Frias L, Ribeca P, Capella-Gutiérrez S, Rodríguez JM, Câmara F, Lowy E, Cozzuto L, Erb I, Tress ML, Rodriguez-Ales JL, Ruiz-Orera J, Reverter F, Casas-Marce M, Soriano L, Arango JR, Derdak S, Galán B, Blanc J, Gut M, Lorente-Galdos B, Andrés-Nieto M, López-Otín C, Valencia A, Gut I, García JL, Guigó R, Murphy WJ, Ruiz-Herrera A, Marques-Bonet T, Roma G, Notredame C, Mailund T, Albà MM, Gabaldón T, Alioto T, Godoy JA. Genome Biol. 2016 Dec 14;17(1):251.
  1. Mammalian meiotic recombination: a toolbox for genome evolution. Capilla L, Garcia Caldés M, Ruiz-Herrera A. Cytogenet Genome Res. 2016;150(1):1-16. doi: 10.1159/000452822.
  1. Meiotic behaviour of evolutionary sex-autosome translocations in Bovidae. Vozdova M, Ruiz-Herrera A, Fernandez J, Cernohorska H, Frohlich J, Sebestova H, Kubickova S, Rubes J. Chromosome Res. 2016 Sep;24(3):325-38. doi: 10.1007/s10577-016-9524-x.
  1. The time scale of recombination rate evolution in great apes. Stevison LS, Woerner AE, Kidd JM, Kelley JL, Veeramah KR, McManus KF; Great Ape Genome Project, Bustamante CD, Hammer MF, Wall JD. Mol Biol Evol. 2016 Apr;33(4):928-45. doi: 10.1093/molbev/msv331.
  1. Telomere homeostasis in mammalian germ cells: a review. Reig-Viader R, Garcia-Caldés M, Ruiz-Herrera A. Chromosoma. 2016 Jun;125(2):337-51. doi: 10.1007/s00412-015-0555-4.
  1. Extreme selective sweeps independently targeted the X chromosomes of the great apes. Nam K, Munch K, Hobolth A, Dutheil JY, Veeramah KR, Woerner AE, Hammer MF; Great Ape Genome Diversity Project, Mailund T, Schierup MH. Proc Natl Acad Sci U S A. 2015 May 19;112(20):6413-8. doi: 10.1073/pnas.1419306112.
  1. An Integrative Breakage Model of genome architecture, reshuffling and evolution: The Integrative Breakage Model of genome evolution, a novel multidisciplinary hypothesis for the study of genome plasticity. Farré M, Robinson TJ, Ruiz-Herrera A. Bioessays. 2015 May;37(5):479-88. doi: 10.1002/bies.201400174.
  1. Use of targeted SNP selection for an improved anchoring of the melon (Cucumis melo L.) scaffold genome assembly. Argyris JM, Ruiz-Herrera A, Madriz-Masis P, Sanseverino W, Morata J, Pujol M, Ramos-Onsins SE, Garcia-Mas J. BMC Genomics. 2015 Jan 22;16:4. doi: 10.1186/s12864-014-1196-3.
  1. On the origin of Robertsonian fusions in nature: evidence of telomere shortening in wild house mice. Sánchez-Guillén RA, Capilla L, Reig-Viader R, Martínez-Plana M, Pardo-Camacho C, Andrés-Nieto M, Ventura J, Ruiz-Herrera A. J Evol Biol. 2015 Jan;28(1):241-9. doi: 10.1111/jeb.12568.
  1. Telomere homeostasis is compromised in spermatocytes from patients with idiopathic infertility. Reig-Viader R, Capilla L, Vila-Cejudo M, Garcia F, Anguita B, Garcia-Caldés M, Ruiz-Herrera A. Fertil Steril. 2014 Sep;102(3):728-738.e1. doi: 10.1016/j.fertnstert.2014.06.005.
  1. Unraveling the effect of genomic structural changes in the rhesus macaque – implications for the adaptive role of inversions. Ullastres A, Farré M, Capilla L, Ruiz-Herrera A. BMC Genomics. 2014 Jun 26;15:530. doi: 10.1186/1471-2164-15-530.
  1. Genetic recombination variation in wild Robertsonian mice: on the role of chromosomal fusions and Prdm9 allelic background. Capilla L, Medarde N, Alemany-Schmidt A, Oliver-Bonet M, Ventura J, Ruiz-Herrera A. Proc Biol Sci. 2014 Jul 7;281(1786). pii: 20140297. doi: 10.1098/rspb.2014.0297.
  1. Telomeric repeat-containing RNA (TERRA) and telomerase are components of telomeres during mammalian gametogenesis. Reig-Viader R, Vila-Cejudo M, Vitelli V, Buscà R, Sabaté M, Giulotto E, Caldés MG, Ruiz-Herrera A. Biol Reprod. 2014 May;90(5):103. doi: 10.1095/biolreprod.113.116954.
  1. Validation and genotyping of multiple human polymorphic inversions mediated by inverted repeats reveals a high degree of recurrence. Aguado C, Gayà-Vidal M, Villatoro S, Oliva M, Izquierdo D, Giner-Delgado C, Montalvo V, García-González J, Martínez-Fundichely A, Capilla L, Ruiz-Herrera A, Estivill X, Puig M, Cáceres M. PLoS Genet. 2014 Mar 20;10(3):e1004208. doi: 10.1371/journal.pgen.1004208.

Aim of the research work

The characterization of how chromatin conformation and DNA-protein interactions have evolved during mammalian diversification is providing a new interpretive hypothesis on the mechanism(s) responsible for the origin of genome architecture and plasticity. Distant loci within the genome interact in a regulatory manner during the cell cycle, affecting their ultimate function thus providing fertile grounds for exploring the dynamics of genome composition, the evolutionary relationships between species and, in the long run, speciation.

It is in this context we couch our main research goal – understanding the evolutionary plasticity and function of the higher-order structural organization of mammalian genome architecture and how this is transmitted to the offspring. We address these questions through a multidisciplinary approach, combining computational and experimental methods such as available genome databases and a battery of molecular, cytogenetic and cell biology, and by studying the genomes of different mammalian species.

Aurora lab

Research identification links

http://grupsderecerca.uab.cat/evolgenom/

https://scholar.google.es/citations?user=i5EWfDsAAAAJ&hl=ca

Researcher ID K-3728-2012

Código Orcid orcid.org/0000-0003-3868-6151