GROUP DESCRIPTION

The origin of new genes can often occur in a sudden manner. This generates novel interactions between these new molecular entities and the cellular environment of the organism in which they are originated. This is what we call “unexpected molecular encounters” or “first-time molecular interactions”.

We think that these unexpected interactions are a key aspect of evolution, a common starting point for evolutionary change. However, we can only investigate those molecular encounters that were successful and survived, all the unexpected encounters that ended soon after they first happened, which are very likely the vast majority of cases, remain unexplored.

To overcome this, instead of studying naturally occurring events, in the lab we generate unexpected encounters artificially, by putting in contact molecular structures that had never interacted before. We focus on how new genes, such as new Transcription Factors (TFs) and genes exapted from Transposable Elements (TEs), can be newly integrated into an existing biological system. To that end, we use a variety of functional genomic approaches and developmental model systems such as zebrafish and flies.

GROUP OBJECTIVES

The lab aims to understand the earliest stages of molecular novelties: how new genes are integrated for the first time into a biological system.

We also study how changes in gene regulation during development impacts the evolution of animals.

RESEARCH GROUP MEMBERS

Group Leader

Ignacio (Nacho) Maeso

I am an Associate Professor at the Genetics, Microbiology and Statistics Department at the University of Barcelona. My research interests focus on the early stages of the origin of molecular novelties and how biological systems establish new interactions with other systems for the first time. I also have a keen interest on the evolution of gene regulation in animals.

Postdoctoral Researcher

Marta Portela

I am interested in the evolution of gene regulation, gene regulatory networks and transcription factors. I use functional genomics techniques and bioinformatic analyses to understand how new elements are incorporated into regulatory networks.

PhD Student (co-supervised with Manuel Irimia)

Manuel Fernández-Moreno

Fascinated by the evolutionary role of transposons and convergent evolution. Pursuing a PhD in transposon biology, unravelling how retroviral genes have been repurposed for neuroplasticity through a combination of two model organisms and in silico approaches.

RESEARCH LINES

  1. How new TFs interact with new host genomes.
    We express ectopic TFs from plants and mamals in zebrafish embryos and characterize the interactions of these unexpected molecular encounters.
  2. Recurrent evolution of exapted genes from TEs
    We study how ARC genes have repeatedly evolved trough recurrent exaptation of TE gag genes.
  3. Evolution of gene regulation in animals
    We use comparative functional genomics and EvoDevo to shed light into the evolution of different animal lineages.
  4. Biological individuals & the Genotype-Phenotype theory
    We investigate a new nested model for the Genotype-Phenotype theory and how it can impact on our current conceptions of genetic identity and biological individuals.

PROJECTS

  • 2023-2025 REARCTE (CNS2022-136105). MICIU. PI: I. Maeso.
  • 2022-2025 GENCOUNTERS (PID2021-128728NB-I00). MICINN. PI: I. Maeso.
  • 2021-2022 The ground zero of transposable element invasions: a new fertile ground for cis-regulatory evolution (PY20_00419). Junta de Andalucía, PAIDI 2020. PI: I. Maeso. 75.000 €
  • 2019-2021: FIREIN (PGC2018-099392-A-I00). MICIU. PI: I. Maeso. 127.050 €, 1 PhD contract.
  • 2018-2022: Programa Ramón y Cajal (RYC-2016-20089), MINECO. PI: I. Maeso

PUBLICATIONS

  1. Magri MS, Voronov D, Foley S, Martínez-García PM, Franke M, Cary GA, Santos-Pereira JM, Cuomo C, Fernández-Moreno M, Gil-Galvez A, Acemel RD, Paganos P, Ku C, Ranđelović J, Rusciano ML, Firbas PN, Gómez-Skarmeta JL, Hinman VF†, Arnone MI†, Maeso I†. Deep conservation of cis-regulatory elements and chromatin organization in echinoderms uncover ancestral regulatory features of animal genomes (2025) Nature Ecol. & Evol. In press https://doi.org/10.1038/s41559-025-02941-y 
  1. Esteban-Collado, J., Fernández-Mañas, M., Fernández-Moreno, M., Maeso, I., Corominas, M., Serras, F. Reactive oxygen species activate the Drosophila TNF receptor Wengen for damage-induced regeneration. (2024) EMBO J. 43 (17): 3604-3626. https://doi.org/10.1038/s44318-024-00155-9
  2. Voronov D, Paganos P, Magri MS, Cuomo C, Maeso, I., Gómez-Skarmeta JL, Arnone MI. Integrative multi-omics increase resolution of the sea urchin posterior gut gene regulatory network at single-cell level. (2024) Development 151(16): dev202278. https://doi.org/10.1242/dev.202278
  3. D. Yu, Y., [24 other authors], I. Maeso, M. Irimia, B. Fromm, K.J Peterson, S. Das, M. Hirano, J.P Rast, M. D Cooper, J. Paps, D. Pisani, S. Kuratani, FJ Martin, W. Wang, P.CJ Donoghue, YE Zhang, J. Pascual-Anaya. Hagfish genome elucidates vertebrate whole-genome duplication events and their evolutionary consequences. (2024) Nat Ecol Evol, 1-17. https://doi.org/10.1038/s41559-023-02299-z
  4. (BC) Ricote, D.†, Maeso, I†. A New Perspective on Type-Token Distinction in the Genotype and Phenotype Concepts. (2023) In: Viejo, J.M., Sanjuán, M. (eds) Life and Mind. Interdisciplinary Evolution Research, vol 8. Springer, Cham. https://doi.org/10.1007/978-3-031-30304-3_11.
  1. K. Skvortsova, S. Bertrand, D. Voronov, P.E Duckett, S.E Ross, M.S. Magri, I. Maeso, R.J Weatheritt, J.L. Gómez Skarmeta, M.I. Arnone, H. Escriva, O. Bogdanovic. Active DNA demethylation of developmental cis-regulatory regions predates vertebrate origins. Science Adv.; 8(48): eabn2258 (2022). DOI: 10.1126/sciadv.abn2258
  2. M Brasó-Vives, [8 other authors], I Maeso, H Escriva, M Irimia, M Robinson-Rechavi. Parallel evolution of amphioxus and vertebrate small-scale gene duplications. Genome Biol 23, 243 (2022). https://doi.org/10.1186/s13059-022-02808-6
  1. Touceda-Suárez, M., Kita, E.M., Acemel, R.D., Firbas, P.N., Magri, M.S., Naranjo, S., Tena, J.J., Gómez-Skarmeta, J.L.†, Maeso, I.†, Irimia, M†. Ancient genomic regulatory blocks are a major source for gene deserts in vertebrates after whole genome duplications. (2020) Mol. Bio. Evol. 37(10):2857-2864. https://doi.org/10.1093/molbev/msaa123
  1. Almudi, I.†, Vizueta, J., [22 other authors], Maeso, I., Casares F†. Genomic adaptations to aquatic and aerial life in mayflies and the origin of insect wings. (2020) Nature Comms 11- 26312020. https://doi.org/10.1038/s41467-020-16284-8
  1. Marlétaz, F.*, Firbas, P.*, Maeso, I.*†, Tena, J.J.*, Bogdanovic, O.*, Perry, M.*, [52 other authors], Escrivá, H.†, Gómez-Skarmeta, J.L.†, Irimia, M†. Amphioxus functional genomics and the origins of vertebrate cis-regulation. (2018) Nature 564: 64-70. https://doi.org/10.1038/s41586-018-0734-6