GROUP LEADER: Manuel Irimia (ICREA Research Professor)
POST-DOCS: Bárbara Pernaute, Thomas Spruce, Yamile Marquez, Elisabeth Kita
TECHNICIANS: Jon Permanyer, Marta Miret, Cristina Rodriguez, André Gohr
STUDENTS: Javier Tapial, Chris Wyatt, Laura López-Blanch, Victoria Rodriguez-Vaello, Antonio Torres-Méndez, Patryk Polinski, Federica Mantica, Simon Bajew.
Our group is interested in understanding the roles that transcriptomic diversification, particularly through alternative splicing and whole genome duplications, plays in vertebrate embryonic development, and how novel transcript variants have contributed to shape our unique development and body plan during evolution.
To address this question, our lab combines high throughput next-generation sequencing (NGS) analyses with cellular and developmental biology assays in multiple vertebrate and non-vertebrate models, with a particular focus on neural and pluripotent systems. In particular, we are currently focusing on two highly contrasting systems: (i) early mammalian embryogenesis and (ii) vertebrate central nervous system (CNS) development. These two developmental contexts show radically distinct characteristics. On the one hand, early embryogenesis captures in vivo pluripotency and the first cell fate decisions, involves relatively simple morphogenetic processes, and shows particularly high evolutionary rates. On the other hand, vertebrate brains are extremely complex systems of highly differentiated cell types that develop through very specialized processes (e.g. neuritogenesis, axon guidance, migration, etc.). Furthermore, neural-specific post-transcriptional events, especially microexons, are exceptionally conserved. Thus, combining both biological systems will provide highly complementary insights into the roles of genome diversification and specialization in development and evolution.
Marletaz F, Firbas P, Maeso I, Tena JJ, Bogdanovic O, Perry M, Wyatt CDR, de la Calle-Mustienes E, Bertrand S, Burguera D, Acemel RD, van Heeringen SJ, Naranjo S, Herrera-Ubeda C, Skvortsova K, Jimenez-Gancedo S, Aldea D, Marquez Y, Buono L, Kozmikova I, Permanyer J, Louis A, Albuixech-Crespo B, Le Petillon Y, Leon A, Subirana L, Balwierz PJ, Duckett PE, Farahani E, Aury JM, Mangenot S, Wincker P, Albalat R, Benito-Gutiérrez È, Cañestro C, Castro F, D’Aniello S, Ferrier DEK, Huang S, Laudet V, Marais GAB, Pontarotti P, Schubert M, Seitz H, Somorjai I, Takahashi T, Mirabeau O, Xu A, Yu JK, Carninci P, Martinez-Morales JR, Crollius HR, Kozmik Z, Weirauch MT, Garcia-Fernàndez J, Lister R, Lenhard B, Holland PWH. Escriva H, Gomez-Skarmeta JL, Irimia M.
“Amphioxus functional genomics and the origins of vertebrate gene regulation.”
Nature, 564:64-70, 2018.
Blazquez L, Emmett W, Faraway R, Pineda JMB, Bajew S, Gohr A, Haberman N, Sibley CR, Bradley RK, Irimia M, Ule J.
“Exon Junction Complex Shapes the Transcriptome by Repressing Recursive Splicing.”
Mol Cell, 72(3):496-509, 2018.
Grau-Bove X, Ruiz-Trillo I, Irimia M.
“Origin of exon skipping-rich transcriptomes in animals driven by evolution of gene architecture.”
Genome Biol, 19(1):135, 2018.
Gohr, A., Irimia, M.
“Matt: Unix tools for alternative splicing analysis.”
Bioinformatics, 35:130-132, 2018.
Fernandez JP, Moreno-Mateos MA, Gohr A, Miao L, Chan SH, Irimia M, Giraldez AJ.
“RES complex is associated with intron definition and required for zebrafish early embryogenesis.”
PLoS Genet, 14(7):e1007473, 2018.
![AmphiENCODE: We sequenced the genome of the Mediterranean amphioxus (Branchiostoma lanceolatum) and characterized DNA methylation, chromatin accessibility, histone modifications and transcriptomes across multiple developmental stages and adult tissues to understand the origin and evolution of the regulation of the vertebrate genome. [Marletaz et al, Nature 2018]](https://annualreport2018.crg.eu/wp-content/uploads/2019/06/4.mirimia-fig-01-300x150.jpg "Fig. 01")
