Dr Alexandre De Mendoza Soler
Senior Lecturer in Bioinformatics
School of Biological and Behavioural Sciences
Queen Mary University of London
Queen Mary University of London
Research
Epigenomics, Macroevolution, Protists, DNA methylation, Transposable Elements, Phylogeny
Interests
I am interested in comparative and evolutionary epigenomics, aiming at understanding how mechanisms of gene regulation evolve, and why. To do this, we explore genome regulation in non-traditional model systems, from unicellular eukaryotes (protists) to animals.I teach in the modules Genes and Bioinformatics (BIO223) and Functional Genomics & Epigenetics (BIO327).
Publications
Publications of specific relevance to the Centre for Evolutionary and Functional Genomics2024
Gao Y, Tan DS, Girbig M, Hu H, Zhou X, Xie Q, Yeung SW, Lee KS, Ho SY, Cojocaru V, Yan J, Hochberg GKA, de Mendoza A and Jauch R (2024). The emergence of Sox and POU transcription factors predates the origins of animal stem cells. Nature Communications, Springer Nature vol. 15 (1) 14-11-2024
Guynes K, Sarre LA, Carrillo-Baltodano AM, Davies BE, Xu L, Liang Y, Martín-Zamora FM, Hurd PJ, de Mendoza A and Martín-Durán JM (2024). Annelid methylomes reveal ancestral developmental and aging-associated epigenetic erosion across Bilateria. Genome Biology, Springer Nature vol. 25 (1), 204-204. 01-08-2024
Sarre LA, Kim IV, Ovchinnikov V, Olivetta M, Suga H, Dudin O, Sebé-Pedrós A and de Mendoza A (2024). DNA methylation enables recurrent endogenization of giant viruses in an animal relative. Science Advances, American Association for the Advancement of Science (AAAS) vol. 10 (28) 12-07-2024
Dossmann L, Emperle M, Dukatz M, de Mendoza A, Bashtrykov P and Jeltsch A (2024). Specific DNMT3C flanking sequence preferences facilitate methylation of young murine retrotransposons. Communications Biology, Springer Nature vol. 7 (1) 16-05-2024
Yu D, Ren Y, Uesaka M, Beavan AJS, Muffato M, Shen J, Li Y, Sato I, Wan W, Clark JW, Keating JN, Carlisle EM, Dearden RP, Giles S, Randle E, Sansom RS, Feuda R, Fleming JF, Sugahara F, Cummins C, et al. (2024). Hagfish genome elucidates vertebrate whole-genome duplication events and their evolutionary consequences. Nature Ecology & Evolution, Springer Nature vol. 8 (3), 519-535. 12-01-2024
2023
Buckberry S, Liu X, Poppe D, Tan JP, Sun G, Chen J, Nguyen TV, de Mendoza A, Pflueger J, Frazer T, Vargas-Landín DB, Paynter JM, Smits N, Liu N, Ouyang JF, Rossello FJ, Chy HS, Rackham OJL, Laslett AL, Breen J, et al. (2023). Transient naive reprogramming corrects hiPS cells functionally and epigenetically. Nature, Springer Nature vol. 620 (7975), 863-872. 16-08-2023
de Mendoza A (2023). A mammalian DNA methylation landscape. Science, American Association for the Advancement of Science vol. 381 (6658), 602-603. 11-08-2023
2022
Dukatz M, Dittrich M, Stahl E, Adam S, de Mendoza A, Bashtrykov P and Jeltsch A (2022). DNA methyltransferase DNMT3A forms interaction networks with the CpG site and flanking sequence elements for efficient methylation. Journal of Biological Chemistry, American Society for Biochemistry and Molecular Biology vol. 298 (10) 01-10-2022
de Mendoza A, Nguyen TV, Ford E, Poppe D, Buckberry S, Pflueger J, Grimmer MR, Stolzenburg S, Bogdanovic O, Oshlack A, Farnham PJ, Blancafort P and Lister R (2022). Large-scale manipulation of promoter DNA methylation reveals context-specific transcriptional responses and stability. Genome Biology, BMC vol. 23 (1) 26-07-2022
2021
De Mendoza Soler A, Poppe D, Buckberry S, Pflueger J, Albertin CB, Daish T, Bertrand S, de la Calle-Mustiennes E, Gomez-Skarmeta JL, Nery JR, Ecker JR, Baer B, Ragsdale CW, Grützner F, Escriva H, Venkatesh B, Bogdanovic O and Lister R (2021). The emergence of the brain non-CpG methylation system in vertebrates., Editors: Domingues V. Nature Ecology and Evolution, Nature Research 18-01-2021
2020
Ross SE, Angeloni A, Geng F-S, de Mendoza A and Bogdanovic O (2020). Developmental remodelling of non-CG methylation at satellite DNA repeats. Nucleic Acids Research, Oxford University Press (OUP) vol. 48 (22) 04-12-2020
Ruiz-Trillo I and de Mendoza A (2020). Towards understanding the origin of animal development. Development (Cambridge, England) vol. 147 (23) 03-12-2020
Hadjieconomou D, King G, Gaspar P, Mineo A, Blackie L, Ameku T, Studd C, De Mendoza Soler A, Diao F, White BH, Brown AEX, Plaçais P-Y, Préat T and Miguel-Aliaga I (2020). Enteric neurons increase maternal food intake during reproduction. Nature, Nature Research 28-10-2020
Kenny NJ, Francis WR, Rivera-Vicéns RE, Juravel K, de Mendoza A, Díez-Vives C, Lister R, Bezares-Calderón LA, Grombacher L, Roller M, Barlow LD, Camilli S, Ryan JF, Wörheide G, Hill AL, Riesgo A and Leys SP (2020). Tracing animal genomic evolution with the chromosomal-level assembly of the freshwater sponge Ephydatia muelleri. Nature Communications, Nature Research (part of Springer Nature) vol. 11 (1) 27-07-2020
Almudi I, Vizueta J, Wyatt CDR, de Mendoza A, Marlétaz F, Firbas PN, Feuda R, Masiero G, Medina P, Alcaina-Caro A, Cruz F, Gómez-Garrido J, Gut M, Alioto TS, Vargas-Chavez C, Davie K, Misof B, González J, Aerts S, Lister R, et al. (2020). Genomic adaptations to aquatic and aerial life in mayflies and the origin of insect wings. Nature Communications, Nature Research (part of Springer Nature) vol. 11 (1) 26-05-2020
Ross SE, Angeloni A, de Mendoza A and Bogdanovic O (2020). Pervasive non-CpG methylation at zebrafish mosaic satellite repeats. 14-05-2020
2019
de Mendoza A, Lister R and Bogdanovic O (2019). Evolution of DNA Methylome Diversity in Eukaryotes. Journal of Molecular Biology, Elsevier vol. 432 (6), 1687-1705. 11-11-2019
de Mendoza A and Sebé-Pedrós A (2019). Origin and evolution of eukaryotic transcription factors. Current Opinion in Genetics and Development, Elsevier vol. 58-59, 25-32. 01-10-2019
de Mendoza A, Hatleberg WL, Pang K, Leininger S, Bogdanovic O, Pflueger J, Buckberry S, Technau U, Hejnol A, Adamska M, Degnan BM, Degnan SM and Lister R (2019). Convergent evolution of a vertebrate-like methylome in a marine sponge. Nature Ecology and Evolution, Nature Research vol. 3 (10), 1464-1473. 26-09-2019
De Mendoza A, Pflueger J and Lister R (2019). Capture of a functionally active methyl-CpG binding domain by an arthropod retrotransposon family. Genome Research, Cold Spring Harbor Laboratory Press vol. 29 (8), 1277-1286. 25-06-2019
de Mendoza A and Sebé-Pedrós A (2019). The Protistan Cellular and Genomic Roots of Animal Multicellularity. Old Questions and Young Approaches to Animal Evolution 15-38. 01-01-2019
2018
De Mendoza A, Bonnet A, Vargas-Landin DB, Ji N, Hong F, Yang F, Li L, Hori K, Pflueger J, Buckberry S, Ohta H, Rosic N, Lesage P, Lin S and Lister R (2018). Recurrent acquisition of cytosine methyltransferases into eukaryotic retrotransposons. Nature Communications, Nature Research (part of Springer Nature) vol. 9 (1) 01-12-2018
2017
Knaupp AS, Buckberry S, Pflueger J, Lim SM, Ford E, Larcombe MR, Rossello FJ, de Mendoza A, Alaei S, Firas J, Holmes ML, Nair SS, Clark SJ, Nefzger CM, Lister R and Polo JM (2017). Transient and Permanent Reconfiguration of Chromatin and Transcription Factor Occupancy Drive Reprogramming. Cell Stem Cell, Elsevier vol. 21 (6), 834-845.e6. 01-12-2017
Ford E, Grimmer MR, Stolzenburg S, Bogdanovic O, de Mendoza A, Farnham PJ, Blancafort P and Lister R (2017). Frequent lack of repressive capacity of promoter DNA methylation identified through genome-wide epigenomic manipulation. 16-08-2017
2016
de Mendoza A, Jones JW and Friedrich M (2016). Methuselah/Methuselah-like G protein-coupled receptors constitute an ancient metazoan gene family. Scientific Reports, Springer Nature vol. 6 (1) 26-02-2016
Gold DA, Grabenstatter J, de Mendoza A, Riesgo A, Ruiz-Trillo I and Summons RE (2016). Sterol and genomic analyses validate the sponge biomarker hypothesis. Proceedings of the National Academy of Sciences of the United States of America, Proceedings of the National Academy of Sciences vol. 113 (10), 2684-2689. 22-02-2016
2015
Torruella G, de Mendoza A, Grau-Bové X, Antó M, Chaplin MA, del Campo J, Eme L, Pérez-Cordón G, Whipps CM, Nichols KM, Paley R, Roger AJ, Sitjà-Bobadilla A, Donachie S and Ruiz-Trillo I (2015). Phylogenomics Reveals Convergent Evolution of Lifestyles in Close Relatives of Animals and Fungi. Current Biology, Elsevier vol. 25 (18), 2404-2410. 01-09-2015
de Mendoza A, Suga H, Permanyer J, Irimia M and Ruiz-Trillo I (2015). Complex transcriptional regulation and independent evolution of fungal-like traits in a relative of animals. eLife, eLife vol. 4 01-01-2015
Sebé-Pedrós A and de Mendoza A (2015). Transcription Factors and the Origin of Animal Multicellularity. Evolutionary Transitions to Multicellular Life 379-394. 01-01-2015
2014
de Mendoza A, Sebé-Pedrós A and Ruiz-Trillo I (2014). The Evolution of the GPCR Signaling System in Eukaryotes: Modularity, Conservation, and the Transition to Metazoan Multicellularity. Genome Biology and Evolution, Oxford University Press (OUP) vol. 6 (3), 606-619. 23-02-2014
de Mendoza A and Ruiz-Trillo I (2014). Forward genetics for back-in-time questions. eLife, eLife vol. 3 01-01-2014
2013
Desvoyes B, de Mendoza A, Ruiz-Trillo I and Gutierrez C (2013). Novel roles of plant RETINOBLASTOMA-RELATED (RBR) protein in cell proliferation and asymmetric cell division. Journal of Experimental Botany, Oxford University Press (OUP) vol. 65 (10), 2657-2666. 09-12-2013
de Mendoza A, Sebé-Pedrós A, Šestak MS, Matejčić M, Torruella G, Domazet-Lošo T and Ruiz-Trillo I (2013). Transcription factor evolution in eukaryotes and the assembly of the regulatory toolkit in multicellular lineages. Proceedings of the National Academy of Sciences of the United States of America, Proceedings of the National Academy of Sciences vol. 110 (50), e4858-e4866. 25-11-2013
Martín-Durán JM, de Mendoza A, Sebé-Pedrós A, Ruiz-Trillo I and Hejnol A (2013). A Broad Genomic Survey Reveals Multiple Origins and Frequent Losses in the Evolution of Respiratory Hemerythrins and Hemocyanins. Genome Biology and Evolution, Oxford University Press (OUP) vol. 5 (7), 1435-1442. 01-07-2013
Suga H, Chen Z, de Mendoza A, Sebé-Pedrós A, Brown MW, Kramer E, Carr M, Kerner P, Vervoort M, Sánchez-Pons N, Torruella G, Derelle R, Manning G, Lang BF, Russ C, Haas BJ, Roger AJ, Nusbaum C and Ruiz-Trillo I (2013). The Capsaspora genome reveals a complex unicellular prehistory of animals. Nature Communications, Springer Nature vol. 4 (1) 01-01-2013
2012
Suga H, Dacre M, de Mendoza A, Shalchian-Tabrizi K, Manning G and Ruiz-Trillo I (2012). Genomic Survey of Premetazoans Shows Deep Conservation of Cytoplasmic Tyrosine Kinases and Multiple Radiations of Receptor Tyrosine Kinases. Science Signaling, American Association for the Advancement of Science (AAAS) vol. 5 (222) 01-05-2012
2011
de Mendoza A and Ruiz-Trillo I (2011). The Mysterious Evolutionary Origin for the GNE Gene and the Root of Bilateria. Molecular Biology and Evolution, Oxford University Press (OUP) vol. 28 (11), 2987-2991. 25-05-2011
de Mendoza A and Ruiz-Trillo I (2011). New genomes, new taxa and deep questions in the eukaryotic tree of life: a meeting report on the EMBO comparative genomics conference. EvoDevo, Springer Nature vol. 2 (1) 01-01-2011
2010
Sebé-Pedrós A, de Mendoza A, Lang BF, Degnan BM and Ruiz-Trillo I (2010). Unexpected Repertoire of Metazoan Transcription Factors in the Unicellular Holozoan Capsaspora owczarzaki. Molecular Biology and Evolution, Oxford University Press (OUP) vol. 28 (3), 1241-1254. 17-11-2010
de Mendoza A, Suga H and Ruiz-Trillo I (2010). Evolution of the MAGUK protein gene family in premetazoan lineages. BMC Ecology and Evolution, Springer Nature vol. 10 (1) 01-04-2010
Grants of specific relevance to the Centre for Evolutionary and Functional Genomics
Deciphering the evolution of cytosine DNA methylation across eukaryotes through experimental and epi - ERC StG 2020 Alex de MendozaAlexandre De Mendoza Soler
£1,213,073 EU Commission - Horizon 2020 (01-09-2021 - 31-08-2026)
A confocal microscope for multidisciplinary dynamic studies of complex biological systemsConrad Mullineaux, Caroline Brennan, Alexandre De Mendoza Soler, Viji Draviam Sastry, Maurice Elphick, Christoph Engl, Maria Isabel Palacios De Castro, Matteo Palma, Marina Resmini, Alexander Ruban, Peter Thorpe, Angelika Stollewerk, Jose Martin Duran, Paulo Baptista Ribeiro, Susana Alves Godinho, Richard Grose, Stephanie Kermorgant, Peter McCormick and Tyson Sharp
£390,834 BBSRC Biotechnology and Biological Sciences Research Council (01-08-2022 - 31-07-2023)