Publications
Publications of specific relevance to the Centre for Evolutionary and Functional Genomics
2025
Chromatin loops are an ancestral hallmark of the animal regulatory genomeKim IV, Navarrete C, Grau-Bové X, Iglesias M, Elek A, Zolotarov G, Bykov NS, Montgomery SA, Ksiezopolska E, Cañas-Armenteros D, Soto-Angel JJ, Leys SP, Burkhardt P, Suga H,
de Mendoza A, Marti-Renom MA and Sebé-Pedrós A
Nature,
Springer Nature, 1-9.
07-05-2025 2024
Reconstructing the last common ancestor of all eukaryotes.Richards TA, Eme L, Archibald JM, Leonard G, Coelho SM,
de Mendoza A, Dessimoz C, Dolezal P, Fritz-Laylin LK, Gabaldón T, Hampl V, Kops GJPL, Leger MM, Lopez-Garcia P, McInerney JO, Moreira D, Muñoz-Gómez SA, Richter DJ, Ruiz-Trillo I, Santoro AE,
et al. Plos Biology,
Public Library of Science (Plos) vol. 22 (11), e3002917-e3002917.
25-11-2024 The emergence of Sox and POU transcription factors predates the origins of animal stem cellsGao 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
Nature Communications,
Springer Nature vol. 15 (1)
14-11-2024 Annelid methylomes reveal ancestral developmental and aging-associated epigenetic erosion across BilateriaGuynes K, Sarre LA,
Carrillo-Baltodano AM, Davies BE,
Xu L, Liang Y, Martín-Zamora FM,
Hurd PJ,
de Mendoza A and Martín-Durán JM
Genome Biology,
Springer Nature vol. 25 (1), 204-204.
01-08-2024 DNA methylation enables recurrent endogenization of giant viruses in an animal relativeSarre LA, Kim IV, Ovchinnikov V, Olivetta M, Suga H, Dudin O, Sebé-Pedrós A and
de Mendoza A Science Advances,
American Association For The Advancement of Science (Aaas) vol. 10 (28), eado6406-eado6406.
12-07-2024 Specific DNMT3C flanking sequence preferences facilitate methylation of young murine retrotransposonsDossmann L, Emperle M, Dukatz M,
de Mendoza A, Bashtrykov P and Jeltsch A
Communications Biology,
Springer Nature vol. 7 (1)
16-05-2024 Hagfish genome elucidates vertebrate whole-genome duplication events and their evolutionary consequencesYu 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. Nature Ecology & Evolution,
Springer Nature vol. 8 (3), 519-535.
12-01-2024 2023
Transient naive reprogramming corrects hiPS cells functionally and epigeneticallyBuckberry 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. Nature,
Springer Nature vol. 620 (7975), 863-872.
16-08-2023 A mammalian DNA methylation landscapede Mendoza A Science,
American Association For The Advancement of Science vol. 381 (6658), 602-603.
11-08-2023 2022
DNA methyltransferase DNMT3A forms interaction networks with the CpG site and flanking sequence elements for efficient methylationDukatz M, Dittrich M, Stahl E, Adam S,
de Mendoza A, Bashtrykov P and Jeltsch A
Journal of Biological Chemistry,
American Society For Biochemistry and Molecular Biology vol. 298 (10)
01-10-2022Large-scale manipulation of promoter DNA methylation reveals context-specific transcriptional responses and stabilityde 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
Genome Biology,
Bmc vol. 23 (1)
26-07-2022 2021
The emergence of the brain non-CpG methylation system in vertebratesDe 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
Nature Ecology and Evolution,
Nature Research Editors: Domingues V.
18-01-2021 2020
Developmental remodelling of non-CG methylation at satellite DNA repeatsRoss SE, Angeloni A, Geng F-S,
de Mendoza A and Bogdanovic O
Nucleic Acids Research,
Oxford University Press (OUP) vol. 48 (22)
04-12-2020 Towards understanding the origin of animal developmentRuiz-Trillo I and
de Mendoza A Development (Cambridge, England) vol. 147 (23)
03-12-2020 Enteric neurons increase maternal food intake during reproductionHadjieconomou 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
Nature,
Nature Research 28-10-2020 Tracing animal genomic evolution with the chromosomal-level assembly of the freshwater sponge Ephydatia muelleriKenny 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
Nature Communications,
Nature Research (Part of Springer Nature) vol. 11 (1)
27-07-2020 Genomic adaptations to aquatic and aerial life in mayflies and the origin of insect wingsAlmudi 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. Nature Communications,
Nature Research (Part of Springer Nature) vol. 11 (1)
26-05-2020 Pervasive non-CpG methylation at zebrafish mosaic satellite repeatsRoss SE, Angeloni A,
de Mendoza A and Bogdanovic O
,
Cold Spring Harbor Laboratory 14-05-2020 2019
Evolution of DNA Methylome Diversity in Eukaryotesde Mendoza A, Lister R and Bogdanovic O
Journal of Molecular Biology,
Elsevier vol. 432 (6), 1687-1705.
11-11-2019 Origin and evolution of eukaryotic transcription factorsde Mendoza A and Sebé-Pedrós A
Current Opinion in Genetics and Development,
Elsevier vol. 58-59, 25-32.
01-10-2019 Convergent evolution of a vertebrate-like methylome in a marine spongede 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
Nature Ecology and Evolution,
Nature Research vol. 3 (10), 1464-1473.
26-09-2019 Capture of a functionally active methyl-CpG binding domain by an arthropod retrotransposon familyDe Mendoza A, Pflueger J and Lister R
Genome Research,
Cold Spring Harbor Laboratory Press vol. 29 (8), 1277-1286.
25-06-2019 The Protistan Cellular and Genomic Roots of Animal Multicellularityde Mendoza A and Sebé-Pedrós A
In
Old Questions and Young Approaches to Animal Evolution,
Springer Nature 15-38.
01-01-2019 2018
Recurrent acquisition of cytosine methyltransferases into eukaryotic retrotransposonsDe 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
Nature Communications,
Nature Research (Part of Springer Nature) vol. 9 (1)
01-12-2018 2017
Transient and Permanent Reconfiguration of Chromatin and Transcription Factor Occupancy Drive ReprogrammingKnaupp 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
Cell Stem Cell,
Elsevier vol. 21 (6), 834-845.e6.
01-12-2017 Frequent lack of repressive capacity of promoter DNA methylation identified through genome-wide epigenomic manipulationFord E, Grimmer MR, Stolzenburg S, Bogdanovic O,
de Mendoza A, Farnham PJ, Blancafort P and Lister R
,
Cold Spring Harbor Laboratory 16-08-2017 2016
Methuselah/Methuselah-like G protein-coupled receptors constitute an ancient metazoan gene familyde Mendoza A, Jones JW and Friedrich M
Scientific Reports,
Springer Nature vol. 6 (1)
26-02-2016 Sterol and genomic analyses validate the sponge biomarker hypothesisGold DA, Grabenstatter J,
de Mendoza A, Riesgo A, Ruiz-Trillo I and Summons RE
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
Phylogenomics Reveals Convergent Evolution of Lifestyles in Close Relatives of Animals and FungiTorruella 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
Current Biology,
Elsevier vol. 25 (18), 2404-2410.
01-09-2015 Complex transcriptional regulation and independent evolution of fungal-like traits in a relative of animalsde Mendoza A, Suga H, Permanyer J, Irimia M and Ruiz-Trillo I
Elife,
Elife vol. 4
01-01-2015 Transcription Factors and the Origin of Animal MulticellularitySebé-Pedrós A and
de Mendoza A In
Evolutionary Transitions to Multicellular Life,
Springer Nature 379-394.
01-01-2015 2014
The Evolution of the GPCR Signaling System in Eukaryotes: Modularity, Conservation, and the Transition to Metazoan Multicellularityde Mendoza A, Sebé-Pedrós A and Ruiz-Trillo I
Genome Biology and Evolution,
Oxford University Press (OUP) vol. 6 (3), 606-619.
23-02-2014 Forward genetics for back-in-time questionsde Mendoza A and Ruiz-Trillo I
Elife,
Elife vol. 3
01-01-2014 2013
Novel roles of plant RETINOBLASTOMA-RELATED (RBR) protein in cell proliferation and asymmetric cell divisionDesvoyes B,
de Mendoza A, Ruiz-Trillo I and Gutierrez C
Journal of Experimental Botany,
Oxford University Press (OUP) vol. 65 (10), 2657-2666.
09-12-2013 Transcription factor evolution in eukaryotes and the assembly of the regulatory toolkit in multicellular lineagesde Mendoza A, Sebé-Pedrós A, Šestak MS, Matejčić M, Torruella G, Domazet-Lošo T and Ruiz-Trillo I
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 A Broad Genomic Survey Reveals Multiple Origins and Frequent Losses in the Evolution of Respiratory Hemerythrins and HemocyaninsMartín-Durán JM,
de Mendoza A, Sebé-Pedrós A, Ruiz-Trillo I and Hejnol A
Genome Biology and Evolution,
Oxford University Press (OUP) vol. 5 (7), 1435-1442.
01-07-2013 The Capsaspora genome reveals a complex unicellular prehistory of animalsSuga 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
Nature Communications,
Springer Nature vol. 4 (1)
01-01-2013 2012
Genomic Survey of Premetazoans Shows Deep Conservation of Cytoplasmic Tyrosine Kinases and Multiple Radiations of Receptor Tyrosine KinasesSuga H, Dacre M,
de Mendoza A, Shalchian-Tabrizi K, Manning G and Ruiz-Trillo I
Science Signaling,
American Association For The Advancement of Science (Aaas) vol. 5 (222)
01-05-2012 2011
The Mysterious Evolutionary Origin for the GNE Gene and the Root of Bilateriade Mendoza A and Ruiz-Trillo I
Molecular Biology and Evolution,
Oxford University Press (OUP) vol. 28 (11), 2987-2991.
25-05-2011 New genomes, new taxa and deep questions in the eukaryotic tree of life: a meeting report on the EMBO comparative genomics conferencede Mendoza A and Ruiz-Trillo I
Evodevo,
Springer Nature vol. 2 (1)
01-01-2011 2010
Unexpected Repertoire of Metazoan Transcription Factors in the Unicellular Holozoan Capsaspora owczarzakiSebé-Pedrós A,
de Mendoza A, Lang BF, Degnan BM and Ruiz-Trillo I
Molecular Biology and Evolution,
Oxford University Press (OUP) vol. 28 (3), 1241-1254.
17-11-2010 Evolution of the MAGUK protein gene family in premetazoan lineagesde Mendoza A, Suga H and Ruiz-Trillo I
Bmc Ecology and Evolution,
Springer Nature vol. 10 (1)
01-04-2010
