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Article

Complete male-to-female sex reversal in XY mice lacking the miR-17~92 cluster.
Hurtado, A., Mota-Gómez, I., Lao, M., Real, F.M., Jedamzick, J., Burgos, M., Lupiáñez, D.G., Jiménez, R. and Barrionuevo, F.J.
Nature Communications 15 (1): 3809. 7 May 2024

Cell adhesion and immune response, two main functions altered in the transcriptome of seasonally regressed testes of two mammalian species.
Real, F.M., Lao-Pérez, M., Burgos, M., Mundlos, S., Lupiáñez, D.G., Jiménez, R. and Barrionuevo, F.J.
Journal of Experimental Zoology Part B: Molecular and Developmental Evolution 340 (3): 231-244. May 2023

The little skate genome and the evolutionary emergence of wing-like fins.
Marlétaz, F., de la Calle-Mustienes, E., Acemel, R.D., Paliou, C., Naranjo, S., Martínez-García, P.M., Cases, I., Sleight, V.A., Hirschberger, C., Marcet-Houben, M., Navon, D., Andrescavage, A., Skvortsova, K., Duckett, P.Ed., González-Rajal, Á., Bogdanovic, O., Gibcus, J.H., Yang, L., Gallardo-Fuentes, L., Sospedra, I., Lopez-Rios, J., Darbellay, F., Visel, A., Dekker, J., Shubin, N., Gabaldón, T., Nakamura, T., Tena, J.J., Lupianez, D.G., Rokhsar, D.S. and Gómez-Skarmeta, J.L.
Nature 616 (7957): 495-503. 20 April 2023

Dynamic antagonism between key repressive pathways maintains the placental epigenome.
Weigert, R., Hetzel, S., Bailly, N., Haggerty, C., Ilik, I.A., Yung, P.Y.K., Navarro, C., Bolondi, A., Kumar, A.S., Anania, C., Brändl, B., Meierhofer, D., Lupianez, D.G., Müller, F.J., Aktas, T., Elsässer, S.J., Kretzmer, H., Smith, Z.D. and Meissner, A.
Nature Cell Biology 25 : 579–591. April 2023

Analysis of copy number variation in men with non-obstructive azoospermia.
Wyrwoll, M.J., Wabschke, R., Röpke, A., Wöste, M., Ruckert, C., Perrey, S., Rotte, N., Hardy, J., Astica, L., Lupianez, D.G., Wistuba, J., Westernströer, B., Schlatt, S., Berman, A.J., Müller, A.M., Kliesch, S., Yatsenko, A.N., Tüttelmann, F. and Friedrich, C.
Andrology 10 (8): 1593-1604. November 2022

Sox9 is required for nail bed differentiation and digit tip regeneration.
Lao, M., Hurtado, A., de Castro, A.C., Burgos, M., Jiménez, R. and Barrionuevo, F.J.
Journal of Investigative Dermatology 142 (10): 2613-2622. October 2022

Assessing evolutionary and developmental transcriptome dynamics in homologous cell types.
Feregrino, C. and Tschopp, P.
Developmental Dynamics 251 (9): 1472-1489. September 2022

C/EBPβ regulates lipid metabolism and Pparg isoform 2 expression in alveolar macrophages.
Dörr, D., Obermayer, B., Weiner, J.M., Zimmermann, K., Anania, C., Wagner, L.K., Lyras, E.M., Sapozhnikova, V., Lara-Astiaso, D., Prósper, F., Lang, R., Lupiáñez, D.G., Beule, D., Höpken, U.E., Leutz, A. and Mildner, A.
Science Immunology 7 (75): eabj0140. September 2022

In vivo dissection of a clustered-CTCF domain boundary reveals developmental principles of regulatory insulation.
Anania, C., Acemel, R.D., Jedamzick, J., Bolondi, A., Cova, G., Brieske, N., Kühn, R., Wittler, L., Real, F.M. and Lupiáñez, D.G.
Nature Genetics 54 (7): 1026-1036. July 2022

Multiomic atlas with functional stratification and developmental dynamics of zebrafish cis-regulatory elements.
Baranasic, D., Hörtenhuber, M., Balwierz, P.J., Zehnder, T., Mukarram, A.K., Nepal, C., Várnai, C., Hadzhiev, Y., Jimenez-Gonzalez, A., Li, N., Wragg, J., D'Orazio, F.M., Relic, D., Pachkov, M., Díaz, N., Hernández-Rodríguez, B., Chen, Z., Stoiber, M., Dong, M., Stevens, I., Ross, S.E., Eagle, A., Martin, R., Obasaju, O., Rastegar, S., McGarvey, A.C., Kopp, W., Chambers, E., Wang, D., Kim, H.R., Acemel, R.D., Naranjo, S., Łapiński, M., Chong, V., Mathavan, S., Peers, B., Sauka-Spengler, T., Vingron, M., Carninci, P., Ohler, U., Lacadie, S.A., Burgess, S.M., Winata, C., van Eeden, F., Vaquerizas, J.M., Gómez-Skarmeta, J.L., Onichtchouk, D., Brown, B.J., Bogdanovic, O., van Nimwegen, E., Westerfield, M., Wardle, F.C, Daub, C.O., Lenhard, B. and Müller, F.
Nature Genetics 54 (7): 1037-1050. July 2022

The mole genome reveals regulatory rearrangements associated with adaptive intersexuality.
Real, F.M., Haas, S.A., Franchini, P., Xiong, P., Simakov, O., Kuhl, H., Schöpflin, R., Heller, D., Moeinzadeh, M.H., Heinrich, V., Krannich, T., Bressin, A., Hartmann, M.F., Wudy, S.A., Dechmann, D.K.N., Hurtado, A., Barrionuevo, F.J., Schindler, M., Harabula, I., Osterwalder, M., Hiller, M., Wittler, L., Visel, A., Timmermann, B., Meyer, A., Vingron, M., Jiménez, R., Mundlos, S. and Lupiáñez, D.G.
Science 370 (6513): 208-214. 9 October 2020

GOPHER: Generator Of Probes for capture Hi-C Experiments at high Resolution.
Hansen, P., Ali, S., Blau, H., Danis, D., Hecht, J., Kornak, U., Lupiáñez, D.G., Mundlos, S., Steinhaus, R. and Robinson, P.N.
BMC Genomics 20 (1): 40. 14 January 2019

First genome-wide CNV mapping in FELIS CATUS using next generation sequencing data.
Genova, F., Longeri, M., Lyons, L.A., Bagnato, A. and Strillacci, M.G.
BMC Genomics 19 (1): 895. 10 December 2018

Unraveling the transcriptional regulation of TWIST1 in limb development.
Hirsch, N., Eshel, R., Bar Yaacov, R., Shahar, T., Shmulevich, F., Dahan, I., Levaot, N., Kaplan, T., Lupiáñez, D.G. and Birnbaum, R..
PLoS Genetics 14 (10): e1007738. 29 October 2018

Dynamic 3D chromatin architecture contributes to enhancer specificity and limb morphogenesis.
Kragesteen, B.K., Spielmann, M., Paliou, C., Heinrich, V., Schöpflin, R., Esposito, A., Annunziatella, C., Bianco, S., Chiariello, A.M., Jerković, I., Harabula, I., Guckelberger, P., Pechstein, M., Wittler, L., Chan, Wi.L., Franke, M., Lupiáñez, D.G., Kraft, K., Timmermann, B., Vingron, M., Visel, A., Nicodemi, M., Mundlos, S. and Andrey, G.
Nature Genetics 50 (10): 1463-1473. October 2018

Polymer physics predicts the effects of structural variants on chromatin architecture.
Bianco, S., Lupiáñez, D.G., Chiariello, A.M., Annunziatella, C., Kraft, K., Schöpflin, R., Wittler, L., Andrey, G., Vingron, M., Pombo, A., Mundlos, S. and Nicodemi, M.
Nature Genetics 50 (5): 662-667. May 2018

Composition and dosage of a multipartite enhancer cluster control developmental expression of Ihh (Indian hedgehog).
Will, A.J., Cova, G., Osterwalder, M., Chan, W.L., Wittler, L., Brieske, N., Heinrich, V., de Villartay, J.P., Vingron, M., Klopocki, E., Visel, A., Lupiáñez, D.G. and Mundlos, S.
Nature Genetics 49 (10): 1539-1545. October 2017

Exome sequencing and CRISPR/Cas genome editing identify mutations of ZAK as a cause of limb defects in humans and mice.
Spielmann, M., Kakar, N., Tayebi, N., Leettola, C., Nürnberg, G., Sowada, N., Lupiáñez, D.G., Harabula, I., Flöttmann, R., Horn, D., Chan, W.L., Wittler, L., Yilmaz, R., Altmüller, J., Thiele, H., van Bokhoven, H., Schwartz, C.E., Nürnberg, P., Bowie, J.U., Ahmad, J., Kubisch, C., Mundlos, S. and Borck, G.
Genome Research 26 (2): 183-191. February 2016

Disruptions of topological chromatin domains cause pathogenic rewiring of gene-enhancer interactions.
Lupiáñez, D.G., Kraft, K., Heinrich, V., Krawitz, P., Brancati, F., Klopocki, E., Horn, D., Kayserili, H., Opitz, J.M., Laxova, R., Santos-Simarro, F., Gilbert-Dussardier, B., Wittler, L., Borschiwer, M., Haas, S.A., Osterwalder, M., Franke, M., Timmermann, B., Hecht, J., Spielmann, M., Visel, A. and Mundlos, S.
Cell 161 (5): 1012-1025. 21 May 2015

Deletions, inversions, duplications: engineering of structural variants using CRISPR/Cas in mice.
Kraft, K., Geuer, S., Will, A.J., Chan, W.L., Paliou, C., Borschiwer, M., Harabula, I., Wittler, L., Franke, M., Ibrahim, D.M., Kragesteen, B.K., Spielmann, M., Mundlos, S., Lupiáñez, D.G. and Andrey, G.
Cell Reports 10 (5): 833-839. 10 February 2015

A microRNA (mmu-miR-124) prevents Sox9 expression in developing mouse ovarian cells.
Real, F.M., Sekido, R., Lupiáñez, D.G., Lovell-Badge, R., Jiménez, R. and Burgos, M.
Biology of Reproduction 89 (4): 78. 1 October 2013

Positive and negative unintended human-induced effects on Iberian mole abundance at the edge of its distribution area.
García-López de Hierro, L., Moleón, M., Lupiáñez, D.G., Virgós, E. and Jiménez, R.
Mammalian Biology 78 (4): 276-282. June 2013

Identification of live germ-cell desquamation as a major mechanism of seasonal testis regression in mammals: a study in the Iberian mole (Talpa occidentalis).
Dadhich, R.K., Barrionuevo, F.J., Real, F.M., Lupiañez, D.G., Ortega, E., Burgos, M. and Jiménez, R.
Biology of Reproduction 88 (4): 101. 1 April 2013

Morphology and ultrastructure of the chorioallantoic placenta of the Iberian mole (Talpa occidentalis) with special reference to heterophagous areolas and the nature of interhaemal barrier.
Siniza, S., Lupianez, D.G., Jimenez, R. and Zeller, U.
Journal of Anatomy 221 (2): 164-173. August 2012

Pattern and density of vascularization in mammalian testes, ovaries, and ovotestes.
Lupianez, D.G., Real, F.M., Dadhich, R.K., Carmona, F.D., Burgos, M., Barrionuevo, F.J. and Jimenez, R.
Journal of Experimental Zoology Part B : Molecular and Developmental Evolution 318 (3): 170-181. May 2012

Expression of genes controlling testicular development in adult testis of the seasonally breeding iberian mole.
Dadhich, R.K., Barrionuevo, F.J., Lupianez, D.G., Real, F.M., Burgos, M. and Jimenez, R.
Sexual Development 5 (2): 77-88. March 2011

SOX9 is not required for the cellular events of testicular organogenesis in XX mole ovotestes.
Carmona, F.D., Lupianez, D.G., Real, F.M., Burgos, M., Zurita, F. and Jimenez, R.
Journal of Experimental Zoology Part B : Molecular and Developmental Evolution 312 (7): 734-748. 15 November 2009

The spatio-temporal pattern of testis organogenesis in mammals - insights from the mole.
Carmona, F.D., Lupianez, D.G., Martin, J.E., Burgos, M., Jimenez, R. and Zurita, F.
International Journal of Developmental Biology 53 (7): 1035-1044. 2009

Meiosis onset is postponed to postnatal stages during ovotestis development in female moles.
Zurita, F., Carmona, F.D., Lupianez, D.G., Barrionuevo, F.J., Guioli, S., Burgos, M. and Jimenez, R.
Sexual Development 1 (1): 66-76. 2007

Review

Cancer evolution: a multifaceted affair.
Ciriello, G., Magnani, L., Aitken, S.J., Akkari, L., Behjati, S., Hanahan, D., Landau, D.A., Lopez-Bigas, N., Lupiáñez, D.G., Marine, J.C., Martin-Villalba, A., Natoli, G., Obenauf, A.C., Oricchio, E., Scaffidi, P., Sottoriva, A., Swarbrick, A., Tonon, G., Vanharanta, S. and Zuber, J.
Cancer Discovery 14 : 1-13. January 2024

Evolution of 3D chromatin organization at different scales.
Acemel, R.D. and Lupianez, D.G.
Current Opinion in Genetics & Development 78 : 102019. February 2023

Non-coding RNAs: lncRNAs, miRNAs, and piRNAs in sexual development.
Burgos, M., Hurtado, A., Jiménez, R. and Barrionuevo, F.J.
Sexual Development 15 (5-6): 335-350. December 2021

Order and disorder: abnormal 3D chromatin organization in human disease.
Anania, C. and Lupianez, D.G.
Briefings in Functional Genomics 19 (2): 128-138. March 2020

A (3D-nuclear) space odyssey: making sense of Hi-C maps.
Mota-Gómez, I. and Lupiáñez, D.G.
Genes 10 (6): 415. 29 May 2019

Structural variation in the 3D genome.
Spielmann, M., Lupiáñez, D.G. and Mundlos, S.
Nature Reviews Genetics 19 (7): 453-467. July 2018

Breaking TADs: how alterations of chromatin domains result in disease.
Lupiáñez, D.G., Spielmann, M. and Mundlos, S.
Trends in Genetics 32 (4): 225-237. April 2016

Comment

Marsupial genomes reveal how a skin membrane for gliding evolved.
Lupiáñez, D.G.
Nature 629 (8010): 43-44. 2 May 2024

Preprint

Comparative single-cell analyses reveal evolutionary repurposing of a conserved gene program in bat wing development.
Schindler, M., Feregrino, C., Aldrovandi, S., Lo, B.W., Monaco, A.A., Ringel, A.R., Morales, A., Zehnder, T., Behncke, R.Y., Glaser, J., Barclay, A., Andrey, G., Kragesteen, B.K., Hägerling, R., Haas, S., Vingron, M., Ulitsky, I., Marti-Renom, M., Hechavarria, J., Fasel, N., Hiller, M., Lupianez, D.G., Mundlos, S. and Real, F.M.
bioRxiv : 2024.10.10.617585. 13 October 2024

The little skate genome and the evolutionary emergence of wing-like fin appendages.
Marletaz, F., de la Calle-Mustienes, E., Acemel, R.D., Nakamura, T., Paliou, C., Naranjo, S., Martinez-Garcia, P.M., Cases, I., Sleight, V.A., Hirschberger, C., Marcet-Houben, M., Navon, D., Andrescavage, A., Skvortsova, K., Duckett, P.E., Gonzalez-Rajal, A., Bogdanovic, O., Gibcus, J.H., Yang, L., Gallardo-Fuentes, L., Sospedra, I., Lopez-Rios, J., Darbellay, F., Visel, A., Dekker, J., Shubin, N., Gabaldon, T., Tena, J.J., Lupianez, D.G., Rokhsar, D.S. and Gomez-Skarmeta, J.L.
bioRxiv : 2022.03.21.485123. 22 March 2022

Crowdfunded whole-genome sequencing of the celebrity cat Lil BUB identifies causal mutations for her osteopetrosis and polydactyly.
Bridavsky, M., Kuhl, H., Woodruf, A., Kornak, U., Timmermann, B., Mages, N., Lupiáñez, D.G., Symmons, O. and Ibrahim, D.M.
bioRxiv : 556761. 22 February 2019