Comparative 3D genome analysis between neural retina and retinal pigment epithelium reveals differential cis-regulatory interactions at retinal disease loci

Autor: Eva D’haene, Víctor López-Soriano, Pedro Manuel Martínez-García, Soraya Kalayanamontri, Alfredo Dueñas Rey, Ana Sousa-Ortega, Silvia Naranjo, Stijn Van de Sompele, Lies Vantomme, Quinten Mahieu, Sarah Vergult, Ana Neto, José Luis Gómez-Skarmeta, Juan Ramón Martínez-Morales, Miriam Bauwens, Juan Jesús Tena, Elfride De Baere

Publikováno v: Genome Biology, Vol 25, Iss 1, Pp 1-24 (2024)

Abstract Background Vision depends on the interplay between photoreceptor cells of the neural retina and the underlying retinal pigment epithelium (RPE). Most genes involved in inherited retinal diseases display specific spatiotemporal expression wit

Externí odkaz: https://doaj.org/article/a3d8d2ce3b6a449b865a48720cdd33d6

Analysis of gene network bifurcation during optic cup morphogenesis in zebrafish

Autor: Lorena Buono, Jorge Corbacho, Silvia Naranjo, María Almuedo-Castillo, Tania Moreno-Marmol, Berta de la Cerda, Estefanía Sanbria-Reinoso, Rocío Polvillo, Francisco-Javier Díaz-Corrales, Ozren Bogdanovic, Paola Bovolenta, Juan-Ramón Martínez-Morales

Publikováno v: Nature Communications, Vol 12, Iss 1, Pp 1-16 (2021)

The gene regulatory network controlling the bifurcation of common progenitors into the neural retina and retinal-pigmented epithelium programs remains poorly understood. Here the authors study transcriptome dynamics and chromatin accessibility during

Externí odkaz: https://doaj.org/article/9deb9ca050074c8e90fd83b3d7611510

Regulatory landscape fusion in rhabdomyosarcoma through interactions between the PAX3 promoter and FOXO1 regulatory elements

Autor: Cristina Vicente-García, Barbara Villarejo-Balcells, Ibai Irastorza-Azcárate, Silvia Naranjo, Rafael D. Acemel, Juan J. Tena, Peter W. J. Rigby, Damien P. Devos, Jose L. Gómez-Skarmeta, Jaime J. Carvajal

Publikováno v: Genome Biology, Vol 18, Iss 1, Pp 1-18 (2017)

Abstract Background The organisation of vertebrate genomes into topologically associating domains (TADs) is believed to facilitate the regulation of the genes located within them. A remaining question is whether TAD organisation is achieved through t

Externí odkaz: https://doaj.org/article/8d136abfe5eb422f8b04820f5a4b27da

The little skate genome and the evolutionary emergence of wing-like fins

Autor: Ferdinand Marlétaz, Elisa de la Calle-Mustienes, Rafael D. Acemel, Christina Paliou, Silvia Naranjo, Pedro Manuel Martínez-García, Ildefonso Cases, Victoria A. Sleight, Christine Hirschberger, Marina Marcet-Houben, Dina Navon, Ali Andrescavage, Ksenia Skvortsova, Paul Edward Duckett, Álvaro González-Rajal, Ozren Bogdanovic, Johan H. Gibcus, Liyan Yang, Lourdes Gallardo-Fuentes, Ismael Sospedra, Javier Lopez-Rios, Fabrice Darbellay, Axel Visel, Job Dekker, Neil Shubin, Toni Gabaldón, Tetsuya Nakamura, Juan J. Tena, Darío G. Lupiáñez, Daniel S. Rokhsar, José Luis Gómez-Skarmeta

Skates are cartilaginous fish whose body plan features enlarged wing-like pectoral fins, enabling them to thrive in benthic environments1,2. However, the molecular underpinnings of this unique trait remain unclear. Here we investigate the origin of t

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::89f1bfcf673c5cdf0b7b2bf7b8f2b39d
http://edoc.mdc-berlin.de/23267/2/23267suppl.zip

Multiomic atlas with functional stratification and developmental dynamics of zebrafish cis-regulatory elements

Autor: Damir Baranasic, Matthias Hörtenhuber, Piotr J. Balwierz, Tobias Zehnder, Abdul Kadir Mukarram, Chirag Nepal, Csilla Várnai, Yavor Hadzhiev, Ada Jimenez-Gonzalez, Nan Li, Joseph Wragg, Fabio M. D’Orazio, Dorde Relic, Mikhail Pachkov, Noelia Díaz, Benjamín Hernández-Rodríguez, Zelin Chen, Marcus Stoiber, Michaël Dong, Irene Stevens, Samuel E. Ross, Anne Eagle, Ryan Martin, Oluwapelumi Obasaju, Sepand Rastegar, Alison C. McGarvey, Wolfgang Kopp, Emily Chambers, Dennis Wang, Hyejeong R. Kim, Rafael D. Acemel, Silvia Naranjo, Maciej Łapiński, Vanessa Chong, Sinnakaruppan Mathavan, Bernard Peers, Tatjana Sauka-Spengler, Martin Vingron, Piero Carninci, Uwe Ohler, Scott Allen Lacadie, Shawn M. Burgess, Cecilia Winata, Freek van Eeden, Juan M. Vaquerizas, José Luis Gómez-Skarmeta, Daria Onichtchouk, Ben James Brown, Ozren Bogdanovic, Erik van Nimwegen, Monte Westerfield, Fiona C. Wardle, Carsten O. Daub, Boris Lenhard, Ferenc Müller

Publikováno v: 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 & Müller, F 2022, ' Multiomic atlas with functional stratification and developmental dynamics of zebrafish cis-regulatory elements ', Nature Genetics, vol. 54, no. 7, pp. 1037-1050 . https://doi.org/10.1038/s41588-022-01089-w
Nature Genetics, 54, 1037–1050
Digital.CSIC. Repositorio Institucional del CSIC
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14 pages, 8 figures, supplementary information https://doi.org/10.1038/s41588-022-01089-w.-- Data availability: Raw and aligned sequencing data are available at https://danio-code.zfin.org/dataExport/. The raw sequencing data produced for this study

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::a5c9b0ff730aa047c825365d177a9878
https://edoc.unibas.ch/89500/