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

Authors: 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

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

Subject Terms: 3D genome structure, Hi-C, HiChIP, UMI-4C, Neural retina, Retinal pigment epithelium (RPE), Biology (General), QH301-705.5, Genetics, QH426-470

File Description: electronic resource

Relation: https://doaj.org/toc/1474-760X

Access URL: https://doaj.org/article/a3d8d2ce3b6a449b865a48720cdd33d6

A proteogenomic atlas of the human neural retina

Authors: Tabea V. Riepe, Merel Stemerdink, Renee Salz, Alfredo Dueñas Rey, Suzanne E. de Bruijn, Erica Boonen, Tomasz Z. Tomkiewicz, Michael Kwint, Jolein Gloerich, Hans J. C. T. Wessels, Emma Delanote, Elfride De Baere, Filip van Nieuwerburgh, Sarah De Keulenaer, Barbara Ferrari, Stefano Ferrari, Frauke Coppieters, Frans P. M. Cremers, Erwin van Wyk, Susanne Roosing, Erik de Vrieze, Peter A. C. ‘t Hoen

Source: Frontiers in Genetics, Vol 15 (2024)

Subject Terms: neural retina, isoform, alternative splicing, multi-omics, long-read sequencing, proteogenomics, Genetics, QH426-470

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fgene.2024.1451024/full; https://doaj.org/toc/1664-8021

Access URL: https://doaj.org/article/597f13c9088a47f6afda9d373f062809

Multi-omics analysis in human retina uncovers ultraconserved cis-regulatory elements at rare eye disease loci

Authors: Victor Lopez Soriano, Alfredo Dueñas Rey, Rajarshi Mukherjee, Genomics England Research Consortium, Frauke Coppieters, Miriam Bauwens, Andy Willaert, Elfride De Baere

Source: Nature Communications, Vol 15, Iss 1, Pp 1-14 (2024)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/38cbf5e245e84d6bb6d38d770e602435

Combining a prioritization strategy and functional studies nominates 5’UTR variants underlying inherited retinal disease

Authors: Alfredo Dueñas Rey, Marta del Pozo Valero, Manon Bouckaert, Katherine A Wood, Filip Van den Broeck, Malena Daich Varela, Huw B Thomas, Mattias Van Heetvelde, Marieke De Bruyne, Stijn Van de Sompele, Miriam Bauwens, Hanne Lenaerts, Quinten Mahieu, Dragana Josifova, Genomics England Research Consortium, Carlo Rivolta, Raymond T O’Keefe, Jamie Ellingford, Andrew R Webster, Gavin Arno, Carmen Ayuso, Julie De Zaeytijd, Bart P Leroy, Elfride De Baere, Frauke Coppieters

Source: Genome Medicine, Vol 16, Iss 1, Pp 1-21 (2024)

Subject Terms: 5’untranslated region (5’UTR), Upstream open reading frame (uORF), Non-coding variation, Whole genome sequencing (WGS), Whole exome sequencing (WES), In silico prioritization, Medicine, Genetics, QH426-470

File Description: electronic resource

Relation: https://doaj.org/toc/1756-994X

Access URL: https://doaj.org/article/3ef1b0b6663c4cf89d5498ab57ec00ff

Nigral transcriptomic profiles in Engrailed-1 hemizygous mouse models of Parkinson’s disease reveal upregulation of oxidative phosphorylation-related genes associated with delayed dopaminergic neurodegeneration

Authors: Lautaro Francisco Belfiori, Alfredo Dueñas Rey, Dorottya Mária Ralbovszki, Itzia Jimenez-Ferrer, Filip Fredlund, Sagar Shivayogi Balikai, Dag Ahrén, Kajsa Atterling Brolin, Maria Swanberg

Source: Frontiers in Aging Neuroscience, Vol 16 (2024)

Subject Terms: Parkinson’s disease, substantia nigra, neurodegeneration, transcriptomics, genetic susceptibility, mitochondria, Neurosciences. Biological psychiatry. Neuropsychiatry, RC321-571

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fnagi.2024.1337365/full; https://doaj.org/toc/1663-4365

Access URL: https://doaj.org/article/3a6bbb21d16d411381688c34692a243c

Author Correction: Multi-omics analysis in human retina uncovers ultraconserved cis-regulatory elements at rare eye disease loci

Authors: Victor Lopez Soriano, Alfredo Dueñas Rey, Rajarshi Mukherjee, Genomics England Research Consortium, Frauke Coppieters, Miriam Bauwens, Andy Willaert, Elfride De Baere

Source: Nature Communications, Vol 15, Iss 1, Pp 1-1 (2024)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/71dc04aaf10049c79f8782552148860f

CEP162 deficiency causes human retinal degeneration and reveals a dual role in ciliogenesis and neurogenesis

Authors: Nafisa Nuzhat, Kristof Van Schil, Sandra Liakopoulos, Miriam Bauwens, Alfredo Dueñas Rey, Stephan Käseberg, Melanie Jäger, Jason R. Willer, Jennifer Winter, Hanh M. Truong, Nuria Gruartmoner, Mattias Van Heetvelde, Joachim Wolf, Robert Merget, Sabine Grasshoff-Derr, Jo Van Dorpe, Anne Hoorens, Heidi Stöhr, Luke Mansard, Anne-Françoise Roux, Thomas Langmann, Katharina Dannhausen, David Rosenkranz, Karl M. Wissing, Michel Van Lint, Heidi Rossmann, Friederike Häuser, Peter Nürnberg, Holger Thiele, Ulrich Zechner, Jillian N. Pearring, Elfride De Baere, Hanno J. Bolz

Source: The Journal of Clinical Investigation, Vol 133, Iss 8 (2023)

Subject Terms: Cell biology, Genetics, Medicine

File Description: electronic resource

Relation: https://doaj.org/toc/1558-8238

Access URL: https://doaj.org/article/5751fc3eb5124e36990ef17731c43da6

Long-Read Sequencing to Unravel Complex Structural Variants of CEP78 Leading to Cone-Rod Dystrophy and Hearing Loss

Authors: Giulia Ascari, Nanna D. Rendtorff, Marieke De Bruyne, Julie De Zaeytijd, Michel Van Lint, Miriam Bauwens, Mattias Van Heetvelde, Gavin Arno, Julie Jacob, David Creytens, Jo Van Dorpe, Thalia Van Laethem, Toon Rosseel, Tim De Pooter, Peter De Rijk, Wouter De Coster, Björn Menten, Alfredo Dueñas Rey, Mojca Strazisar, Mette Bertelsen, Lisbeth Tranebjaerg, Elfride De Baere

Source: Frontiers in Cell and Developmental Biology, Vol 9 (2021)

Subject Terms: CEP78, inherited retinal disease, cone-rod dystrophy with hearing loss, long-read sequencing, structural variants, single-cell gene expression analysis, Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fcell.2021.664317/full; https://doaj.org/toc/2296-634X

Access URL: https://doaj.org/article/483ae383a34a48e1a6bbe9032362f8b3

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Loss of ctnnd2b affects neuronal differentiation and behavior in zebrafish

Authors: Raquel Vaz, Steven Edwards, Alfredo Dueñas-Rey, Wolfgang Hofmeister, Anna Lindstrand

Source: Frontiers in Neuroscience, Vol 17 (2023)

Subject Terms: CTNND2, CRISPR/Cas9, zebrafish, neuronal development, swimming behavior, Neurosciences. Biological psychiatry. Neuropsychiatry, RC321-571

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fnins.2023.1205653/full; https://doaj.org/toc/1662-453X

Access URL: https://doaj.org/article/336a2fe6a59f47a1882811abcd7de73b