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Universitat Pompeu Fabra

3 ARTICLES PUBLISHED IN JoVE

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Biology

Genome-wide Analysis using ChIP to Identify Isoform-specific Gene Targets
Michael L. Beshiri 1, Abul Islam 2, Dannielle C. DeWaal 1, William F. Richter 1, Jennifer Love 3, Nuria Lopez-Bigas 2, Elizaveta V. Benevolenskaya 1
1Department of Biochemistry and Molecular Genetics, University of Illinois Chicago - UIC, 2Research Unit on Biomedical Informatics, Universitat Pompeu Fabra, 3Genome Technology Core, Whitehead Institute for Biomedical Research

Here we are presenting a chromatin immunoprecipitation (ChIP) procedure for genome-wide location analysis of protein isoforms that differ in a histone-binding domain. We are applying it to ChIP-Seq analysis to identify the targets of the KDM5A/JARID1A/RBP2 histone demethylase.

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Genetics

Identification of Enhancer-Promoter Contacts in Embryoid Bodies by Quantitative Chromosome Conformation Capture (4C)
Tian V. Tian 1,2,3, Enrique Vidal 1,2, Thomas Graf 1,2, Grégoire Stik 1,2
1Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 2Universitat Pompeu Fabra, 3Vall d'Hebron Institute of Oncology

We report the application of quantitative chromosome conformation capture followed by high-throughput sequencing in embryoid bodies generated from embryonic stem cells. This technique allows to identify and quantitate the contacts between putative enhancers and promoter regions of a given gene during embryonic stem cell differentiation.

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Developmental Biology

Early Unguided Human Brain Organoid Neurovascular Niche Modeling into the Permissive Chick Embryo Chorioallantoic Membrane
Luciano Fiore 1,2, Jan Arderiu 3, Andrea Martí-Sarrias 3,4, Isabel Turpín 3,4, Ruth I. Pareja 3,5, Arcadi Navarro 5,6,7,8, Mariana Holubiec 2,9, Julieta Bianchelli 9, Tomas Falzone 2,9, Gonzalo Spelzini 1,2, Gabriel Scicolone 1,2, Sandra Acosta 3,4
1Instituto de Biología Celular y Neurociencias “Prof. E. De Robertis” (IBCN), CONICET - Universidad de Buenos Aires, 2Facultad de Medicina, Departamento de Biología Celular, Histología, Embriología y Genética, Universidad de Buenos Aires, 3Institute of Neurosciences, Pathology and Experimental Therapeutics Dept, University of Barcelona, 4Functional Neurogenomics Group, Neurodevelopmental Disorders, IDIBELL, L’Hospitalet de Llobregat, 5IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra, 6Institució Catalana de Recerca i Estudis Avançats (ICREA) and Universitat Pompeu Fabra, 7Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 8BarcelonaBeta Brain Research Center, Pasqual Maragall Foundation, 9Instituto de Investigación en Biomedicina (IBioBA) – CONICET – Instituto Partner de la Sociedad Max Planck

Here, we present a protocol to engraft human brain organoids at multiple maturation stages into the chick chorioallantoic membrane (CAM). Brain organoids were grown following unguided standardized protocols.

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