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Universitat Pompeu Fabra

3 ARTICLES PUBLISHED IN JoVE

Biology

Genome-wide Analysis using ChIP to Identify Isoform-specific Gene Targets

Michael L. Beshiri¹, Abul Islam², Dannielle C. DeWaal¹, William F. Richter¹, Jennifer Love³, Nuria Lopez-Bigas², Elizaveta V. Benevolenskaya¹

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.

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.

Developmental Biology

Early Unguided Human Brain Organoid Neurovascular Niche Modeling into the Permissive Chick Embryo Chorioallantoic Membrane

Luciano Fiore^1,2, Jan Arderiu³, 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 Bianchelli⁹, 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.