Whitehead Institute for Biomedical Research View Institution's Website 7 articles published in JoVE Genetics A Method to Study de novo Formation of Chromatin Domains Ozgur Oksuz1,2,3, Danny Reinberg1,2 1Howard Hughes Medical Institute, New York University School of Medicine, 2Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, 3Whitehead Institute for Biomedical Research This method is designed to follow formation of PRC2-mediated chromatin domains in cell lines, and the method can be adapted to many other systems. Genetics CRISPR-mediated Genome Editing of the Human Fungal Pathogen Candida albicans Ben A. Evans*1, Ethan S. Pickerill*1, Valmik K. Vyas2, Douglas A. Bernstein1 1Department of Biology, Ball State University, 2Whitehead Institute for Biomedical Research Efficient genome engineering of Candida albicans is critical to understanding the pathogenesis and development of therapeutics. Here, we described a protocol to quickly and accurately edit the C. albicans genome using CRISPR. The protocol allows investigators to introduce a wide variety of genetic modifications including point mutations, insertions, and deletions. Neuroscience An Assay for Permeability of the Zebrafish Embryonic Neuroepithelium Jessica T. Chang1,2, Hazel Sive1,2 1Department of Biology, Massachusetts Institute of Technology, 2Whitehead Institute of Biomedical Research We describe a live whole animal quantitative measurement for permeability of the embryonic zebrafish brain. The technique analyzes the ability to retain cerebrospinal fluid and molecules of different molecular weights within the neural tube lumen and quantifies their movement out of the ventricles. This method is useful for determining differences in epithelial permeability and maturation during development and disease. Immunology and Infection Transnuclear Mice with Pre-defined T Cell Receptor Specificities Against Toxoplasma gondii Obtained Via SCNT Oktay Kirak1, Eva-Maria Frickel1, Gijsbert M. Grotenbreg1,2, Heikyung Suh1, Rudolf Jaenisch1,3, Hidde L. Ploegh1,3 1Whitehead Institute for Biomedical Research, 2Departments of Microbiology and Biological Sciences, National University of Singapore, 3Department of Biology, Massachusetts Institute of Technology We demonstrate here that epigenetic reprogramming via Somatic Cell Nuclear Transfer (SCNT) can be used as a tool to generate mouse models with pre-defined T cell receptor (TCR) specificities. These transnuclear mice express the corresponding TCR from their endogenous locus under the control of the endogenous promoter. 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. Biology Zebrafish Brain Ventricle Injection Jennifer H. Gutzman1, Hazel Sive1,2 1Whitehead Institute for Biochemical Research, 2MIT - Massachusetts Institute of Technology After neural tube formation, the neuroepithelium constricts and folds while the tube fills with embryonic cerebrospinal fluid (eCSF) to form the embryonic brain ventricles. We developed this ventricle injection technique to better visualize the fluid filled space in contrast to the neuroepithelial shape in a live embryo. Biology Screening for Amyloid Aggregation by Semi-Denaturing Detergent-Agarose Gel Electrophoresis Randal Halfmann1,2,3, Susan Lindquist1,2,3 1Whitehead Institute for Biomedical Research, 2Department of Biology, MIT - Massachusetts Institute of Technology, 3Howard Hughes Medical Institute SDD-AGE is a useful technique for the detection and characterization of amyloid-like polymers in cells. Here we demonstrate an adaptation that makes this technique amenable to large-scale applications.