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Whitehead Institute for Biomedical Research

8 ARTICLES PUBLISHED IN JoVE

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Biology

Generating iPS Cells from MEFS through Forced Expression of Sox-2, Oct-4, c-Myc, and Klf4
G. Grant Welstead 1, Tobias Brambrink 1, Rudolf Jaenisch 1
1Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology

This video shows the procedure for generating induced pluripotent stem cells using inducible lentivirus that express Oct4, Sox2, c-Myc and Klf4.

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Biology

Interview: Protein Folding and Studies of Neurodegenerative Diseases
Susan Lindquist 1
1Whitehead Institute for Biomedical Research, MIT - Massachusetts Institute of Technology

In this interview, Dr. Lindquist describes relationships between protein folding, prion diseases and neurodegenerative disorders. The problem of the protein folding is at the core of the modern biology. In addition to their traditional biochemical functions, proteins can mediate transfer of biological information and therefore can be considered a genetic material. This recently discovered function of proteins has important implications for studies of human disorders. Dr. Lindquist also describes current experimental approaches to investigate the mechanism of neurodegenerative diseases based on genetic studies in model organisms.

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Biology

Screening for Amyloid Aggregation by Semi-Denaturing Detergent-Agarose Gel Electrophoresis
Randal Halfmann 1,2,3, Susan Lindquist 1,2,3
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.

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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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Immunology and Infection

Transnuclear Mice with Pre-defined T Cell Receptor Specificities Against Toxoplasma gondii Obtained Via SCNT
Oktay Kirak 1, Eva-Maria Frickel 1, Gijsbert M. Grotenbreg 1,2, Heikyung Suh 1, Rudolf Jaenisch 1,3, Hidde L. Ploegh 1,3
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.

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Genetics

CRISPR-mediated Genome Editing of the Human Fungal Pathogen Candida albicans
Ben A. Evans *1, Ethan S. Pickerill *1, Valmik K. Vyas 2, Douglas A. Bernstein 1
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.

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Biology

Detecting and Characterizing Protein Self-Assembly In Vivo by Flow Cytometry
Shriram Venkatesan *1, Tejbir S. Kandola *1, Alejandro Rodríguez-Gama 1, Andrew Box 1, Randal Halfmann 1,2
1Stowers Institute for Medical Research, 2Department of Molecular and Integrative Physiology, The University of Kansas School of Medicine

This article describes a FRET-based flow cytometry protocol to quantify protein self-assembly in both S. cerevisiae and HEK293T cells.

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Genetics

A Method to Study de novo Formation of Chromatin Domains
Ozgur Oksuz 1,2,3, Danny Reinberg 1,2
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.

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