3 articles published in JoVE
Real-time Analysis of Transcription Factor Binding, Transcription, Translation, and Turnover to Display Global Events During Cellular Activation Kathrin Davari*1, Johannes Lichti*1, Caroline C. Friedel2, Elke Glasmacher1,3 1Institute for Diabetes and Obesity (IDO), German Center for Diabetes Research (DZD), Helmholtz Zentrum München, 2Institute for Informatics, Ludwig-Maximilians-Universität München, 3Roche Pharma Research and Early Development, Large Molecule Research, Roche Innovation Center Penzberg This protocol describes the combinatorial use of ChIP-seq, 4sU-seq, total RNA-seq, and ribosome profiling for cell lines and primary cells. It enables tracking changes in transcription-factor binding, de novo transcription, RNA processing, turnover and translation over time, and displaying the overall course of events in activated and/or rapidly changing cells.
A Universal Protocol for Large-scale gRNA Library Production from any DNA Source Anna Köferle1, Stefan H. Stricker1,2 1MCN Junior Research Group, Munich Center for Neurosciences, Ludwig-Maximilian-Universität, BioMedical Center, 2Epigenetic Engineering, Institute of Stem Cell Research, Helmholtz Zentrum, German Research Center for Environmental Health Methods for generating large-scale gRNA libraries should be simple, efficient and cost-effective. We describe a protocol for the production of gRNA libraries based on enzymatic digestion of target DNA. This method, CORALINA (comprehensive gRNA library generation through controlled nuclease activity) presents an alternative to costly custom oligonucleotide synthesis.
Combining Wet and Dry Lab Techniques to Guide the Crystallization of Large Coiled-coil Containing Proteins Jenna K. Zalewski1, Simone Heber1,2, Joshua H. Mo1, Keith O'Conor1, Jeffrey D. Hildebrand1, Andrew P. VanDemark1 1Department of Biological Sciences, University of Pittsburgh, 2Institute of Structural Biology, German Research Center for Environmental Health We describe a framework incorporating straightforward biochemical and computational analysis to guide the characterization and crystallization of large coiled-coil domains. This framework can be adapted for globular proteins or extended to incorporate a variety of high-throughput techniques.