Francis Crick Institute

4 ARTICLES PUBLISHED IN JoVE

Biology

iCLIP - Transcriptome-wide Mapping of Protein-RNA Interactions with Individual Nucleotide Resolution

Julian Konig¹, Kathi Zarnack², Gregor Rot³, Tomaz Curk³, Melis Kayikci¹, Blaz Zupan³, Daniel J. Turner⁴, Nicholas M. Luscombe², Jernej Ule¹

¹Laboratory of Molecular Biology, Medical Research Council - MRC, ²European Bioinformatics Institute, EMBL Heidelberg, ³Computer and Information Science, University of Ljubljana, ⁴Wellcome Trust Genome Campus, Wellcome Trust Sanger Institute

The spatial arrangement of RNA-binding proteins on a transcript is a key determinant of post-transcriptional regulation. Therefore, we developed individual-nucleotide resolution UV crosslinking and immunoprecipitation (iCLIP) that allows precise genome-wide mapping of the binding sites of an RNA-binding protein.

Environment

Streamlined Sampling and Cultivation of the Pelagic Cosmopolitan Larvacean, Oikopleura dioica

Aki Masunaga¹, Andrew W. Liu¹, Yongkai Tan¹, Andrew Scott¹, Nicholas M. Luscombe^1,2,3

¹Okinawa Institute of Science and Technology Graduate University, ²Francis Crick Institute, ³UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London

Oikopleura dioica is a tunicate model organism in various fields of biology. We describe sampling methods, species identification, culturing setup, and culturing protocols for the animals and algal feed. We highlight key factors that helped strengthen the culture system and discuss the possible problems and resolutions.

Immunology and Infection

Assessing Respiratory Immune Responses to Haemophilus Influenzae

Lovisa Dousha^1,2, Roleen Sharma^1,2, Steven Lim^2,3, James Ngui^2,4, Ashley M. Buckle⁵, Paul T. King^1,2

¹Monash Lung and Sleep, Monash Medical Centre, ²Monash University Department of Medicine, Monash Medical Centre, ³Flow Cytometry Science Technology Platform, Francis Crick Institute, ⁴Clinical Immunology, Monash Medical Centre, ⁵Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University

Haemophilus influenzae induces inflammation in the respiratory tract. This article will focus on the use of flow cytometry and confocal microscopy to define immune responses by phagocytes and lymphocytes in response to this bacterium.

Biochemistry

Hybrid Ensemble and Single-molecule Assay to Image the Motion of Fully Reconstituted CMG

Daniel Ramírez Montero¹, Humberto Sánchez¹, Edo van Veen¹, Theo van Laar¹, Belén Solano¹, John F. X. Diffley², Nynke H. Dekker^1,3

¹Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, ²Chromosome Replication Laboratory, Francis Crick Institute, ³Department of Physics and Kavli Institute of Nanoscience Discovery, University of Oxford

We report a hybrid ensemble and single-molecule assay to directly image and quantify the motion of fluorescently labeled, fully reconstituted Cdc45/Mcm2-7/GINS (CMG) helicase on linear DNA molecules held in place in an optical trap.