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In JoVE (1)
Other Publications (3)
Articles by Alexander Ulrich in JoVE
JoVE General
PAR-CliP - A Method to Identify Transcriptome-wide the Binding Sites of RNA Binding Proteins
1Howard Hughes Medical Institute, Laboratory of RNA Molecular Biology, Rockefeller University, 2Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine, 3Biozentrum der Universität Basel and Swiss Institute of Bioinformatics (SIB), 4Biozentrum der Universität Basel and Swiss Institute of Bioinformatics (SIB), 5Genomics Resource Center, Rockefeller University
RNA transcripts are subject to extensive posttranscriptional regulation that is mediated by a multitude of trans-acting RNA-binding proteins (RBPs). Here we present a generalizable method to identify precisely and on a transcriptome-wide scale the RNA binding sites of RBPs.
Other articles by Alexander Ulrich on PubMed
Antigenic Mimicry of the HIV Envelope by AIDS-associated Pathogens
Only one broadly neutralizing anti-HIV antibody, 2G12, recognises the envelope sugars of HIV. In the present study, we show that 2G12 also recognises Candida albicans and Candida tropicalis with high affinity (11 nmol/l) through a carbohydrate-dependent interaction (50% inhibitory concentration for D-fructose, 12 mmol/l). This is the first report of a neutralizing HIV antibody displaying cross-reactivity with another pathogen, revealing that the carbohydrate neutralization determinant of HIV, defined by 2G12, is more widespread amongst immunogenic, microbial surfaces than previously recognized.
Superposition of Two TRNASer Acceptor Stem Crystal Structures: Comparison of Structure, Ligands and Hydration
We solved the X-ray structures of two Escherichia coli tRNA(Ser) acceptor stem microhelices. As both tRNAs are aminoacylated by the same seryl-tRNA-synthetase, we performed a comparative structure analysis of both duplexes to investigate the helical conformation, the hydration patterns and magnesium binding sites. It is well accepted, that the hydration of RNA plays an important role in RNA-protein interactions and that the extensive solvent content of the minor groove has a special function in RNA. The detailed comparison of both tRNA(Ser) microhelices provides insights into the structural arrangement of the isoacceptor tRNA aminoacyl stems with respect to the surrounding water molecules and may eventually help us to understand their biological function at atomic resolution.
Transcriptome-wide Identification of RNA-binding Protein and MicroRNA Target Sites by PAR-CLIP
RNA transcripts are subject to posttranscriptional gene regulation involving hundreds of RNA-binding proteins (RBPs) and microRNA-containing ribonucleoprotein complexes (miRNPs) expressed in a cell-type dependent fashion. We developed a cell-based crosslinking approach to determine at high resolution and transcriptome-wide the binding sites of cellular RBPs and miRNPs. The crosslinked sites are revealed by thymidine to cytidine transitions in the cDNAs prepared from immunopurified RNPs of 4-thiouridine-treated cells. We determined the binding sites and regulatory consequences for several intensely studied RBPs and miRNPs, including PUM2, QKI, IGF2BP1-3, AGO/EIF2C1-4 and TNRC6A-C. Our study revealed that these factors bind thousands of sites containing defined sequence motifs and have distinct preferences for exonic versus intronic or coding versus untranslated transcript regions. The precise mapping of binding sites across the transcriptome will be critical to the interpretation of the rapidly emerging data on genetic variation between individuals and how these variations contribute to complex genetic diseases.
