High-Resolution Profiling of Protein-RNA Interactions

  • Mathias Munschauer

Part of the Springer Theses book series (Springer Theses)

Table of contents

  1. Front Matter
    Pages i-xxiii
  2. Mathias Munschauer
    Pages 1-47
  3. Mathias Munschauer
    Pages 89-120
  4. Back Matter
    Pages 121-121

About this book

Introduction

The work reported in this book represents an excellent example of how creative experimentation and technology development, complemented by computational data analysis, can yield important insights that further our understanding of biological entities from a systems perspective. The book describes how the study of a single RNA-binding protein and its interaction sites led to the development of the novel ‘protein occupancy profiling’ technology that for the first time captured the mRNA sequence space contacted by the ensemble of expressed RNA binders. Application of protein occupancy profiling to eukaryotic cells revealed that extensive sequence stretches in 3’ UTRs can be contacted by RBPs and that evolutionary conservation as well as negative selection act on protein-RNA contact sites, suggesting functional importance. Comparative analysis of the RBP-bound sequence space has the potential to unravel putative cis-acting RNA elements without a priori knowledge of the bound regulators. Here, Dr. Munschauer provides a comprehensive introduction to the field of post-transcriptional gene regulation, examines state-of-the-art technologies, and combines the conclusions from several journal articles into a coherent and logical story from the frontiers of systems-biology inspired life science. This thesis, submitted to the Department of Biology, Chemistry and Pharmacy at Freie Universität Berlin, was selected as outstanding work by the Berlin Institute for Medical Systems Biology at the Max-Delbrueck Center for Molecular Medicine, Germany.

 

Keywords

LIN28B Binding Sites Next-generation Sequencing PAR-CLIP Post-Transcriptional Regulatome Post-transcriptional Regulation Protein Occupancy Profiling RNA Binding Proteins Small Non-coding RNAs mRNA Complexes miRNA Binding Sites

Authors and affiliations

  • Mathias Munschauer
    • 1
  1. 1.Broad Institute of MIT and HarvardCambridgeUSA

Bibliographic information

  • DOI https://doi.org/10.1007/978-3-319-16253-9
  • Copyright Information Springer International Publishing Switzerland 2015
  • Publisher Name Springer, Cham
  • eBook Packages Engineering
  • Print ISBN 978-3-319-16252-2
  • Online ISBN 978-3-319-16253-9
  • Series Print ISSN 2190-5053
  • Series Online ISSN 2190-5061
  • About this book
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