Ribosome Profiling Methods and Protocols

This book provides a single-source reference on the current state of the ribosome profiling method by describing experimental protocols for the quantitative analysis of translation in a variety of model organisms. In addition, the volume presents a detailed overview of the existing software tools and includes detailed description of methods for statistical analysis, data processing, and visualization of ribosome profiling data. Written for the highly successful Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. 

Part I: Experimental Protocols

 

1. Monitoring Bacterial Translation Rates Genome-Wide

            Eugene Oh

 

2. Identification of Translation Start Sites in Bacterial Genomes

            Sezen Meydan, Dorota Klepacki, Alexander S. Mankin, and Nora Vázquez-Laslop

 

3. Genome-Wide Ribosome Profiling of the Plasmodium falciparum Intraerythrocytic Developmental Cycle

            Florence Caro and Joseph L. DeRisi

 

4. Performing Ribosome Profiling to Assess Translation in Vegetative and Meiotic Yeast Cells

            Emily Nicole Powers and Gloria Ann Brar

 

5. Quantitative Comparisons of Translation Activity by Ribosome Profiling with Internal Standards

            Yinuo J. Wang and Wendy V. Gilbert

 

6. Genome-Wide Analysis of Translation in Replicatively Aged Yeast

            Hanna Barlit, Manish K. Rai, Sara Shoushtari, Carine Beaupere, and Vyacheslav M. Labunskyy

 

7. Tissue-Specific Ribosome Profiling in Drosophila

            Xun Chen and Dion Dickman

 

8. Measuring Organ-Specific Translation Elongation Rate in Mice

            Maxim Gerashchenko and Vadim N. Gladyshev

 

9. Active Ribosome Profiling with RiboLace: From Bench to Data Analysis

            Massimiliano Clamer, Fabio Lauria, Toma Tebaldi, and Gabriella Viero

 

10. Poly-A Tailing and Adaptor Ligation Methods for Ribo-Seq Library Construction

            Jingfan Qiu and Shu-Bing Qian

 

11. Choice of Ribonucleases for Ribosome Profiling Experiments

            Maxim Gerashchenko

 

Part II: Bioinformatics and Statistical Analysis

 

12. Codon Resolution Analysis of Ribosome Profiling Data

            Alexander Bartholomäus and Zoya Ignatova

 

13. Assessing Ribosome Distribution Along Transcripts with Polarity Scores and Regression Slope Estimates

            Ilya E. Vorontsov, Artyom A. Egorov, Aleksandra S. Anisimova, Irina A. Eliseeva, Vsevolod J. Makeev, Vadim N. Gladyshev, Sergey E. Dmitriev, and Ivan V. Kulakovskiy

 

14. Unsupervised Bayesian Prediction of RNA Translation from Ribosome Profiling Data

            Etienne Boileau and Christoph Dieterich

 

15. uORF-seqr: A Machine Learning-Based Approach to the Identification of Upstream Open Reading Frames in Yeast

            Pieter Spealman, Armaghan Naik, and Joel McManus

 

16. Genome-Wide Analysis of Actively Translated Open Reading Frames Using RiboTaper/ORFquant

            Dermot Harnett, Eelco Meerdink, Lorenzo Calviello, Dominique Sydow, and Uwe Ohler