Post-Transcriptional Gene Regulation (3^rd Ed., 3rd ed. 2022) Methods in Molecular Biology Series, Vol. 2404

Part I: Bioinformatics

1. Introduction to Bioinformatics Resources for Post-Transcriptional Regulation of Gene Expression

            Eliana Destefanis and Erik Dassi

2. Predicting RNA Secondary Structure UsingIn Vitro and In VivoData

            Riccardo Delli Ponti and Gian Gaetano Tartaglia

3. RBPmap: A Tool for Mapping and Predicting the Binding Sites of RNA-Binding Proteins Considering the Motif Environment

            Inbal Paz, Amir Argoetti, Noa Cohen, Niv Even, and Yael Mandel-Gutfreund

Part II: Expression Studies

4. Analysis of mRNA Translation by Polysome Profiling

            Anne Cammas, Pauline Herviou, Leïla Dumas, and Stefania Millevoi

5. Exploring Ribosome-Positioning on Translating Transcripts with Ribosome Profiling

            Alexander L. Cope, Sangeevan Vellappan, John S. Favate, Kyle S. Skalenko, Srujana S. Yadavalli, and Premal Shah

6. Identification of RNA Binding Partners of CRISPR-Cas Proteins in Prokaryotes Using RIP-Seq

            Sahil Sharma and Cynthia M. Sharma

7. Rapidly Characterizing CRISPR-Cas13 Nucleases Using Cell-Free Transcription-Translation Systems

            Katharina G. Wandera and Chase L. Beisel

Part III: Interactomics

8. Studying RNP Composition with RIP

            Annalisa Rossi and Alberto Inga

9. PAR-CLIP: A Method for Transcriptome-Wide Identification of RNA Binding Protein Interaction Sites

            Charles Danan, Sudhir Manickavel, and Markus Hafner

10. A Pipeline for Analyzing eCLIP and iCLIP Data with htseq-clip and DEWSeq

            Sudeep Sahadevan, Thileepan Sekaran, and Thomas Schwarz

11. Identification of miRNAs Bound to an RNA of Interest by MicroRNA Capture Affinity Technology (miR-CATCH)

            Andrea Zeni, Margherita Grasso, and Michela A. Denti

12. Identifying the Protein Interactomes of Target RNAs Using HyPR-MS

            Katherine B. Henke, Rachel M. Miller, Rachel A. Knoener, Mark Scalf, Michele Spiniello, and Lloyd M. Smith

Part IV: The RNA Lifecycle

13. Visualization and Quantification of Subcellular RNA Localization Using Single Molecule RNA Fluorescence In Situ Hybridization

            Ankita Arora, Raeann Goering, Pedro Tirado Velez, and J. Matthew Taliaferro

14. Single-Molecule RNA Imaging Using Mango II Arrays

            Adam D. Cawte, Haruki Iino, Peter J. Unrau, and David S. Rueda

15. Genome-Wide Identification of Polyadenylation Dynamics with TED-Seq

            Yeonui Kwak and Hojoong Kwak

16.In Vivo RNA Structure Probing with DMS-MaPseq

            Paromita Gupta and Silvia Rouskin

17. Transcriptome-Wide Profiling of RNA Stability

            Nina Fasching, Jan Petržílek, Niko Popitsch, Veronika Herzog, and Stefan L. Ameres

18. High-Throughput Quantitation of Yeast uORF Regulatory Impacts Using FACS-uORF

            Gemma E. May and C. Joel McManus

Part V: RNA Modifications

19. m⁶A RNA Immunoprecipitation Followed by High-Throughput Sequencing to Map N⁶-Methyladenosine

            Devi Prasad Bhattarai and Francesca Aguilo

20. Detecting m⁶A with In Vitro DART-Seq

            Matthew Tegowski1, Huanyu Zhu, and Kate D. Meyer

21. Target-Specific Profiling of RNA m⁵C Methylation Level Using Amplicon Sequencing

            Tennille Sibbritt, Ulrike Schumann, Andrew Shafik, Marco Guarnacci, Susan J. Clark, and Thomas Preiss

22. Transcriptome-Wide Identification of 2'-O-Methylation Sites with RibOxi-Seq

            Yinzhou Zhu, Christopher L. Holley, and Gordon G. Carmichael

Includes cutting-edge techniques

Provides step-by-step detail essential for reproducible results

Contains key implementation advice from the experts