Chimeric RNA

1. Front Matter

   Pages i-xii

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2. Identification and Characterization

   1. Front Matter

      Pages 1-1

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   2. Prediction, Characterization, and In Silico Validation of Chimeric RNAs

      • Sandeep Singh, Hui Li

      Pages 3-12

   3. Identification of Fusion Transcripts from Unaligned RNA-Seq Reads Using ChimeRScope

      • Neetha Nanoth Vellichirammal, Abrar Albahrani, You Li, Chittibabu Guda

      Pages 13-25

   4. Identification of Chimeric RNAs Using RNA-Seq Reads and Protein–Protein Interactions of Translated Chimeras

      • Milana Frenkel-Morgenstern

      Pages 27-40

   5. Gene Fusion Discovery with INTEGRATE

      • Jin Zhang, Christopher A. Maher

      Pages 41-68

   6. Case Study: Systematic Detection and Prioritization of Gene Fusions in Cancer by RNA-Seq: A DIY Toolkit

      • Pankaj Vats, Arul M. Chinnaiyan, Chandan Kumar-Sinha

      Pages 69-79

3. Experimental Validation

   1. Front Matter

      Pages 81-81

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   2. Detection and Measurement of Chimeric RNAs by RT-PCR

      • Justin Elfman, Hui Li

      Pages 83-94

   3. Detection of Group II Intron-Generated Chimeric mRNAs in Bacterial Cells

      • Félix LaRoche-Johnston, Caroline Monat, Benoit Cousineau

      Pages 95-107

   4. RNase Protection Assay

      • Jianzhu Zhao, Jun Tang, Justin Elfman, Hui Li

      Pages 109-116

   5. Validation of Chimeric Fusion Peptides Using Proteomics Data

      • Sandeep Singh, Hui Li

      Pages 117-124

   6. NanoString nCounter Technology: High-Throughput RNA Validation

      • Angela Goytain, Tony Ng

      Pages 125-139

4. Functional and Mechanistic Studies

   1. Front Matter

      Pages 141-141

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   2. Knockdown of Chimeric RNA by RNAi

      • Fujun Qin, Xinrui Shi, Hui Li

      Pages 143-154

   3. Overexpression of Chimeric RNA by Retroviral Transduction

      • Hao Wu, Hui Li

      Pages 155-166

   4. Separation of Nuclear and Cytoplasmic Fractions for Chimeric RNA Characterization

      • Fujun Qin, Xinrui Shi, Hui Li

      Pages 167-175

   5. Confirmation of Transcriptional Read-Through Events by RT-PCR

      • Xinrui Shi, Fujun Qin, Hui Li

      Pages 177-186

   6. Validating Gene Fusion as the Source of Chimeric RNAs

      • Sachin Kumar Gupta, Jocelyn Duen-Ya Jea, Laising Yen

      Pages 187-207

5. Translational Applications

   1. Front Matter

      Pages 209-209

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This book provides numerous methods for identification, validation, and functional characterization of chimeric RNAs, herein described as any transcript which contains the nucleotide sequence of two distinct parental genes. Beginning with identification and characterization through bioinformatics tools, the book continues with experimental validation using RT-PCR, hybridization methods for RNA, and the use of mass spectrometry data for fusion protein validation, as well as functional and mechanistic studies of chimeric RNAs and translational applications. 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. 

Authoritative and practical, Chimeric RNA: Methods and Protocols is an ideal guide to this expansive field and an inspiration to researchers seeking to further our knowledge of these remarkable features of the transcriptome.

• Gene fusion
• Transcription-mediated fusions
• Fusion transcripts
• Bioinformatics
• Translational applications

• Department of Paathology, School of Medicine, University of Virginia, Charlottesville, VA, USA, Department of Biochemistry and Molecular Genetics, School of Medicine, University of Virginia, Charlottesville, USA

  Hui Li

• Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, USA

  Justin Elfman

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