Chimeric RNA : methods and protocols [electronic resource]

  • Li, Hui , Elfman, Justin
  • Humana Press
  • 2020
Chimeric RNA : methods and protocols [electronic resource]


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 prools, and tips on troubleshooting and avoiding known pitfalls.


Prediction, Characterization, and In Silico Validation of Chimeric RNAs
Identification of Fusion Transcripts from Unaligned RNA-Seq Reads Using ChimeRScope
Identification of Chimeric RNAs Using RNA-Seq Reads and Protein-Protein Interactions of Translated Chimeras
Gene Fusion Discovery with INTEGRATE
Case Study: Systematic Detection and Prioritization of Gene Fusions in Cancer by RNA-Seq: A DIY Toolkit
Detection and Measurement of Chimeric RNAs by RT-PCR
Detection of Group II Intron-Generated Chimeric mRNAs in Bacterial Cells
RNase Protection Assay
Validation of Chimeric Fusion Peptides Using Proteomics Data
NanoString nCounter Technology: High-Throughput RNA Validation
Knockdown of Chimeric RNA by RNAi
Overexpression of Chimeric RNA by Retroviral Transduction
Separation of Nuclear and Cytoplasmic Fractions for Chimeric RNA Characterization
Confirmation of Transcriptional Read-Through Events by RT-PCR
Validating Gene Fusion as the Source of Chimeric RNAs
Chimeric RNA and Exosomes-Based Liquid Biopsy
SMaRT for Therapeutic Purposes
Case Study: Landscape of Chimeric RNAs in Bladder Cancer
Case Study: The Recurrent Fusion RNA DUS4L-BCAP29 in Non-Cancer Human Tissues and Cells.