Chimeric RNA

TRAMA

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.

SOMMARIO

Part I: Identification and Characterization   1. Prediction, Characterization, and In Silico Validation of Chimeric RNAs             Sandeep Singh and Hui Li   2. Identification of Fusion Transcripts from Unaligned RNA-Seq Reads Using ChimeRScope             Neetha Nanoth Vellichirammal, Abrar Albahrani, You Li, and Chittibabu Guda   3. Identification of Chimeric RNAs Using RNA-Seq Reads and Protein-Protein Interactions of Translated Chimeras             Milana Frenkel-Morgenstern   4. Gene Fusion Discovery with INTEGRATE             Jin Zhang and Christopher A. Maher   5. Case Study: Systematic Detection and Prioritization of Gene Fusions in Cancer by RNA-Seq: A DIY Toolkit             Pankaj Vats, Arul M. Chinnaiyan, and Chandan Kumar-Sinha   Part II: Experimental Validation   6. Detection and Measurement of Chimeric RNAs by RT-PCR             Justin Elfman and Hui Li   7. Detection of Group II Intron-Generated Chimeric mRNAs in Bacterial Cells             Félix LaRoche-Johnston, Caroline Monat, and Benoit Cousineau   8. RNase Protection Assay             Jianzhu Zhao, Jun Tang, Justin Elfman, and Hui Li   9. Validation of Chimeric Fusion Peptides Using Proteomics Data             Sandeep Singh   10. NanoString nCounter Technology: High-Throughput RNA Validation             Angela Goytain and Tony Ng   Part III: Functional and Mechanistic Studies   11. Knockdown of Chimeric RNA by RNAi             Xinrui Shi, Fujun Qin, and Hui Li   12. Overexpression of Chimeric RNA by Retroviral Transduction             Hao Wu and Hui Li   13. Separation of Nuclear and Cytoplasmic Fractions for Chimeric RNA Characterization             Xinrui Shi, Fujun Qin, and Hui Li   14. Confirmation of Transcriptional Read-Through Events by RT-PCR             Xinrui Shi, Fujun Qin, and Hui Li   15. Validating Gene Fusion as the Source of Chimeric RNAs             Sachin Kumar Gupta, Jocelyn Duen-Ya Jea, and Laising Yen   Part IV: Translational Applications   16. Chimeric RNA and Exosomes-Based Liquid Biopsy             Xiurong Ke, Xiao Xiong, Yusheng Lin, and Hao Zhang   17. SMaRT for Therapeutic Purposes             Lisa M. Riedmayr   18. Case Study: Landscape of Chimeric RNAs in Bladder Cancer             Dingjun Zhu and Hui Li   19. Case Study: The Recurrent Fusion RNA DUS4L-BCAP29 in Non-Cancer Human Tissues and Cells             Yue Tang, Fangxia Guan, and Hui Li

ALTRE INFORMAZIONI

• Condizione: Nuovo
• ISBN: 9781493999033
• Collana: Methods in Molecular Biology
• Dimensioni: 254 x 178 mm Ø 722 gr
• Formato: Copertina rigida
• Illustration Notes: XII, 262 p. 56 illus., 52 illus. in color.
• Pagine Arabe: 262
• Pagine Romane: xii