mRNA 3’ End Processing and Stability, Volume 655 in the Methods in Enzymology series, highlights new advances in the field, with this new volume presenting interesting chapters on a variety of timely topics. Each chapter is written by an international board of authors.
1. Cover image - p. i 2. Title page - p. ii 3. Table of Contents - p. iii 4. Series Page - p. iii 5. Copyright - p. iii 6. Contributors - p. iii 7. Preface - p. xix 8. Chapter One: Application and design considerations for 3′-end sequencing using click-chemistry - p. 1 9. Chapter Two: PAS-seq 2: A fast and sensitive method for global profiling of polyadenylated RNAs - p. 25 10. Chapter Three: TRENDseq—A highly multiplexed high throughput RNA 3′ end sequencing for mapping alternative polyadenylation - p. 37 11. Chapter Four: QPAT-seq, a rapid and deduplicatable method for quantification of poly(A) site usages - p. 73 12. Chapter Five: Using TIF-Seq2 to investigate association between 5´ and 3´mRNA ends - p. 88 13. Chapter Six: Single-molecule polyadenylated tail sequencing (SM-PAT-Seq) to measure polyA tail lengths transcriptome-wide - p. 119 14. Chapter Seven: 3′ End sequencing of pA+ and pA− RNAs - p. 139 15. Chapter Eight: Comprehensive profiling of mRNA polyadenylation in specific cell types in vivo by cTag-PAPERCLIP - p. 165 16. Chapter Nine: A computational pipeline to infer alternative poly-adenylation from 3′ sequencing data - p. 185 17. Chapter Ten: Systematic refinement of gene annotations by parsing mRNA 3′ end sequencing datasets - p. 205 18. Chapter Eleven: Computational analysis of alternative polyadenylation from standard RNA-seq and single-cell RNA-seq data - p. 225 19. Chapter Twelve: Quantifying alternative polyadenylation in RNAseq data with LABRAT - p. 245 20. Chapter Thirteen: Poly(A) tail dynamics: Measuring polyadenylation, deadenylation and poly(A) tail length - p. 265 21. Chapter Fourteen: Reconstitution and biochemical assays of an active human histone pre-mRNA 3′-end processing machinery - p. 291 22. Chapter Fifteen: Comprehensive RNP profiling in cells identifies U1 snRNP complexes with cleavage and polyadenylation factors active in telescripting - p. 325 23. Chapter Sixteen: Simultaneous studies of gene expression and alternative polyadenylation in primary human immune cells - p. 349 24. Chapter Seventeen: RIPiT-Seq: A tandem immunoprecipitation approach to reveal global binding landscape of multisubunit ribonucleoproteins - p. 401 25. Chapter Eighteen: Generation of 3′UTR knockout cell lines by CRISPR/Cas9-mediated genome editing - p. 427 26. Chapter Nineteen: Modulation of alternative cleavage and polyadenylation events by dCas9-mediated CRISPRpas - p. 459
mRNA 3’ End Processing and Stability, Volume 655 in the Methods in Enzymology series, highlights new advances in the field, with this new volume presenting interesting chapters on a variety of timely topics. Each chapter is written by an international board of authors.
1. Cover image - p. i 2. Title page - p. ii 3. Table of Contents - p. iii 4. Series Page - p. iii 5. Copyright - p. iii 6. Contributors - p. iii 7. Preface - p. xix 8. Chapter One: Application and design considerations for 3′-end sequencing using click-chemistry - p. 1 9. Chapter Two: PAS-seq 2: A fast and sensitive method for global profiling of polyadenylated RNAs - p. 25 10. Chapter Three: TRENDseq—A highly multiplexed high throughput RNA 3′ end sequencing for mapping alternative polyadenylation - p. 37 11. Chapter Four: QPAT-seq, a rapid and deduplicatable method for quantification of poly(A) site usages - p. 73 12. Chapter Five: Using TIF-Seq2 to investigate association between 5´ and 3´mRNA ends - p. 88 13. Chapter Six: Single-molecule polyadenylated tail sequencing (SM-PAT-Seq) to measure polyA tail lengths transcriptome-wide - p. 119 14. Chapter Seven: 3′ End sequencing of pA+ and pA− RNAs - p. 139 15. Chapter Eight: Comprehensive profiling of mRNA polyadenylation in specific cell types in vivo by cTag-PAPERCLIP - p. 165 16. Chapter Nine: A computational pipeline to infer alternative poly-adenylation from 3′ sequencing data - p. 185 17. Chapter Ten: Systematic refinement of gene annotations by parsing mRNA 3′ end sequencing datasets - p. 205 18. Chapter Eleven: Computational analysis of alternative polyadenylation from standard RNA-seq and single-cell RNA-seq data - p. 225 19. Chapter Twelve: Quantifying alternative polyadenylation in RNAseq data with LABRAT - p. 245 20. Chapter Thirteen: Poly(A) tail dynamics: Measuring polyadenylation, deadenylation and poly(A) tail length - p. 265 21. Chapter Fourteen: Reconstitution and biochemical assays of an active human histone pre-mRNA 3′-end processing machinery - p. 291 22. Chapter Fifteen: Comprehensive RNP profiling in cells identifies U1 snRNP complexes with cleavage and polyadenylation factors active in telescripting - p. 325 23. Chapter Sixteen: Simultaneous studies of gene expression and alternative polyadenylation in primary human immune cells - p. 349 24. Chapter Seventeen: RIPiT-Seq: A tandem immunoprecipitation approach to reveal global binding landscape of multisubunit ribonucleoproteins - p. 401 25. Chapter Eighteen: Generation of 3′UTR knockout cell lines by CRISPR/Cas9-mediated genome editing - p. 427 26. Chapter Nineteen: Modulation of alternative cleavage and polyadenylation events by dCas9-mediated CRISPRpas - p. 459
