Yeast Functional Genomics

<p>Preface…<br>Table of Contents…<br>Contributing Authors…<br><br>Part I Transcriptomic Analyses<br><br>1. Single-Cell RNA-Sequencing in Yeast using the 10x Genomics Chromium Device<br>Lieselotte Vermeersch, Abbas Jariani, Jana Helsen, Benjamin M. Heineike, and Kevin J. Verstrepen<br><br>2. Genome-Wide Profiling of Transcription Initiation with STRIPE-seq<br>Robert A. Policastro and Gabriel E. Zentner<br><br>3. A Modified Crosslinking Analysis of cDNAs (CRAC) Protocol for Detecting RNA-Protein Interactions and Transcription at Single Nucleotide Resolution<br>Drice Challal, Jessie Colin, Tommaso Villa and Domenico Libri<br><br>4. High-Resolution Deep Sequencing of Nascent Transcription in Yeast with BioGRO-seq<br>Antonio Jordán-Pla and José E. Pérez-Ortín<br><br>5. Direct Sequencing of RNA and RNA Modification Identification using Nanopore<br>Thidathip Wongsurawat, Piroon Jenjaroenpun, and Intawat Nookaew<br><br>6. UNAGI: Yeast Transcriptome Reconstruction and Gene Discovery using Nanopore Sequencing<br>Mohamad Al kadi, Nicolas Jung, and Daisuke Okuzaki<br><br>7. Identification of Taxonomically Restricted Transcripts from Illumina RNA Sequencing Data<br>William R. Blevins<br><br>Part II DNA Replication and Protein/DNA Interactions<br><br>8. FORK-seq: Single Molecule Profiling of DNA Replication<br>Magali Hennion, Bertrand Theulot, Jean-Michel Arbona, Benjamin Audit, and Olivier Hyrien<br><br>9. CUT&RUN Profiling of the Budding Yeast Epigenome<br>Sandipan Brahma and Steven Henikoff<br><br>10. ChIP-SICAP: A New Tool to Explore Gene-Regulatory Networks in Candida albicans and Other Yeasts<br>Lasse van Wijlick, Ansh Goyal, Sophie Bachellier-Bassi, and Christophe d’Enfert<br><br>Part III Translation Dynamics, Protein Complexes, and Proteomics<br><br>11. Purification of Ribosome-Nascent-Chain Complex for Ribosome Profiling and Selective Ribosome Profiling<br>Hagit Bar-Yosef, Johannes Venezian, Kevin Klann, and Ayala Shiber<br><br>12. Single-Step Affinity Purification (ssAP) and Mass Spectrometry of Macromolecular Complexes in the Yeast S. cerevisiae<br>Christian Trahan and Marlene Oeffinger<br><br>13. Composition and Dynamics of Protein Complexes Measured by Quantitative Mass Spectrometry of Affinity Purified Samples<br>Abdelkader Namane and Cosmin Saveanu<br><br>14. Deep Mutational Scanning of Protein-Protein Interaction Stability between Partner Expressed from Their Endogenous Loci In Vivo<br>Alexandre K Dubé, Rohan Dandage, Soham Dibyachintan, Ugo Dionne, Philippe C. Després, and Christian R. Landry<br><br>15. Proteomic Mapping by APEX2-Catalyzed Proximity Labeling in Saccharomyces cerevisiae Semi-Permeabilized Cells<br>Birgit Singer-Krüger and Ralf-Peter Jansen<br><br>16. Quantitative Proteomics in Yeast: From bSLIM and Proteome Discoverer Outputs to Graphical Assessment of the Significance of Protein Quantification Scores<br>Nicolas Sénécaut, Pierre Poulain, Laurent Lignières, Samuel Terrier, Véronique Legros, Guillaume Chevreux, Gaëlle Lelandais, and Jean-Michel Camadro<br><br>17. A Strong Cation Exchange Chromatography Protocol for Examining N-Terminal Proteoforms&nbsp;<br>Esperanza Fernández, Annelies Bogaert, Evy Timmerman, An Staes, Francis Impens, and Kris Gevaert<br><br>Part IV Genotypic Screens and Phenotypic Profiling<br><br>18. RNA Interference (RNAi) as a Tool for High-Resolution Phenotypic Screening of the Pathogenic Yeast Candida glabrata<br>Andreas Tsouris, Joseph Schacherer, and Olena P. Ishchuk<br><br>19. High Throughput Gene Mutagenesis Screening using Base Editing<br>Philippe C. Després, Alexandre K. Dubé, Nozomu Yachie, and Christian R. Landry<br><br>20. SAturated Transposon Analysis in Yeast (SATAY) for Deep Functional Mapping of Yeast Genomes&nbsp;<br>Agnès H. Michel and Benoît Kornmann<br><br>21. High-Throughput, High-Precision Colony Phenotyping with Pyphe<br>Stephan Kamrad, Jürg Bähler, and Markus Ralser<br><br>22. Bulk-Fitness Measurements using Barcode Sequencing Analysis in Yeast<br>Claire A. Chochinov and Alex N. Nguyen Ba<br><br>Part V In Silico Integration of Functional Genomics Data<br><br>23. Prediction of Gene and Genomic Regulation in Candida Species, using the PathoYeastract Database: A Comparative Genomics Approach<br>Pedro Pais, Jorge Oliveira, Romeu Viana, Inês V. Costa, Isabel Sá-Correia, Pedro T. Monteiro, and Miguel C. Teixeira<br><br>24. Enabling Studies of Genome-Scale Regulatory Network Evolution in Large Phylogenies with MRTLE<br>Shilu Zhang, Sara Knaack, and Sushmita Roy<br><br>25. Omics Analyses, How to Navigate through a Constant Data Deluge<br>Thomas Denecker and Gaëlle Lelandais<br><br>Subject Index List…</p>