Yeast Functional Genomics

Preface…
Table of Contents…
Contributing Authors…

Part I Transcriptomic Analyses

1. Single-Cell RNA-Sequencing in Yeast using the 10x Genomics Chromium Device
Lieselotte Vermeersch, Abbas Jariani, Jana Helsen, Benjamin M. Heineike, and Kevin J. Verstrepen

2. Genome-Wide Profiling of Transcription Initiation with STRIPE-seq
Robert A. Policastro and Gabriel E. Zentner

3. A Modified Crosslinking Analysis of cDNAs (CRAC) Protocol for Detecting RNA-Protein Interactions and Transcription at Single Nucleotide Resolution
Drice Challal, Jessie Colin, Tommaso Villa and Domenico Libri

4. High-Resolution Deep Sequencing of Nascent Transcription in Yeast with BioGRO-seq
Antonio Jordán-Pla and José E. Pérez-Ortín

5. Direct Sequencing of RNA and RNA Modification Identification using Nanopore
Thidathip Wongsurawat, Piroon Jenjaroenpun, and Intawat Nookaew

6. UNAGI: Yeast Transcriptome Reconstruction and Gene Discovery using Nanopore Sequencing
Mohamad Al kadi, Nicolas Jung, and Daisuke Okuzaki

7. Identification of Taxonomically Restricted Transcripts from Illumina RNA Sequencing Data
William R. Blevins

Part II DNA Replication and Protein/DNA Interactions

8. FORK-seq: Single Molecule Profiling of DNA Replication
Magali Hennion, Bertrand Theulot, Jean-Michel Arbona, Benjamin Audit, and Olivier Hyrien

9. CUT&RUN Profiling of the Budding Yeast Epigenome
Sandipan Brahma and Steven Henikoff

10. ChIP-SICAP: A New Tool to Explore Gene-Regulatory Networks in Candida albicans and Other Yeasts
Lasse van Wijlick, Ansh Goyal, Sophie Bachellier-Bassi, and Christophe d’Enfert

Part III Translation Dynamics, Protein Complexes, and Proteomics

11. Purification of Ribosome-Nascent-Chain Complex for Ribosome Profiling and Selective Ribosome Profiling
Hagit Bar-Yosef, Johannes Venezian, Kevin Klann, and Ayala Shiber

12. Single-Step Affinity Purification (ssAP) and Mass Spectrometry of Macromolecular Complexes in the Yeast S. cerevisiae
Christian Trahan and Marlene Oeffinger

13. Composition and Dynamics of Protein Complexes Measured by Quantitative Mass Spectrometry of Affinity Purified Samples
Abdelkader Namane and Cosmin Saveanu

14. Deep Mutational Scanning of Protein-Protein Interaction Stability between Partner Expressed from Their Endogenous Loci In Vivo
Alexandre K Dubé, Rohan Dandage, Soham Dibyachintan, Ugo Dionne, Philippe C. Després, and Christian R. Landry

15. Proteomic Mapping by APEX2-Catalyzed Proximity Labeling in Saccharomyces cerevisiae Semi-Permeabilized Cells
Birgit Singer-Krüger and Ralf-Peter Jansen

16. Quantitative Proteomics in Yeast: From bSLIM and Proteome Discoverer Outputs to Graphical Assessment of the Significance of Protein Quantification Scores
Nicolas Sénécaut, Pierre Poulain, Laurent Lignières, Samuel Terrier, Véronique Legros, Guillaume Chevreux, Gaëlle Lelandais, and Jean-Michel Camadro

17. A Strong Cation Exchange Chromatography Protocol for Examining N-Terminal Proteoforms 
Esperanza Fernández, Annelies Bogaert, Evy Timmerman, An Staes, Francis Impens, and Kris Gevaert

Part IV Genotypic Screens and Phenotypic Profiling

18. RNA Interference (RNAi) as a Tool for High-Resolution Phenotypic Screening of the Pathogenic Yeast Candida glabrata
Andreas Tsouris, Joseph Schacherer, and Olena P. Ishchuk

19. High Throughput Gene Mutagenesis Screening using Base Editing
Philippe C. Després, Alexandre K. Dubé, Nozomu Yachie, and Christian R. Landry

20. SAturated Transposon Analysis in Yeast (SATAY) for Deep Functional Mapping of Yeast Genomes 
Agnès H. Michel and Benoît Kornmann

21. High-Throughput, High-Precision Colony Phenotyping with Pyphe
Stephan Kamrad, Jürg Bähler, and Markus Ralser

22. Bulk-Fitness Measurements using Barcode Sequencing Analysis in Yeast
Claire A. Chochinov and Alex N. Nguyen Ba

Part V In Silico Integration of Functional Genomics Data

23. Prediction of Gene and Genomic Regulation in Candida Species, using the PathoYeastract Database: A Comparative Genomics Approach
Pedro Pais, Jorge Oliveira, Romeu Viana, Inês V. Costa, Isabel Sá-Correia, Pedro T. Monteiro, and Miguel C. Teixeira

24. Enabling Studies of Genome-Scale Regulatory Network Evolution in Large Phylogenies with MRTLE
Shilu Zhang, Sara Knaack, and Sushmita Roy

25. Omics Analyses, How to Navigate through a Constant Data Deluge
Thomas Denecker and Gaëlle Lelandais

Subject Index List…