Yeast Functional Genomics

This second edition volume discusses the latest techniques and protocols used in the field that were not covered in the previous edition. The chapters in this book are organized into five parts. Part One looks at transcriptomic analyses and Part Two covers DNA replication and protein/DNA interactions. Part Three discusses translation dynamics, protein complexes, and proteomics. Part Four looks at genotypic screens and phenotypic profiling, and Part Five explores in silico integration of functional genomics data. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary material and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.

Cutting edge and practical, Yeast Functional Genomics: Methods and Protocols, Second Edition is a valuable resource for all researchers interested in learning more about the evolving field of yeast.

Chapters 1, 9, 16, 20, 22, 24, and 25 are available open access under a Creative Commons Attribution 4.0 International License via link.springer.com.

Includes cutting-edge methods and protocols Provides step-by-step detail essential for reproducible results Contains key notes and implementation advice from the experts

Inhalt
Single-Cell RNA-Sequencing in Yeast using the 10x Genomics Chromium Device.- Genome-Wide Profiling of Transcription Initiation with STRIPE-seq.- A Modified Crosslinking Analysis of cDNAs (CRAC) Protocol for Detecting RNA-Protein Interactions and Transcription at Single Nucleotide Resolution.- High-Resolution Deep Sequencing of Nascent Transcription in Yeast with BioGRO-seq.- Direct Sequencing of RNA and RNA Modification Identification using Nanopore.- UNAGI: Yeast Transcriptome Reconstruction and Gene Discovery using Nanopore Sequencing.- Identification of Taxonomically Restricted Transcripts from Illumina RNA Sequencing Data.- FORK-seq: Single Molecule Profiling of DNA Replication.- CUT&RUN Profiling of the Budding Yeast Epigenome.- ChIP-SICAP: A New Tool to Explore Gene-Regulatory Networks in Candida albicans and Other Yeasts.- Purification of Ribosome-Nascent-Chain Complex for Ribosome Profiling and Selective Ribosome Profiling.- Single-Step Affinity Purification (ssAP) and Mass Spectrometry of Macromolecular Complexes in the Yeast S. cerevisiae.- Composition and Dynamics of Protein Complexes Measured by Quantitative Mass Spectrometry of Affinity Purified Samples.- Deep Mutational Scanning of Protein-Protein Interaction Stability between Partner Expressed from Their Endogenous Loci In Vivo.- Proteomic Mapping by APEX2-Catalyzed Proximity Labeling in Saccharomyces cerevisiae Semi-Permeabilized Cells.- Quantitative Proteomics in Yeast: From bSLIM and Proteome Discoverer Outputs to Graphical Assessment of the Significance of Protein Quantification Scores.- A Strong Cation Exchange Chromatography Protocol for Examining N-Terminal Proteoforms.- RNA Interference (RNAi) as a Tool for High-Resolution Phenotypic Screening of the Pathogenic Yeast Candida glabrata.- High Throughput Gene Mutagenesis Screening using Base Editing.- Saturated Transposon Analysis in Yeast (SATAY) for Deep Functional Mapping of Yeast Genomes.- High-Throughput, High-Precision Colony Phenotyping with Pyphe.- Bulk-Fitness Measurements using Barcode Sequencing Analysis in Yeast.- Prediction of Gene and Genomic Regulation in Candida Species, using the PathoYeastract Database: A Comparative Genomics Approach.- Enabling Studies of Genome-Scale Regulatory Network Evolution in Large Phylogenies with MRTLE.- Omics Analyses, How to Navigate through a Constant Data Deluge.