Main description:

This volume provides a collection of protocols for the study of DNA-DNA contact maps, replication profiles, transcription rates, RNA secondary structures, protein-RNA interactions, ribosome profiling and quantitative proteomes and metabolomes. Written for the 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, Yeast Functional Genomics: Methods and Protocols aims to ensure successful results in the further study of this vital field.

Contents:

1. Using RNA-seq for Analysis of Differential Gene Expression in Fungal Species

Can Wang, Markus S. Schroeder, Stephen Hammel, and Geraldine Butler

2. Enhancing Structural Annotation of Yeast Genomes with RNA-Seq Data

Hugo Devillers, Nicolas Morin, and Cecile Neuveglise

3. Pathogen Gene Expression Profiling During Infection Using a Nanostring Ncounter Platform

Wenjie Xu, Norma V. Solis, Scott G. Filler, and Aaron P. Mitchell

4. Comparative Transcriptomics in Yeasts

Dawn A. Thompson

5. Mapping the Transcriptome-Wide Landscape of RBP Binding sites using gPAR-CLIP-seq: Experimental Procedures

Ting Ha and John K. Kim

6. Mapping the Transcriptome-wide Landscape of RBP Binding Sites using gPAR-CLIP-seq: Bioinformatic Analysis

Mallory A. Freeberg and John K. Kim

7. Translation Analysis at the Genome Scale by Ribosome Profiling

Agnes Baudin-Baillieu, Isabelle Hatin, Rachel Legendre, and Olivier Namy

8. Biotin-Genomic Run-on (Bio-GRO): A High-Resolution Method for the Analysis of Nascent Transcription in Yeast

Antonio Jordan-Pla, Ana Miguel, Eva Serna, Vicent Pelechano, and Jose E. Perez-Ortin

9. Genome-wide Probing of RNA Structures in Vitro Using Nucleases and Deep Sequencing

Yue Wan, Kun Qu, Zhengqing Ouyang and Howard Y. Chang

10. Genome-wide Chromatin Immunoprecipitation in Candida albicans and other Yeasts

Matthew B. Lohse, Pisiwat Kongsomboonvech, Maria Madrigal, Aaron D. Hernday, and Clarissa J. Nobile

11. ChIPseq in Yeast Species: from Chromatin Immumoprecipitation to High-Throughput Sequencing and Bioinformatics Data Analyses

Gaelle Lelandais, Corinne Blugeon, and Jawad Merhej

12. Systematic Determination of Transcription factor DNA-binding Specificities in Yeast

Lourdes Pena-Castillo and Gwenael Badis

13. Generation and Analysis of Chromosomal Contact Maps of Yeast Species

Axel Cournac, Martial Marbouty, Julien Mozziconacci, and Romain Koszul

14. A Versatile Procedure to Generate Genome-Wide Spatio-Temporal Program of Replication in Yeast Species

Nicolas Agier and Gilles Fischer

15. Single-Step Affinity Purification (ssAP) and Mass Spectrometry of Macromolecular Complexes in the Yeast S. cerevisiae

Christian Trahan, Lisbeth-Carolina Aguilar, and Marlene Oeffinger

16. Label-Free Quantitative Proteomics in Yeast

Thibaut Leger, Camille Garcia, Mathieu Videlier, and Jean-Michel Camadro

17. Profiling of Yeast Lipids by Shotgun LipidomicsKlose Christian and Tarasov Kirill

18. Identification of Links between Cellular Pathways by Genetic Interaction Mapping (GIM)

Christophe Malabat and Cosmin Saveanu

19. On The Mapping of Epistatic Genetic Interactions in Natural Isolates: Combining Classical Genetics and Genomics

Jing Hou and Joseph Schacherer

20. Experimental Evolution and Resequencing Analysis of Yeast

Celia Payen and Maitreya J. Dunham

21. Reconstruction and Analysis of the Evolution of Modular Transcriptional Regulatory Programs using Arboretum

Sara A. Knaack, Dawn A. Thompson, and Sushmita Roy

22. Predicting Gene and Genomic Regulation in Saccharomyces cerevisiae, using the YEASTRACT Database: A Step By Step Guided Analysis

Miguel C. Teixeira, Pedro T. Monteiro, and Isabel Sa-Correia