Eukaryotic Transcriptional and Post-transcriptional Gene Expression Regulation

1. Fluorescence Reporter-Based Genome-Wide RNA Interference Screening to Identify Alternative Splicing Regulators

Ashish Misra and Michael R. Green

2. Tandem Affinity Purification Approach Coupled To Mass Spectrometry to Identify Post-translational Modifications of Histones Associated with Chromatin-binding Proteins

Sophie Beyer, Philippe Robin, and Slimane Ait-Si-Ali

3. Efficient Preparation of High-Complexity ChIP-Seq Profiles from Early Xenopus Embryos

George E. Gentsch and James C Smith

4. Systematic Discovery Of Chromatin-bound Protein Complexes from ChIP-seq Datasets

Eugenia Giannopoulou and Olivier Elemento

5. Assay for Transposase-Accessible Chromatin with high throughput sequencing (ATAC-seq) Protocol for Zebrafish Embryos

Canan Doganli, Melissa Sandova, Sean Thomas, and Daniel Hart

6. Establishment of time- and cell-specific RNAi in Caenorhabditis elegans

Masayuki Hamakawa and Takaaki Hirotsu

7. Cell-penetrating Peptide-mediated Delivery of Cas9 Protein and Guide RNA for Genome Editing

Bharathi Suresh, Suresh Ramakrishna, and Hyongbum Kim

8. Epigenetic Analysis of Endocrine Cell Subtypes from Human Pancreatic Islets

Jia Zhang and Klaus H. Kaestner

9. eIF3 Regulation of Protein Synthesis, Tumorigenesis, and Therapeutic Response

Ji-Ye Yin, Zizheng Dong, and Jian-Ting Zhang

10. High Resolution Gene Expression Profiling of RNA Synthesis, Processing, and Decay by Metabolic Labeling of Newly Transcribed RNA using 4-thiouridine

Andrzej J. Rutkowski and Lars Dölken

11. Accurate Detection of Differential Expression and Splicing using Low-level Features

Tomi Suomi and Laura L. Elo

12. Profiling Changes in Histone Post-translational Modifications by Top-Down Mass Spectrometry

Mowei Zhou, Si Wu, ^{David L. Stenoien, Zhaorui Zhang, Lanelle Connolly, Michael Freitag, andLjiljana Pasa-Tolic}

13. Determining if an mRNA is a Substrate of Nonsense-mediated mRNA Decay in Saccharomyces cerevisiae

Marcus J.O. Johansson

14. Optimizing In Vitro Pre-mRNA 3’ Cleavage Efficiency: Reconstitution from Anion-Exchange Separated HeLa Cleavage Factors and from Adherent HeLa Cell Nuclear Extract

Mihwa Na, Susana T. Valente, and Kevin Ryan

15. Unbiased Interrogation of 3D Genome Topology using Chromosome Conformation Capture Coupled to High-throughput Sequencing (3C-Seq)

Rutger W.W. Brouwer, Mirjam C.G.N. van den Hout, Wilfred F.J. van IJcken, Eric Soler, and Ralph Stadhouders

16. Using an Inducible CRISPR-Cas9-KRAB Effector System to Dissect Transcriptional Regulation in Human Embryonic Stem Cells

Krishna Mohan Parsi, Erica Hennessy, Nicola Kearns, and René Maehr

17. In vitro assay to Study Histone Ubiquitination during Transcriptional Regulation

Jogender Singh Tushir and Sanchita Bhatnagar

18. Determination of Alternate Splicing Events using Transcriptome Arrays

Rebecca S. DeVaux, Marcy Kuentzel, Jason Herschkowitz, and Sridar V. Chittur

19. Large-scale RNA Interference Screening to Identify Transcriptional Regulators of a Tumor Suppressor Gene

Matteo Forloni, Thuy Ho, Lisha Sun, and Narendra Wajapeyee

20. Transcriptional Analysis-based Integrative Genomics Approach to Identify Tumor Promoting Metabolic Genes

Romi Gupta and Narendra Wajapeyee