Plant Synthetic Promoters: Methods and Protocols

ISBN-13: 9781493963942 / Angielski / Twarda / 2016 / 325 str.

Reinhard Hehl

Opis

This book assembles experimental and bioinformatics protocols for the design and experimental testing of synthetic promoters. The identification of cis-regulatory elements potentially achieving the desired expression of a gene is at the core of synthetic promoter design. For this, several bioinformatics chapters are presented. The experimental verification of the proposed expression profile conferred by the cis-regulatory elements requires the assembly of synthetic promoters. Several chapters are dedicated to the assembly of synthetic promoters, also including specific software tools to facilitate promoter design. Transient and transgenic reporter gene technology is a prominent approach to test the spatial and temporal expression driven by synthetic promoters, and several chapters address this approach. Written for the highly successful Methods in Molecular Biology series, chapters include the kind of detail and expert implementation advice to ensure successful results in the lab.
Practical and cutting-edge, Plant Synthetic Promoters: Methods and Protocols covers all steps required from the identification of cis-regulatory elements, over synthetic promoter design, to the experimental analysis of synthetic promoter function.

Spis treści

1. What Have We Learned About Synthetic Promoter Construction?

Paul J. Rushton

2. Quantitative Analysis of Cis-Regulatory Element Activity Using Synthetic Promoters in Transgenic Plants

Geoffrey Benn and Katayoon Dehesh

3. The Identification of Cis-Regulatory Sequence Motifs in Gene Promoters Based on SNP Information

Paula Korkuć and Dirk Walther

4. Quantitative Analysis of Protein-DNA Interaction by qDPI-ELISA

5. Analyzing Synthetic Promoters Using Arabidopsis Protoplasts

Ralf Stracke, Katharina Thiedig, Melanie Kuhlmann, and Bernd Weisshaar

6. Selecting Hypomethylated Genomic Regions Using MRE-Seq

Elisabeth Wischnitzki, Kornel Burg, Maria Berenyi, and Eva Maria Sehr

7. Spatio-Temporal Imaging of Promoter Activity in Intact Plant Tissues

Tou Cheu Xiong, Frédéric Sanchez, Jean-François Briat, Frédéric Gaymard, and Christian Dubos

8. Novel Synthetic Promoters from the Cestrum Yellow Leaf-Curling Virus

Dipak Kumar Sahoo, Shayan Sarkar, Indu B. Maiti, and Nrisingha Dey

9. Fast and Efficient Cloning of Cis-Regulatory Sequences for High Throughput Yeast One-Hybrid Analyses of Transcription Factors

Zsolt Kelemen, Jonathan Przybyla-Toscano, Nicolas Tissot, Loïc Lepiniec, and Christian Dubos

10. The Physcomitrella patens System for Transient Gene Expression Assays

Johanne Thévenin, Wenjia Xu, Louise Vaisman, Loïc Lepiniec, Bertrand Dubreucq, and Christian Dubos

11. Analysis of Microbe-Associated Molecular Pattern-Responsive Synthetic Promoters with the Parsley Protoplast System

Konstantin Kanofsky, Mona Lehmeyer, Jutta Schulze, and Reinhard Hehl

12. A Framework for Discovering, Designing, and Testing MicroProteins to Regulate Synthetic Transcriptional Modules

Elisa Fiume, Niek de Klein, Seung Yon Rhee, and Enrico Magnani

13. Simultaneous Analysis of Multiple Promoters: An Application of the PC-GW Binary Vector Series

Jyoti Dalal

14. GenoCAD Plant Grammar to Design Plant Expression Vectors for Promoter Analysis

Anna Coll, Mandy L. Wilson, Kristina Gruden, and Jean Peccoud

15. Bioinformatic Identification of Conserved Cis-Sequences in Coregulated Genes

Lorenz Bülow and Reinhard Hehl

16. In Silico Expression Analysis

Julio Bolívar, Reinhard Hehl, and Lorenz Bülow

17. FootprintDB: Analysis of Plant Cis-Regulatory Elements, Transcription Factors, and Binding Interfaces

Bruno Contreras-Moreira and Alvaro Sebastian

18. RSAT::Plants: Motif Discovery Within Clusters of Upstream Sequences in Plant Genomes

Bruno Contreras-Moreira, Jaime Castro-Mondragon, Claire Rioualen, Carlos P. Cantalapiedra, and Jacques van Helden

19. RSAT::Plants: Motif Discovery in ChIP-Seq Peaks of Plant Genomes

Jaime Castro-Mondragon, Claire Rioualen, Bruno Contreras-Moreira, and Jacques van Helden