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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.
List of contents
What Have We Learned About Synthetic Promoter Construction?.- Quantitative Analysis of Cis-Regulatory Element Activity Using Synthetic Promoters in Transgenic Plants.- The Identification of Cis-Regulatory Sequence Motifs in Gene Promoters Based on SNP Information.- Quantitative Analysis of Protein-DNA Interaction by qDPI-ELISA.- Analyzing Synthetic Promoters Using Arabidopsis Protoplasts.- Selecting Hypomethylated Genomic Regions Using MRE-Seq.- Spatio-Temporal Imaging of Promoter Activity in Intact Plant Tissues.- Novel Synthetic Promoters from the Cestrum Yellow Leaf-Curling Virus.- Fast and Efficient Cloning of Cis-Regulatory Sequences for High Throughput Yeast One-Hybrid Analyses of Transcription Factors.- The Physcomitrella patens System for Transient Gene Expression Assays.- Analysis of Microbe-Associated Molecular Pattern-Responsive Synthetic Promoters with the Parsley Protoplast System.- A Framework for Discovering, Designing, and Testing MicroProteins to Regulate Synthetic Transcriptional Modules.- Simultaneous Analysis of Multiple Promoters: An Application of the PC-GW Binary Vector Series.- GenoCAD Plant Grammar to Design Plant Expression Vectors for Promoter Analysis.- Bioinformatic Identification of Conserved Cis-Sequences in Coregulated Genes.- In Silico Expression Analysis.- FootprintDB: Analysis of Plant Cis-Regulatory Elements, Transcription Factors, and Binding Interfaces.- RSAT::Plants: Motif Discovery Within Clusters of Upstream Sequences in Plant Genomes.- RSAT::Plants: Motif Discovery in ChIP-Seq Peaks of Plant Genomes.
Summary
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.
