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The Analysis of Regulatory DNA: Current Developments, Knowledge and Applications Uncovering Gene Regulation

  • ID: 2713787
  • Book
  • November 2013
  • 225 Pages
  • Bentham Science Publishers Ltd
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A major goal of integrative research is understanding regulatory networks to such an extent as to allow researchers to model developmental and stress responses. Regulatory networks of living systems include complex and vast interactions between proteins, metabolites, RNA, various signaling molecules and DNA. One aspect of systems biology is understanding the dynamics of protein-DNA interactions affecting gene expression that are caused by transcription factors (TFs) and chromatin remodeling factors.

This Ebook provides a resource for summarizing current knowledge about eukaryotic transcription and explores cis-elements and methods for their analysis, prediction and discovery. The book also presents an overview for exploring gene regulatory networks, chromatin, and miRNAs. Information about state-of-the-art techniques for determining TF — cis-element interactions in vivo and in silico give cutting edge insights on how genomic-scale research is being approached.

The Analysis of Regulatory DNA provides readers with both the necessary background knowledge and provocative, up-to-date insights aimed at sparking new and vibrant experimental designs for understanding and predicting cis-elements in the eukaryotic genome.
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List of Contributors


1. A General Introduction to Eukaryotic Transcription and its Molecular Components
Kenneth W. Berendzen

2. The Consensus RNA Polymerase II Core Promoter and Beyond
Dóra Szakonyi and Kenneth W. Berendzen

3. Gene Regulation by Epigenetic Mechanisms and Chromatin Structure
Audrey Vincent and Isabelle Van Seuningen

4. microRNAs: Macro Regulators in Biological Networks
Jianzhen Xu and Shijun Xu

5. Phylogenetic Footprinting: An Evolutionary Tool for the Identification of cis-Regulatory Elements
Hozana A. Castillo, Carla V. C. Grade, Susanne Dietrich, Frank R. Schubert, Mônica S. Salerno, José Xavier-Neto and Lúcia E. Alvares

6. Limits and Prospects of Methods for the Analysis of DNA-Protein Interaction
Luise H. Brand, Santosh B. Satbhai, Üner Kolukisaoglu and Dierk Wanke

7. Reporter, Inducible and Synthetic Promoters: Engineering Tools to Study Gene Regulation and Biological Systems
Nicolas Jonckheere and Isabelle Van Seuningen

8. Identifying Cis Elements in Eukaryotes Using Old Tricks and High Throughput Sequence Data
Björn Usadel, Kenneth W. Berendzen and Anthony Bolger

9. The Combinatorics of cis-Regulatory Elements: From Cooperatively Acting Motifs to Gene Regulatory Networks
Dirk Walther

10. Structural Insights into Physical Interactions of Transcription Factor-DNA Complexes at an Atomic Level
Nina M. Fischer and Oliver Kohlbacher

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Kenneth Wayne Berendzen, Joachim Kilian, Dierk Wanke
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