Editor: Kenneth Wayne Berendzen

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

eBook: US $69 Special Offer (PDF + Printed Copy): US $147
Printed Copy: US $113
Library License: US $276
ISBN: 978-1-60805-711-5 (Print)
ISBN: 978-1-60805-492-3 (Online)
Year of Publication: 2013
DOI: 10.2174/97816080549231130101

Introduction

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 e-book provides a resource for summarizing current knowledge eukaryotic transcription and explores cis-elements and methods for their analysis, prediction and discovery. The book also presents an overview of exploring gene regulatory networks, chromatin, and miRNAs. Information about state-of-the-art techniques for the determination of 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.

Foreword

- Pp. i-iii (3)
Klaus Harter
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Preface

- Pp. iv-vi (3)
Kenneth W. Berendzen
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List of Contributors

- Pp. vii-ix (3)
Kenneth W. Berendzen
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A General Introduction To Eukaryotic Transcription And Its Molecular Components

- Pp. 3-38 (36)
Kenneth W. Berendzen

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The Consensus Rna Polymerase II Core Promoter And Beyond

- Pp. 39-70 (32)
Dóra Szakonyi and Kenneth W. Berendzen

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Gene Regulation By Epigenetic Mechanisms And Chromatin Structure

- Pp. 71-85 (15)
Audrey Vincent and Isabelle Van Seuningen

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microRNAs: Macro Regulators In Biological Networks

- Pp. 86-100 (15)
Jianzhen Xu and Shijun Xu

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Phylogenetic Footprinting: An Evolutionary Tool For The Identification Of Cis-Regulatory Elements

- Pp. 101-123 (23)
Hozana A. Castillo, Carla V. C. Grade, Susanne Dietrich, Frank R. Schubert, Mônica S. Salerno, José Xavier-Neto and Lúcia E. Alvares

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Limits And Prospects Of Methods For The Analysis Of DNA-Protein Interaction

- Pp. 124-148 (25)
Luise H. Brand, Santosh B. Satbhai, Üner Kolukisaoglu and Dierk Wanke

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Reporter, Inducible And Synthetic Promoters: Engineering Tools To Study Gene Regulation And Biological Systems

- Pp. 149-161 (13)
Nicolas Jonckheere and Isabelle Van Seuningen

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Identifying Cis Elements In Eukaryotes Using Old Tricks And High Throughput Sequence Data

- Pp. 162-175 (14)
Björn Usadel, Kenneth W. Berendzen and Anthony Bolger

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The Combinatorics Of Cis-Regulatory Elements: From Cooperatively Acting Motifs To Gene Regulatory Networks

- Pp. 176-188 (13)
Dirk Walther

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Structural Insights Into Physical Interactions Of Transcription Factor-Dna Complexes At An Atomic Level

- Pp. 189-207 (19)
Nina M. Fischer and Oliver Kohlbacher

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Index

- Pp. 207-212 (6)
Kenneth W. Berendzen, Joachim Kilian and Dierk Wanke
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