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


by

Kenneth W. Berendzen

DOI: 10.2174/97816080549231130101
eISBN: 978-1-60805-492-3, 2013
ISBN: 978-1-60805-711-5



Recommend this eBook to your Library



A major goal of integrative research is understanding regulatory networks to such an extent as to allow researchers to model developme...[view complete introduction]

Table of Contents

Foreword

- Pp. i-iii (3)

Klaus Harter

Download Free

Preface

- Pp. iv-vi (3)

Kenneth W. Berendzen

Download Free

List of Contributors

- Pp. vii-ix (3)

Kenneth W. Berendzen

Download Free

A General Introduction To Eukaryotic Transcription And Its Molecular Components

- Pp. 3-38 (36)

Kenneth W. Berendzen

View Abstract Purchase Chapter

The Consensus Rna Polymerase II Core Promoter And Beyond

- Pp. 39-70 (32)

Dóra Szakonyi and Kenneth W. Berendzen

View Abstract Purchase Chapter

Gene Regulation By Epigenetic Mechanisms And Chromatin Structure

- Pp. 71-85 (15)

Audrey Vincent and Isabelle Van Seuningen

View Abstract Purchase Chapter

microRNAs: Macro Regulators In Biological Networks

- Pp. 86-100 (15)

Jianzhen Xu and Shijun Xu

View Abstract Purchase Chapter

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

View Abstract Purchase Chapter

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

View Abstract Purchase Chapter

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

- Pp. 149-161 (13)

Nicolas Jonckheere and Isabelle Van Seuningen

View Abstract Purchase Chapter

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

View Abstract Purchase Chapter

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

- Pp. 176-188 (13)

Dirk Walther

View Abstract Purchase Chapter

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

- Pp. 189-207 (19)

Nina M. Fischer and Oliver Kohlbacher

View Abstract Purchase Chapter

Index

- Pp. 207-212 (6)

Kenneth W. Berendzen, Joachim Kilian and Dierk Wanke

Download Free

Foreword

Transcription is the complex, multistep process which transfers the genetic information stored in DNA to RNA. The synthesized and processed RNAs encode for proteins as the building blocks of all living cells such as the mRNAs, are structural compounds of many RNA-protein complexes such as ribosomes, are required for protein translation such as the tRNAs and rRNAs or function as regulator of RNA stability and activity such as the microRNAs. Thus, the regulation of eukaryotic transcription and gene expression is expected to be a highly sophisticated process, which is controlled and fine-tuned at multiple molecular and cellular levels.

The eBook begins with a chapter by Kenneth W. Berendzen, who summarizes the vast field of how transcript abundance in eukaryotes is controlled emphasizing on the complexity of this process. This introduction provides a firm basis for the following up chapters. In the chapter “The consensus RNA polymerase II core promoter and beyond”, Szakonyi and Berendzen focus on core elements of Pol II-dependent promoters, present different eukaryotic promoter classes and discuss a plant-specific core promoter which acts, as likely case of intron-mediated enhancement, downstream of the transcription start site.

Epigenetic processes play a major role in the regulation of eukaryotic transcription. In the chapter “Epigenetics and chromatin structure”, Audrey Vincent and Isabelle Van Seuningen describe excitingly the two major mechanisms of epigenetic regulation: DNA methylation and covalent modification of nucleosomal histone proteins, and how these processes are interlinked. microRNAs (miRNAs) have been shown to regulate the number of protein molecules produced by mRNAs. In the chapter “microRNAs: macro regulators in biological networks”, Jianzhen Xu and Shijun Xu shortly describe the different modes of miRNA action and provide a detailed overview on miRNA characteristics for metazoans and plants, focus on unexpected chromatin effects on nuclear miRNAs and present computational tools for analyzing the miRNA’s role in gene networking.

Phylogenetic footprinting is an evolutionary tool which can be used for the identification of functional elements in genomes. Hozanna A. Castillo and colleagues demonstrate in the chapter “Phylogenetic footprinting: an evolutionary tool for the identification of cis -regulatory elements”, how this approach is of great value for the functional characterization of promoters and distal acting enhancers and silencers in vertebrate genomes. In the chapter “Limits and Prospects of Methods for the analysis of DNA-Protein interaction”, Luise H. Brand and colleagues describe and explain state-of-the-art methods for determining cis -element binding sites in vitro and in vivo and their application to high-throughput and genome scale methods.

Synthetic promoters become more and more important to gain control of spatial and temporal gene expression. Nicolas Jonckheere and Isabelle Van Seuningen in their chapter “Reporter, inducible and synthetic promoters: Engineering tools to study gene regulation and biological system”, describe how such promoters are applied to studying eukaryotic transcription in the context of gene transfer and gene therapy, and give an outlook, how engineered promoters will provide the basis for diverse applications in manipulations, tissue engineering and biopharmaceutics. Finding cis -regulatory elements in eukaryotic genes is still a challenge. In the chapter “Identifying cis elements in eukaryotes using old tricks and high throughput sequence data”, Björn Usadel and colleagues firstly describe the general structure of a core promoter and then discuss the approaches how to find functional cis-regulatory elements. They also show how next generation sequencing will help to make cis element identification more reliable.

Cooperative binding of several transcription regulators to one and the same gene promoter is the Dirk Walther’s topic in the chapter “The combinatorics of cis -regulatory elements: from cooperatively acting motifs to gene regulatory networks”. He highlights bioinformatics approaches used to capture the complexity of cooperatively at composite cis-regulatory elements and gives an overview on available Web-based resources that utilize information on transcription factor – target gene binding events for gene regulatory network analysis. In the last chapter “Structural insights into physical interactions of transcription factor-DNA complexes at an atomic level”, Nina Fischer and Oliver Kohlbacher describe and discuss the most promising computational approaches to model protein-DNA interaction interfaces at an atomic level. In an interesting case study, they present a computational modeling technique for the ab initio three-dimensional design of transcription factor-DNA complexes.

I sincerely thank the contributors who made this eBook possible and rewarding. I am sure this eBook will provide the basis for knowledge update, lively discussions and a starting point for further research on eukaryotic transcription.

Prof. Dr. Klaus Harter
Center for Plant Molecular Biology (ZMBP)
University of Tübingen
Tübingen
Germany


Preface

This book is a collaborative contribution to summarize and illustrate current understandings of eukaryotic transcription. Although it is impossible to cover the entire field of eukaryotic transcription, the book strives to capture both basic and novel insights concerning what is currently known. The book gives background information to all known fields of study that influence the regulation of gene transcription from the basic machinery, transcription factors, miRNAs and chromatin as well as providing wetlab and drylab state-of-the-art methods chapters. To this aim, some chapters include novel data is also presented in some chapters as case-studies for underpinning alternative perspectives. Furthermore, there are chapters aimed at those studying connections between transcription factors and their cognate cis elements either from the cis element side or from the transcription factor side.

As a scientist and editor of this book, I am extremely proud and grateful to those that have made it possible. The authors who contributed to this book are from all over the world. Their willingness and perseverance have made it a joy and a rewarding experience. In fact, I have not met many of the authors face-to-face, and it is a great trust and respect they have given me for managing such a project. I am pleased and honored that they have keep to the task, have endured the email traffic over the last three years, and have been committed to seeing this through. In Chapter 1, I have tried to summarize transcription in a nutshell – a particularly difficult task considering the complexity, detail and the vastness of this research field. Transcription is not only a necessary precursor to produce a protein, but it is the regulation and control of gene expression that leads to and is determined by network communication dynamics. One of the basic insights into regulation has been with the discovery and characterization of core-promoters. This topic was approached by Dóra Szakonyi and I in Chapter 2, both as a review and a demonstration of a plant core-promoter that sits within the second intron of a gene, an phenomenal example of intron-mediated enhancement.

The basics of chromatin-based regulation are concisely addressed by Audrey Vincent and Isabelle Van Seuningen in Chapter 3. In addition to explaining the complexity of the histone code, they have complied an extensive reference table of human chromatin-modifying enzymes. Jianzhen Xu and colleague address in Chapter 4 the miRNA biogenesis and its significance in animals and plants. In addition, they include useful collections of online resources for metazoan and plant miRNAs. Castillo and co-workers in Chapter 5 provide a splendid introduction to phylogenetic footprinting and walk us through how to perform an analysis and underpin this with two case-study examples from their own research. Chapter 6 (Brand and co-workers) addresses similar and different approaches to the analysis of protein-DNA binding in vitro and in vivo and features the DPIELISA technique, which has been used by Luise Brand to explore the differential binding of WRKY11 and WRKY50 DNA-binding domains to variant W-boxes.

Chapter 7 by Nicolas Jonckheere and Isabelle Van Seuningen is an excellent summary and example of where animal and plant science are nearly indistinguishable: the techniques used to study of transcriptional regulation in vitro. Here, he summarizes reporter, inducible and synthetic promoters used to study basal regulation and how they are implemented as engineering tools. Usadel and co-workers in Chapter 8 provide the reader with an introduction to basic informatic techniques used to look for known and unknown cis elements is strings of DNA, a must, for any book that would like to underpin the importance of gene regulation by transcription factors. In their outlook, they also give a suggestion at other methods for looking for cis elements that will be incorporating highthroughput sequencing data from multiple samples and multiple species.

In Chapter 9 Dirk Walther precisely and quaintly presents the background and actual bioinformatic approaches needed to study the combinatorics and cooperativity of cis elements. Cooperative cis elements are also known as regulatory modules and are now the desired target of many informatic studies, especially those studies that look at many stimuli or species. He also provides the reader with some selected tools and online resources for the detection of modules to get a laboratory researcher kick-start. Finally, Chapter 10 by Nina Fischer and Oliver Kohlbacher explain and look at how to model DNA-protein interactions by computational methods in silico. This exciting approach allows a researcher to study these physical interactions at an atomic level leading to unprecedented insights into molecular dynamics. Their well-written chapter not only gives the reader the essential background into what techniques are being used, but discuss both the pros and cons of various techniques with plenty of examples, both from published and their own previously unpublished work. Additionally, they look at WRKY DNA-complexes of WRKY11 and WRKY50 via homology modeling providing clues at different specificities and putative functions of WRKY proteins.

I would like to thank all the authors, including those I directly and indirectly interacted with. This has been, for me personally, a very rewarding growth experience. The books itself is a small compendium that can be broadly referenced for background knowledge and methodology for studying gene transcription and I will definitely be referring to it myself and use it for teaching students. I would also like to thank Bentham Science Publishers Manager of Publications Aniza Naveed. She has been extremely patient with my enquiries, requests, and the speed of which I took to complete the entire project, making it possible to sculpt the book into a form that is both intellectually and optically pleasing.

I would like to thank my wife, Virtudes Mira Rodado, for her patience with me and the entire project. Apparently writing a book or even editing a book is still a daunting process and many nights that could have been spent relaxing were converted into the knowledge, text, comments, and figures to create this work.

I hope that this peer-reviewed book provides a good starting point for both attaining a basic foundation in gene transcription for entry level students, students active in the laboratory and established researchers by providing provocative assessments of what is known today about eukaryotic transcription.

Kenneth W. Berendzen
Center for Plant Molecular Biology (ZMBP)
University of Tübingen
Germany

List of Contributors

Editor(s):
Kenneth W. Berendzen
Center for Plant Molecular Biology (ZMBP)
University of Tübingen
Tübingen
Germany




Co-Editor(s):
Joachim Kilian
Center for Plant Molecular Biology (ZMBP)
University of Tübingen
Tübingen
Germany


Dierk Wanke
Center for Plant Molecular Biology (ZMBP)
University of Tübingen
Tübingen
Germany




Contributor(s):
Lúcia E. Alvares
Department of Histology and Embryology
State University of Campinas –UNICAMP
Campinas (São Paulo)
Brazil


Kenneth W. Berendzen
Central Facility Core Manager of Plant Transformation and Flow Cytometry
Center for Plant Molecular Biology (ZMBP)
University of Tübingen
Tübingen
Germany


Anthony Bolger
Research Doctoral Candidate, RWTH Aachen University, Aachen
Germany Luise H. Brand Center for Plant Molecular Biology (ZMBP)
University of Tübingen
Tübingen
Germany


Hozana A. Castillo
Brazilian National Laboratory for Biosciences
Brazilian Association for Synchrotron Light Technology
Campinas (São Paulo)
Brazil


Susanne Dietrich
Institute of Biomedical and Biomolecular Sciences
School of Biological Sciences
University of Portsmouth
Portsmouth
U. K.


Nina M. Fischer
Applied Bioinformatics
Centre for Bioinformatics (ZBIT)
University of Tübingen
Tübingen
Germany


Carla V. C. Grade
Department of Histology and Embryology
State University of Campinas –UNICAMP
Campinas (São Paulo)
Brazil


Nicolas Jonckheere
Team 5 "Mucins, epithelial differentiation and carcinogenesis" laboratory
Inserm UMR837, Jean-Pierre Aubert Research Center
Lille
France


Joachim Kilian
Center for Plant Molecular Biology (ZMBP)
University of Tübingen
Tübingen
Germany


Oliver Kohlbacher
Applied Bioinformatics
Centre for Bioinformatics (ZBIT)
University of Tübingen
Tübingen
Germany


Üner Kolukisaoglu
Center for Plant Molecular Biology (ZMBP)
University of Tübingen
Tübingen
Germany


Mônica S. Salerno
Growth and Lactation
Ruakura Research Centre
AgResearch
Hamilton
New Zealand


Santosh B. Satbhai
Gregor Mendel Institute of Molecular Plant Biology
Vienna
Austria


Isabelle Van Seuningen
Team 5 "Mucins, epithelial differentiation and carcinogenesis" laboratory
Inserm UMR837, Jean-Pierre Aubert Research Center
Lille
France


Frank R. Shubert
Institute of Biomedical and Biomolecular Sciences
School of Biological Sciences
University of Portsmouth
Portsmouth
U. K.


Dóra Szakonyi
Department of Plant Systems Biology
Ghent University
Ghent
Belgium


Björn Usadel
Professor RWTH Aachen University
Co-Director at the Forschungszentrum Jülich
RWTH Aachen University, Forschungszentrum Jülich
Aachen, Germany
Jülich
Germany


Audrey Vincent
Team 5 "Mucins, epithelial differentiation and carcinogenesis" laboratory
Jean-Pierre Aubert Research Center
Inserm UMR837
Lille
France


Dirk Walther
Central Infrastructure Group Bioinformatics
Max Planck Institute for Molecular Plant Physiology
Golm
Germany


Dierk Wanke
Center for Plant Molecular Biology (ZMBP)
University of Tübingen
Tübingen
Germany


José Xavier-Neto
Brazilian National Laboratory for Biosciences
Brazilian Association for Synchrotron Light Technology
Campinas(São Paulo)
Brazil


Jianzhen Xu
College of Bioengineering
Henan University of Technology
Zhengzhou
P.R.China


Shijun Xu
College of Bioengineering
Henan University of Technology
Zhengzhou
P.R.China




Advertisement


Related Journals



Related Books



Webmaster Contact: urooj@benthamscience.org Copyright © 2016 Bentham Science