Epigenetic Regulation and Epigenomics E-Book

• Herausgeber: Wiley-VCH
• Kategorie: Wissenschaft und neue Technologien
• Serie: Current Topics from the Encyclopedia of Molecular Cell Biology and Molecular Medicine
• Sprache: Englisch

Seitenzahl: 2682

Veröffentlichungsjahr: 2012

Beschreibung

Epigenetics is a term in biology referring to heritable traits that do not involve changes in the underlying DNA sequence of the organism. Epigenetic traits exist on top of or in addition to the traditional molecular basis for inheritance. The "epigenome" is a parallel to the word "genome," and refers to the overall epigenetic state of a cell. Cancer and stem cell research have gradually focused attention on these genome modifications. The molecular basis of epigenetics involves modifications to DNA and the chromatin proteins that associate with it. Methylation, for example, can silence a nearby gene and seems to be involved in some cancers.

Epigenetics is beginning to form and take shape as a new scientific discipline, which will have a major impact on Medicine and essentially all fields of biology. Increasingly, researchers are unearthing links between epigenetics and a number of diseases.

Although in recent years cancer has been the main focus of epigenetics, recent data suggests that epigenetic plays a critical role in psychology and psychopathology. It is being realized that normal behaviors such as maternal care and pathologies such as Schizophrenia and Alzheimer's might have an epigenetic basis. It is also becoming clear that nutrition and life experiences have epigenetic consequences.

Discover more online content in the Encyclopedia of Molecular Cell Biology and Molecular Medicine.

Leseprobe

Table of Contents

Related Titles

Title Page

Copyright

Preface and Commentary

List of Contributors

Volume I

Part I: Analytical Methods

1 RNA Methodologies

1 Introduction

2 Subpopulations of RNA

3 Goals in the Purification of RNA

4 Methods of Cellular Disruption and RNA Recovery

5 Inhibition of Ribonuclease Activity

6 Methods for the Analysis of RNA

7 Summary

References

2 AR All Things ChIP

1 Introduction

2 Protein-DNA Binding

3 ChIP Protocol

4 ChIP-PCR, ChIP-Chip, or ChIP-Seq. Which Should be Chosen?

5 Experimental Considerations

6 Calculating IP Enrichment

7 Special Analysis Considerations

8 Conclusions

References

3 Methods for DNA Methylation Analysis

1 Introduction

2 Methods of DNA Methylation Analysis

3 Concluding Remarks

Acknowledgments

References

4 DNA Methylation Analysis by MALDI Mass Spectrometry

1 Introduction to DNA Methylation

2 Epigenetics and Disease

3 DNA Methylation Content Analysis by Mass Spectrometry

4 Specific DNA Methylation Analysis

5 Introduction to MALDI

6 Problems of MALDI Analysis of DNA

7 DNA Sequencing with MALDI Mass Spectrometry Readout

8 Primer Extension for the Interrogation of Specific Positions

9 Quantification

10 Automation of Sample Preparation, Data Accumulation, and Analysis

11 Positioning of MALDI MS for DNA Methylation Analysis

12 Applications of DNA Methylation Analysis by Mass Spectrometry

13 DNA Methylation Analysis for Tumor Classification

14 DNA Methylation Analysis for Prognosis and Response to Treatment

15 Prenatal Diagnosis

16 Conclusions

References

5 Tag Sequencing

1 Library Construction

2 Advanced Sequencing Technologies

3 Data Analysis and Bioinformatics

4 Applications of Tag Sequencing

5 Clinical Applications of Tag Sequencing

6 Future Perspectives

Acknowledgments

References

Part II: Basic Molecular Mechanisms

6 Heterochromatin and Euchromatin—Organization, Boundaries, and Gene Regulation

1 Properties and Functions of Heterochromatin

2 Euchromatin Formation

3 Boundaries between Heterochromatin and Euchromatin

4 Insulating against Active Chromatin

Acknowledgments

References

7 Regulation of Gene Expression

1 Introduction

2 Regulation of Gene Expression in Prokaryotes

3 Regulation of Gene Expression in Eukaryotes

4 RNA Splicing

5 Role of microRNAs (miRNAs) in the Regulation of Gene Expression

6 Chromatin Structure and the Control of Gene Expression

7 Epigenetic Control of Gene Expression

8 Gene Regulation by Hormonal Action

9 Post-Transcriptional Regulation of mRNA

10 Transport of Processed mRNA to the Cytoplasm

11 Regulation of Gene Expression at the Level of Translation

Acknowledgments

References

8 Molecular Genetics of Genomic Imprinting

1 Genomic Imprinting in Mammals

2 Imprinted Genes

3 Molecular Mechanisms

4 Imprinting and Disease

5 Human Reproduction

6 Evolution of Imprinting

References

9 Nuclear Transfer for Cloning Animals

1 Introduction and Brief Historical Overview

2 Key Elements and Critical Aspects of NT Technology

3 Applications of NT in Different Species

4 Future Perspectives of NT

Acknowledgments

References

10 Regulation of Gene Expression at the Beginning of Mammalian Development

1 Preimplantation Development

2 Maternal to Zygotic Gene Transition

3 “Zygotic Clock”: The Time-Dependent Activation of Zygotic Gene Expression

4 Developmental Acquisition of Transcriptional Regulation

5 Transition from Morula to Blastocyst Requires Specification of Two Cell Lineages

6 Conclusions and Perspectives

References

11 RNA Interference in Animals

1 Introduction

2 Small Interfering RNA (siRNA)-Mediated Gene Silencing

3 MicroRNA (miRNA)-Mediated Gene Silencing

4 PIWI-Interacting RNA (piRNA)-Mediated Gene Silencing

5 Conclusions

References

12 AR The Cell Nucleus

1 Introduction

2 Nuclear Function

3 Nuclear Structure

4 Integrating Nuclear Structure and Function

5 Overview

References

13 Chromosome Territory Organization within the Nucleus

1 Origins of Chromosome Research

2 Chromosome Territories: An Early Concept and Its Late Experimental Proof

3 Nonrandom, Higher-Order Chromatin Arrangements in Cultured Cells

4 Chromosome Territory Arrangements Change during Normal Development and Cell Differentiation

5 Chromatin Fibers, Loops, and Domains: What Hierarchies, Structures, and Sizes?

6 Capturing Genome-Wide DNA–DNA and DNA–Protein Interactions

7 Functional Nuclear Organization Studied by Electron Microscopy

8 Functional Nuclear Organization Studied by Light Optical Nanoscopy

9 Where We Stand: Current Models of the Functional Nuclear Organization

10 A Glance at the Future: Nuclear Cartography with Nanometer Resolution

References

14 Epigenetic Reprogramming in Mammalian Development

1 Introduction

2 Epigenetic Reprogramming in Preimplantation Embryos

3 Epigenetic Reprogramming in PGCs

4 Mechanistic Aspects of DNA Methylation Reprogramming

5 Conclusions

References

15 Histone Acetylation and Deacetylation

1 Introduction

2 Histone Acetyltransferases (HATs): “Writers”

3 Histone Deacetylases (HDACs): “Erasers”

4 Epigenetic Therapies: Histone Acetylation–Deacetylation and Disease

5 Summary

References

16 Epigenetic Regulation in Pluripotent Stem Cells

1 Introduction

2 DNA Methylation

3 Histone Modifications and Histone Variants

4 Higher-Order Structure of Chromatin

5 X-Chromosome Inactivation

6 Regulation of ESC Pluripotency and Differentiation by miRNAs

7 Telomere Function and Genomic Stability in ESCs

8 Imprinting and ESC Stability

9 Epigenetic Interconversion among Mouse ESCs, EpiSCs, and Human ESCs

10 Summary

References

17 Imprinting and the Epigenetic Asymmetry between Parental Genomes

1 Introduction

2 Evolution of Genomic Imprinting in Mammals

3 Asynchronous Replication of Imprinted Chromosome Domains

4 DNA Methylation and Chromatin Structure

5 Imprinting Mechanisms and Their Disturbances

6 The Imprinting Cycle

7 Reprogramming Errors and Epigenetic Variation

References

18 Chromatin Dynamics and Higher-Order Chromatin Organization

1 Introduction

2 Structural Levels of Chromatin Organization

3 Chromatin Dynamics

4 Conclusions

Acknowledgments

References

19 Histone Modifications

1 Introduction

2 Histone Acetylation

3 Histone Methylation

4 Histone Phosphorylation

5 Other Histone Modifications

6 Histone Modifications in DNA Processes

7 Histone Modifications and Disease

8 Perspective

References

20 Monozygotic Twins and Epigenetics

1 Introduction

2 Twin Formation

3 The Epigenome

4 The Impact of Environment on the Epigenome

5 Monozygotic Twins and Epigenetic Inheritance

6 Monozygotic Twins and Aging

7 Monozygotic Twins in Research Studies

8 Monozygotic Twins and Complex Diseases

9 Future Directions

References

21 Prions as Epigenetic Regulators of Phenotype in Fungi

1 Prions: An Introduction

2 Prions Regulate a Variety of Biological Processes in Fungi

3 Distinguishing Features of Prion Proteins

4 Molecular Mechanisms of Prion Inheritance

5 Prions: Beyond Fungi

Acknowledgments

References

Volume 2

Part III: The Epigenome

22 Computational Epigenetics

1 Introduction

2 Data Sources

3 Computational Tools

4 Computational Analysis of DNA Methylation

5 Computational Analysis of Histone Modifications

6 Computational Analysis of Cancer Epigenetics

7 Computational Analysis of Stem Cell Epigenetics

8 Conclusion

References

23 The Human Epigenome

1 Introduction

2 DNA Methylation

3 DNA Methylation in Normal Development

4 Nutrition and DNA Methylation

5 Epigenetic Crosstalk: DNA Methylation and Histone Modifications

6 Genome-Wide DNA Methylation Analyses

7 Computational Analysis of the Methylome

8 DNA Methylation in Cancer

9 DNA Methylation as a Biomarker

10 Epigenetic Response to Cancer Therapy

11 Concluding Remarks

References

24 Methylomes

1 An Introduction to Methylomes

2 Technology

3 Applications

4 Future Directions

References

Part IV: Medical Applications

25 Emerging Clinical Applications and Pharmacology of RNA

1 Clinically Relevant Features of RNA

2 Emerging Clinical Applications of RNA

3 The Design, Synthesis, Delivery, and Pharmacokinetics of RNA

4 An RNA Drug for Every Disease?

Acknowledgments

References

26 Epigenetics of the Immune System

1 The Immune System: An Introduction

2 Epigenetic Markings

3 HSCs: Epigenetic Basis for Stem Cell Characteristics

4 B Cells

5 T Cells

6 Conclusions

References

27 Epigenetic Medicine

1 Introduction to the Epigenome

2 The Epigenome: A Biomarker for Exposure

3 Targeting the Epigenome in Complex Disease

4 Cancer as an Epigenetic Disease

5 Summary

References

28 Chromatin Remodeling in Carcinoma Cells

1 Introduction

2 Chromatin

3 Chromatin Remodeling

4 Remodeling the Hallmarks of Cancer

5 Conclusion

References

29 Pharmaco-Epigenomics to Improve Cancer Therapies

1 Introduction

2 The Epigenetic Origin of Cancer

3 Pharmaco-Epigenomics: Translating Epigenetics into Clinical Practice

4 Epigenetic Therapies for Cancer

5 Epigenetic Biomarkers for Cancer Therapy

6 Epigenetic Therapy beyond Cancer Cells

7 Future Perspectives

References

Part V: Model Organisms

30 Parental Genomic Imprinting in Flowering Plants

1 General Context of Parental Genomic Imprinting in Plants

2 Imprinted Genes and Their Function

3 Molecular Mechanisms Controlling Imprinting

4 Biological Significance and the Evolution of Imprinting

Acknowledgments

References

31 Epigenetics of Filamentous Fungi

1 Genome Defense in Filamentous Fungi

2 Epigenetic Phenomena in Filamentous Fungi

3 Parts of the Machinery: Proteins Involved in Silencing

4 Propagation of Epigenetic Marks in Filamentous Fungi

5 RNA-Dependent Silencing Phenomena

6 Transcriptional Silencing or Activation by Changes in Chromatin Structure

7 Concluding Remarks

Acknowledgments

References

Epigenetic Gene Regulation in Bacteria

1 Epigenetic Variation and Lineage Formation in Bacteria

2 DNA Methylation in Bacteria

3 Bacterial Lineage Formation by Hereditary Transmission of Feedback Loops

4 Phenotypic Heterogeneity of Bacteria in Natural Environments

5 Perspectives

References

33 Epigenetics of Ciliates

1 Ciliate Biology

2 Epigenetic Phenomena in Ciliates

3 RNA-Mediated Epigenetic Mechanisms

4 Small RNA-Mediated DNA Rearrangements

5 Chromosome Fragmentation and Elimination of DNA during Conjugation in Oxytricha

6 Perspective

References

Index

Related Titles

Meyers, R.A. (ed.)

Encyclopedia of Molecular Cell Biology

and Molecular Medicine

Online version: www.meyers-emcbmm.com

Sippl, W., Jung, M. (eds.)

Epigenetic Targets in Drug Discovery

ISBN: 978-3-527-32355-5

Kahl, G.

The Dictionary of Genomics, Transcriptomics and Proteomics

ISBN: 978-3-527-32073-8

Giordano, A., Macaluso (eds.)

Cancer Epigenetics

Biomolecular Therapeutics in Human Cancer

ISBN: 978-0-471-71096-7

Niculescu, M.D., Haggarty, P. (eds.)

Nutrition in Epigenetics

ISBN: 978-0-8138-1605-0

The Editor

Dr. Robert A. Meyers

Editor in Chief

RAMTECH Limited

122, Escalle Lane

Larkspur, CA 94939

USA

Cover

Simplified model of the interplay between histone modifications and small RNAs in the maintenance of pericentric heterochromatin in fission yeast (for more information see Chapter 19 “Histone Modifications”, Figure 8)”. Designed and drawn by Andrew Bannister and Blerta Xhemalce, The Gurdon Institute, University of Cambridge, CB2 1QN, UK.

Limit of Liability/Disclaimer of Warranty: While the publisher and author have used their best efforts in preparing this book, they make no representations or warranties with respect to the accuracy or completeness of the contents of this book and specifically disclaim any implied warranties of merchantability or fitness for a particular purpose. No warranty can be created or extended by sales representatives or written sales materials. The Advice and strategies contained herein may not be suitable for your situation. You should consult with a professional where appropriate. Neither the publisher nor authors shall be liable for any loss of profit or any other commercial damages, including but not limited to special, incidental, consequential, or other damages.

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© 2012 Wiley-VCH Verlag & Co. KGaA, Boschstr. 12, 69469 Weinheim, Germany

Wiley-Blackwell is an imprint of John Wiley & Sons, formed by the merger of Wiley's global Scientific, Technical, and Medical business with Blackwell Publishing.

All rights reserved (including those of translation into other languages). No part of this book may be reproduced in any form — by photoprinting, microfilm, or any other means — nor transmitted or translated into a machine language without written permission from the publishers. Registered names, trademarks, etc. used in this book, even when not specifically marked as such, are not to be considered unprotected by law.

Print ISBN: 978-3-527-32682-2

Preface and Commentary

Epigenetics is the term given to heritable traits that occur over rounds of cell division and sometimes transgenerationally, in which the mechanisms are reversible, but do not involve changes to the underlying DNA sequence. This involves regulatory systems such as DNA methylation, histone modification, nucleosome location, and noncoding RNA. The epigenome, meanwhile, is a parallel to the word genome, refers to the overall epigenetic state of a cell and can be considered essentially a network of chemical switches within our cells.

Our compendium is written for university undergraduates, graduate students, faculty and investigators at research institutes. There are 33 articles with a combined length of over 1100 pages and as such is the largest in depth, up to date treatment of epigenetics presently available.

Epigenetics Regulation and Epigenomics differs in content and quality from all others available in five ways 1) the overall coverage was approved by our Board, which includes 11 Nobel Prize winners; 2) the selection of each article and author was validated by several reviewers from major university research centers; 3) each article was then reviewed by peers from other universities; 4) a glossary of terms with definitions is provided at the beginning of each article and 5) the articles average 35 print pages — which provides several times the depth of other such compendia.

The content is divided into five sections of articles covering key epigenetics areas. These sections are Analytical Methods, Basic Molecular Mechanisms, The Epigenome, Medical Applications and Model Organisms.

Analytical Methods articles range from chromatin immunoprecipitation (ChIP), to tag sequencing (impacting epigenomics), DNA methylation analysis, high throughput epigenotyping by mass spectrometry and includes RNA methodologies which provide an understanding of aspects of gene regulation. The Basic Mechanisms section covers the cell nucleus and chromatin organization and dynamics; epigenetics of stem cells; imprinting and histone modifications and methylation; as well as epigenetic aspects of prions, twins, cloning and RNA interference and all types of regulation of gene expression. The Epigenome coverage includes computational epigenetics and the human epigenome. Medical Applications include a comprehensive article on epigenetic medicine and additional detail in several articles on the of epigenetics of cancer, the immune system and aging as well as pharmaco-epigenomics to improve cancer therapies. In fact, drugs that inhibit the DNA methyltransferases, which place methyl groups on the DNA, are now approved for clinical use in the United States for the treatment of certain cancers. This may be the beginning of a new era of cancer treatment involving epigenetic therapy. Pharmacology and emerging clinical application of RNA is also presented in this section. Model Organisms range from bacteria to protozoans as well as fungi and plants.

Our team of authors and peer reviewers are located at top rated epigenetics departments at institutions including the University of Cambridge, the University of Southern California, the University of California at Los Angeles, Washington University, St. Louis, and the National Institutes of Health. The team is truly global with authors or coauthors from the U.S., Sweden, Belgium, Germany, France, the UK, Austria, Spain, Hungary, Japan, India, China, Singapore, Canada and Israel.

Our team hopes that you, the reader, will benefit from our hard work — finding the content useful in your research as well as educational. We wish to thank our Managing Editor, Sarah Mellor, as well as our Executive Editor, Gregor Cicchetti for both their advice and hard work in the course of this project.

Larkspur, California, March 2012

Robert A. Meyers

RAMTECH Limited

List of Contributors

Julia Arand

University of Saarland

Institute for Genetics/Epigenetics

Uni Campus Bld. A2.4

66123 Saarbrücken

Germany

Andrew J. Bannister

University of Cambridge

Wellcome Trust/Cancer Research UK Gurdon Institute

Tennis Court Road

Cambridge, CB2 1QN

UK

Sailen Barik

Cleveland State University

Center for Gene Regulation in Health and Disease and Department of Biological

Geological and Environmental Sciences

College of Sciences and Health Professions

2121 Euclid Avenue

Cleveland, OH 44115

USA

Therese M. Becker

University of Sydney

Westmead Institute for Cancer Research at Westmead Millennium Institute

Westmead Hospital

Westmead

Sydney, New South Wales

Australia

Sven Beichmanis

University of Heidelberg

Kirchhoff-Institute for Physics and BioQuant Center

69120 Heidelberg

Germany

Frédéric Berger

Temasek Life Sciences Laboratory (TLL)

1 Research Link

Singapore 117604

Singapore

Yehudit Bergman

The Hebrew University Medical School

Institute for Medical Research Israel-Canada

Department of Developmental Biology and Cancer Research

Jerusalem

Israel

Autumn Bernal

Duke University

Radiation Oncology

139 Environmental Safety DUMC

Durham, NC 27710

USA

Vira Bitko

NanoBio Corporation

2311 Green Rd

Ste A

Ann Arbor, MI 48105

USA

Erin L. Bredeweg

Oregon State University

Department of Biochemistry and Biophysics

and

Center for Genome Research and

Biocomputing (CGRB)

Corvallis, OR 97331-7305

USA

Romulo Martin Brena

University of Southern California

USC Epigenome Center

Harlyne Norris Medical Research Tower

G511, 1450 Biggy Street

Los Angeles, CA 90033

USA

Michael J. Buck

State University of New York at Buffalo

Department of Biochemistry

and

The Center of Excellence in Bioinformatics and Life Sciences

701 Ellicott Street

Buffalo, NY 14203

USA

Josep Casadesús

Universidad de Sevilla

Departamento de Genética

Facultad de Biología

Apartado 1095

41080 Seville

Spain

Douglas L. Chalker

Washington University in St Louis

Biology Department

1 Brookings Drive

St Louis, MO 63130

USA

Lingyi Chen

Nankai University

The Ministry of Education

Key Laboratory of Bioactive Materials

Laboratory of Stem Cells and Developmental Biology

College of Life Sciences

94 Weijin Road

Tianjin 300071

China

Pao-Yang Chen

Department of Molecular Cell

and Developmental Biology

University of California

610 Charles Young Drive East

Los Angeles, CA 90095

USA

Bart Claes

VIB

Vesalius Research Center

Herestraat 49

Box 912

3000 Leuven

Belgium

and

KU Leuven Campus Gasthuisberg

Vesalius Research Center

Herestraat 49

Box 912

3000 Leuven

Belgium

Nicole Cloonan

The University of Queensland

Queensland Centre for Medical Genomics

Institute for Molecular Bioscience

306 Carmody Road

St Lucia, Queensland 4072

Australia

Lanelle R. Connolly

Oregon State University

Department of Biochemistry and Biophysics

and

Center for Genome Research and Biocomputing (CGRB)

Corvallis, OR 97331-7305

USA

Ignacio Cota

Universidad de Sevilla

Departamento de Genética

Facultad de Biología

Apartado 1095

41080 Seville

Spain

Marion Cremer

Ludwig Maximilians University

Biocenter

Department of Biology II

82152 Martinsried

Germany

Christoph Cremer

University of Heidelberg

Kirchhoff-Institute for Physics and BioQuant Center

69120 Heidelberg

Germany

Thomas Cremer

Ludwig Maximilians University

Biocenter

Department of Biology II

82152 Martinsried

Germany

Mark A. Dawson

University of Cambridge

Wellcome Trust/Cancer Research UK Gurdon Institute

Tennis Court Road

Cambridge, CB2 1QN

UK

and

University of Cambridge

Cambridge Institute for Medical Research

Department of Haematology

Cambridge, CB2 0XY

UK

Melvin L. DePamphilis

National Institute of Child Health and Human Development

National Institutes of Health

Building 6A

Room 3A15

9000 Rockville Pike

Bethesda, MD 20892-2753

USA

Andras Dinnyes

Szent Istvan University

Molecular Animal Biotechnology Laboratory

Hungary

and

BioTalentum Ltd

2100 Gödöllö

Hungary

Jean-Sébastien Doucet

University of Toronto

Centre for Addiction and Mental Health

Department of Pharmacology

Toronto, Ontario

Canada

Karl Ekwall

Karolinska Institutet

Department of Biosciences and Nutrition

Center for Biosciences

Novum

Huddinge

141 57 Stockholm

Sweden

Robert E. Farrell Jr.

Penn State University

Department of Biology

1031 Edgecomb Avenue

NY, PA 17403

USA

Daniel M. Fass

Broad Institute of MIT and Harvard

Stanley Center for Psychiatric Research

7 Cambridge Center

Cambridge, MA 02142

USA

Robert Feil

Centre National de la Recherche Scientific and University of Montpellier

CNRS, UMR 5535

Institute of Molecular Genetics (IGMM)

1919 route de Mende

34293 Montpellier

France

Agustin F. Fernandez

Universidad de Oviedo

Cancer Epigenetics Laboratory

Instituto Universitario de Oncología del Principado de Asturias (IUOPA)

Hospital Universitario Central de Asturias (HUCA)

Bloque Polivalente A

33006 Oviedo

Spain

Mario F. Fraga

National Center for Biotechnology (CNB) and Spanish National Research Council (CSIC)

Department of Immunology and Oncology

Cantoblanco

28049 Madrid

Spain

Michael Freitag

Oregon State University

Department of Biochemistry and Biophysics

and

Center for Genome Research and

Biocomputing (CGRB)

Corvallis, OR 97331-7305

USA

Neha Garg

Devi Ahilya University

School of Biotechnology

Khandwa Road

Indore 452001

India

and

Barkatullah University

Biotechnology Department

Bhopal 462026

India

Sarika Garg

Devi Ahilya University

School of Biotechnology

Khandwa Road

Indore 452001

India

and

Max Planck Unit for Structural

Molecular Biology

C/O DESY

Gebäude 25b

Notkestrasse 85

22607 Hamburg

Germany

and

Present address: University of Saskatchewan

Department of Psychiatry

Rm B45 HSB

107 Wiggins Road

Saskatoon, SK S7N 5E5

Canada

Sean M. Grimmond

The University of Queensland

Queensland Centre for Medical Genomics

Institute for Molecular Bioscience

306 Carmody Road

St Lucia

Queensland 4072

Australia

Ivo G. Gut

Centro Nacional de Analisis Genomico

C/Baldiri Reixac 4

08028 Barcelona

Spain

Thomas Haaf

Julius-Maximilians-University Würzburg

Institute of Human Genetics

Biozentrum

Am Hubland

97074 Würzburg

Germany

Martin Heß

Ludwig Maximilians University

Biocenter

Department of Biology II

82152 Martinsried

Germany

Ryutaro Hirasawa

Centre National de la Recherche Scientific and University of Montpellier

CNRS, UMR 5535

Institute of Molecular Genetics (IGMM)

1919 route de Mende

34293 Montpellier

France

Edward B. Holson

Broad Institute of MIT and Harvard

Stanley Center for Psychiatric Research

7 Cambridge Center

Cambridge, MA 02142

USA

Barbara Hübner

Ludwig Maximilians University

Biocenter

Department of Biology II

82152 Martinsried

Germany

Dean A. Jackson

University of Manchester

Faculty of Life Sciences

MIB 131 Princess Street

Manchester M1 7DN

UK

Randy Jirtle

Duke University

Radiation Oncology

139 Environmental Safety DUMC

Durham, NC 27710

USA

Kotaro J. Kaneko

National Institute of Child Health and Human Development

National Institutes of Health

Building 6A

Room 3A15

9000 Rockville Pike

Bethesda, MD 20892-2753

USA

Melissa M. Kemp

Broad Institute of MIT and Harvard

Chemical Biology

7, Cambridge Center

Cambridge, MA 02142

USA

Matthew J. Kohn

University at Albany

Department of Biomedical Sciences

School of Public Health and NYSTEM

New York State Department of Health

Empire State Plaza

Biggs Laboratory

C345 Albany, NY 12201

USA

Satya K. Kota

Centre National de la Recherche Scientific and University of Montpellier

CNRS, UMR 5535

Institute of Molecular Genetics (IGMM)

1919 route de Mende

34293 Montpellier

France

Keerthana Krishnan

The University of Queensland

Queensland Centre for Medical Genomics

Institute for Molecular Bioscience

306 Carmody Road

St Lucia

Queensland 4072

Australia

Anil Kumar

Devi Ahilya University

School of Biotechnology

Khandwa Road

Indore 452001

India

Diether Lambrechts

VIB Vesalius Research Center

Herestraat 49, Box 912

3000 Leuven

Belgium

and

KU Leuven Campus Gasthuisberg

Vesalius Research Center

Herestraat 49, Box 912

3000 Leuven

Belgium

Konstantin Lepikhov

University of Saarland

Institute for Genetics/Epigenetics

Uni Campus Bld. A2.4

66123 Saarbrücken

Germany

Rena Levin-Klein

The Hebrew University Medical School

Institute for Medical Research Israel-Canada

Department of Developmental Biology and Cancer Research

Jerusalem

Israel

Shen Jean Lim

National University of Singapore

Department of Biochemistry

Yong Loo Lin School of Medicine

8 Medical Drive

Singapore 117597

Singapore

Lin Liu

Nankai University

The Ministry of Education

Key Laboratory of Bioactive Materials

Laboratory of Stem Cells

and

Developmental Biology

College of Life Sciences

94 Weijin Road

Tianjin 300071

China

Alexandra Lusser

Innsbruck Medical University

Division of Molecular Biology

Biocenter

Fritz-Pregl Strasse 3

6020 Innsbruck

Austria

Javier López-Garrido

Universidad de Sevilla

Departamento de Genética

Facultad de Biología

Apartado 1095

41080 Seville

Spain

Yolanda Markaki

Ludwig Maximilians University

Biocenter

Department of Biology II

82152 Martinsried

Germany

Jason A. Motl

Washington University in St Louis

Biology Department

1 Brookings Drive

St Louis, MO 63130

USA

Wesley R. Naeimi

University of Kent

Kent Fungal Group

School of Biosciences

Stacey Building

Canterbury

Kent CT2 7NJ

UK

Björn Oback

AgResearch

Ruakura Research Centre

East Street

Private Bag 3123

Hamilton

New Zealand

Matteo Pellegrini

Department of Molecular Cell and Developmental Biology

University of California

610 Charles Young Drive East

Los Angeles, CA 90095

USA

Pallavi A. Phatale

Oregon State University

Department of Biochemistry and Biophysics

and

Center for Genome Research and Biocomputing (CGRB)

Corvallis, OR 97331-7305

USA

Paolo Piatti

Innsbruck Medical University

Division of Molecular Biology

Biocenter

Fritz-Pregl Strasse 3

6020 Innsbruck

Austria

Kyle R. Pomraning

Oregon State University

Department of Biochemistry and Biophysics

and

Center for Genome Research and Biocomputing (CGRB)

Corvallis, OR 97331-7305

USA

Jason M. Rizzo

State University of New York at Buffalo

Department of Biochemistry

and

The Center of Excellence in Bioinformatics and Life Sciences

701 Ellicott Street

Buffalo, NY 14203

USA

Lothar Schermelleh

Ludwig Maximilians University

Biocenter

Department of Biology II

82152 Martinsried

Germany

Frederick A. Schroeder

Massachusetts General Hospital

Harvard Medical School

185, Cambridge Street

6th Floor

Boston, MA 02114

USA

Annie W. Shieh

Washington University in St Louis

Biology Department

1 Brookings Drive

St Louis, MO 63130

USA

Bernard Siebens

VIB Vesalius Research Center

Herestraat 49

Box 912

3000 Leuven

Belgium

and

KU Leuven Campus Gasthuisberg

Vesalius Research Center

Herestraat 49

Box 912

3000 Leuven

Belgium

Mikiko C. Siomi

Keio University School of Medicine

Department of Molecular Biology

35 Shinanomachi

Shinjuku-ku

Tokyo 160-8582

Japan

David Skaar

Duke University

Radiation Oncology

139 Environmental Safety DUMC

Durham, NC 27710

USA

Kristina M. Smith

Oregon State University

Department of Biochemistry and Biophysics

and

Center for Genome Research and Biocomputing (CGRB)

Corvallis, OR 97331-7305

USA

Jason A. Steen

The University of Queensland

Queensland Centre for Medical Genomics

Institute for Molecular Bioscience

306 Carmody Road

St Lucia

Queensland 4072

Australia

Hilmar Strickfaden

Ludwig Maximilians University

Biocenter

Department of Biology II

82152 Martinsried

Germany

Annelie Strålfors

Karolinska Institutet

Department of Biosciences and Nutrition

Center for Biosciences

Novum

Huddinge

141 57 Stockholm

Sweden

Xiuchun Cindy Tian

University of Connecticut

Department of Animal Science

Center for Regenerative Biology

Storrs, CT 06269

USA

Joo Chuan Tong

National University of Singapore

Department of Biochemistry

Yong Loo Lin School of Medicine

8 Medical Drive

Singapore 117597

Singapore

and

Institute for Infocomm Research

Data Mining Department

1 Fusionopolis Way

No. 21-01

Connexis

South Tower

Singapore 138632

Singapore

Jörg Tost

Centre National de Génotypage

CEA-Institut de Genomique

Laboratory for Epigenetics

Bâtiment G2

2 Rue Gaston Crémieux

91000 Evry

France

and

Fondation Jean Dausset — CEPH

Laboratory for Functional Genomics

27 rue Juliette Dodu 75010

Paris

France

Mick F. Tuite

University of Kent

Kent Fungal Group

School of Biosciences

Stacey Building

Canterbury

Kent CT2 7NJ

UK

Rocio G. Urdinguio

Universidad de Oviedo

Cancer Epigenetics Laboratory

Instituto Universitario de Oncología del Principado de Asturias (IUOPA)

Hospital Universitario Central de Asturias (HUCA)

Bloque Polivalente A

33006 Oviedo

Spain

Florence F. Wagner

Broad Institute of MIT and Harvard

Stanley Center for Psychiatric Research

7 Cambridge Center

Cambridge, MA 02142

USA

Joern Walter

University of Saarland

Institute for Genetics/Epigenetics

Uni Campus Bld. A2.4

66123 Saarbrücken

Germany

Qiu Wang

Duke University

Department of Chemistry

French Family Science Center

Durham, NC 27708-0354

USA

Albert H. C. Wong

University of Toronto

Centre for Addiction and Mental Health

Departments of Psychiatry and Pharmacology

Faculty of Medicine

250 College Street

Toronto

Ontario, M5T 1R8

Canada

David L. A. Wood

The University of Queensland

Queensland Centre for Medical Genomics

Institute for Molecular Bioscience

306 Carmody Road

St Lucia

Queensland 4072

Australia

Mark Wossidlo

University of Saarland

Institute for Genetics/Epigenetics

Uni Campus Bld. A2.4

66123 Saarbrücken

Germany

Blerta Xhemalce

University of Cambridge

Wellcome Trust/Cancer Research UK Gurdon Institute

Tennis Court Road

Cambridge, CB2 1QN

UK

Anette Zeilner

Innsbruck Medical University

Division of Molecular Biology

Biocenter

Fritz-Pregl Strasse 3

6020 Innsbruck

Austria

Andreas Zunhammer

Ludwig Maximilians University

Biocenter

Department of Biology II

82152 Martinsried

Germany

Volume 1

Part I

Analytical Methods

1

RNA Methodologies

Robert E. Farrell, Jr.

Penn State University, Department of Biology, 1031, Edgecomb Avenue, NY, PA 17403, USA

1 Introduction

2 Subpopulations of RNA

2.1 Messenger RNA (mRNA)

2.2 Transfer RNA (tRNA)

2.3 Ribosomal RNA (rRNA)

2.4 Nuclear RNA