Chapter 1. Basic Concepts of Gene Expression

  1. Dr. Stefan Lorkowski9 and
  2. Dr. Paul Cullen10
  1. Dr. Paul Cullen10,*,
  2. Dr. Stefan Lorkowski9,*,
  3. Mario Kratz1,
  4. Michel Werner2,
  5. Christoph Marschall3,
  6. Hanns-Georg Klein3,*,
  7. David Goodlett4,*,
  8. Ruedi Aebersold4 and
  9. Claudia Wenner1

Published Online: 27 MAY 2004

DOI: 10.1002/352760149X.ch1

Analysing Gene Expression: A Handbook of Methods: Possibilities and Pitfalls

Analysing Gene Expression: A Handbook of Methods: Possibilities and Pitfalls

How to Cite

Cullen, P., Lorkowski, S., Kratz, M., Werner, M., Marschall, C., Klein, H.-G., Goodlett, D., Aebersold, R. and Wenner, C. (2002) Basic Concepts of Gene Expression, in Analysing Gene Expression: A Handbook of Methods: Possibilities and Pitfalls (eds S. Lorkowski and P. Cullen), Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim, FRG. doi: 10.1002/352760149X.ch1

Editor Information

  1. 9

    Institute of Arteriosclerosis Research, University of Münster, Domagkstr. 3, 48149 Münster, Germany

  2. 10

    Ogham GmbH, Mendelstr. 11, 48149 Münster, Germany

Author Information

  1. 1

    University of Münster, Münster (Germany)

  2. 2

    Service de Biochimie et Génétique Moléculaire, Gif-sur-Yvette (France)

  3. 3

    IMGM Laboratories GmbH, Martinsried (Germany)

  4. 4

    The Institute for Systems Biology, Seattle (USA)

  5. 9

    Institute of Arteriosclerosis Research, University of Münster, Domagkstr. 3, 48149 Münster, Germany

  6. 10

    Ogham GmbH, Mendelstr. 11, 48149 Münster, Germany

*Ogham GmbH, Mendelstr. 11, 48149 Münster, Germany

Publication History

  1. Published Online: 27 MAY 2004
  2. Published Print: 1 DEC 2002

ISBN Information

Print ISBN: 9783527304882

Online ISBN: 9783527601493

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Keywords:

  • gene expression;
  • basics;
  • regulation;
  • promoters;
  • expression;
  • enhancers;
  • silencers;
  • post-transcriptional regulation;
  • prokaryotes;
  • eukaryotes;
  • splicing;
  • stability and degradation;
  • protein modification;
  • protein expression;
  • mRNA;
  • housekeeping genes;
  • gene expression technologies

Summary

This chapter contains sections titled:

  • Introduction

  • Basics of transcription and translation in the cell

    • Introduction

    • Transcription

    • Translation

    • Summary

  • Regulation of transcription

    • Introduction

    • mRNA expression profiles – the transcriptome

    • Protein expression profiles – the proteome

    • Interaction between genes and proteins – the interactome

    • The transcription machinery and core promoters

    • Regulatory promoters

    • Enhancers

    • Locus control regions

    • Matrix attachment regions

    • Insulators

    • RIDGEs – Regions of increased gene expression

    • Enhanceosomes

    • Chromatin

    • Silencer elements

    • Transcription factors, repressors and co-repressors

    • Epigenetics

    • Summary and conclusions

  • Post-transcriptional regulation

    • Introduction

    • Regulation of RNA stability and degradation

    • Regulation of transcription elongation

    • Differential/alternative pre-mRNA splicing

    • Trans-RNA splicing

    • Regulation of mRNA transport

    • Directed intracellular mRNA localisation

    • Regulation of mRNA polyadenylation

    • Antisense RNA

    • RNA editing

    • Summary and conclusions

  • Post-translational modification of proteins

    • Introduction

    • Proteolytic cleavage of proteins

    • Acylation

    • Prenylation

    • Methylation

    • Sulphation

    • Phosphorylation

    • Ubiquitination

    • Glycosylation

    • Conclusions

  • Correlation of mRNA and protein expression

    • Introduction

    • Levels of mRNA and protein expression: correlations and discrepancies

    • Conclusions

  • Housekeeping genes, internal and external standards

    • What are housekeeping genes?

    • Survey of the most important housekeeping genes

    • Other commonly used housekeeping genes

    • New identified ‘maintenance genes’

    • Methods of quantification

    • Summary

  • Classification of differential gene expression technologies

    • Introduction

    • From single genes to transcriptomes

    • Methods of classification

    • Conclusions

  • Summary

  • References