This textbook aims to describe the fascinating area of eukaryotic gene regulation for graduate students in all areas of the biomedical sciences. Gene expression is essential in shaping the various phenotypes of cells and tissues and as such, regulation of gene expression is a fundamental aspect of nearly all processes in physiology, both in healthy and in diseased states. This pivotal role for the regulation of gene expression makes this textbook essential reading for students of all the biomedical sciences, in order to be better prepared for their specialized disciplines.
A complete understanding of transcription factors and the processes that alter their activity is a major goal of modern life science research. The availability of the whole human genome sequence (and that of other eukaryotic genomes) and the consequent development of next-generation sequencing technologies have significantly changed nearly all areas of the biological sciences. For example, the genome-wide location of histone modifications and transcription factor binding sites, such as provided by the ENCODE consortium, has greatly improved our understanding of gene regulation. Therefore, the focus of this book is the description of the post-genome understanding of gene regulation.
The purpose of this book is to provide, in a condensed form, an overview on the present understanding of the mechanisms of gene regulation. The authors are not aiming to compete with comprehensive treatises, but rather focus on the essentials. Therefore, the authors have favored a high figure-to-text ratio following the rule stating that "a picture tells more than thousand words".
The content of the book is based on the lecture course, which is given by Prof. Carlberg since 2001 at the University of Eastern Finland in Kuopio. The book is subdivided into 4 sections and 13 chapters. Following the Introduction there are three sections, which take a view on gene regulation from the perspective of transcription factors, chromatin and non-coding RNA, respectively. Besides its value as a textbook, Mechanisms of Gene Regulation will be a useful reference for individuals working in biomedical laboratories.
Prof. Carsten Carlberg: Professor for biochemistry at the School of Medicine, Institute of Biomedicine at the University of Eastern Finland. The main research interests of Prof. Carlberg are (epi)genomics of nuclear receptors and their ligands with special focus on vitamin D. So far he published more than 190 papers (H-index 50). Since 2003 he is lecturing yearly the course "Nutrigenomics", which is the basis of this textbook. Together with Dr. Molnar he also published the Springer textbook "Mechanisms of gene regulation". Dr. Ferdinand Molnar: Senior researcher at the School of Pharmacy, Institute of Biopharmacy, University of Eastern Finland. The main research interests of Dr. Molnar are the molecular structure of nuclear receptor proteins and their natural and synthetic ligands, on which he published more than 20 papers (H-index 14). Together with Prof. Carlberg he published the Springer textbook "Mechanisms of gene regulation".
Section A: Introduction I. Overview: What is gene expression? II. The impact of chromatin Section B: Transcription factor view III. The basal transcriptional machinery IV. Transcription factors V. Linking signal transduction and gene regulation VI. Switching genes on and off at the example of nuclear receptors VII. Mapping the genome Section C: Chromatin view VIII. Chromatin modifiers IX. Genomic imprinting X. The epigenome XI: Chromatin remodeling XII. Chromatin architecture Section D: Non-coding RNA view XIII. Regulatory RNA