Preface

The Eukaryotic Gene Expression course is designed to provide scientists from diverse backgrounds with a comprehensive introduction to the concepts, strategies, and techniques employed in eukaryotic gene expression research. The course is intended for researchers who wish to understand the mechanisms involved in regulating the expression of a particular gene or the activities of a particular transcription factor that has been implicated in an important cellular process or whose aberrant function is associated with diseases. The curriculum for this course embodies three components: (1) a rigorous and comprehensive set of laboratory experiments; (2) a series of detailed theoretical lectures by the instructors describing current knowledge, concepts, techniques, and strategies employed in gene expression research; and (3) a series of seminars by invited speakers describing their research, with a emphasis on unique and imaginative approaches at the forefront of gene expression field.

The laboratory experiments included in the course provide hands-on experience with a broad array of techniques that are employed during a typical analysis of transcriptional regulation including but not restricted to nuclear extract preparation, in vitro transcription assays, and measurement of transcription factor binding. Methods for the assembly and analysis of chromatin in vitro and chromatin remodeling assays are used to demonstrate the role of chromatin in transcriptional regulation. Affinity chromatography methods are employed to investigate multi-protein regulatory complexes. Methods for analyzing promoter and enhancer function and gene expression in vivo include cell-based assays, such as transient transfection or reporter plasmids into cultured cells, chromatin immunoprecipitation, and gene silencing by RNA interference. Bioinformatic tools for analyzing genomic data sets will be used to analyze ChIP-chip and Chip-seq data sets. Finally recent methods for assessing the three-dimensional organization of the genome (3C and HiC) will also be used. Overall, the goal of the experimental section is to provide students with sufficient experience to allow them to employ the techniques in their own laboratories.

The lecture component of the course is designed to ensure that students learn the relevant background material, fundamental concepts, and current trends in the field of transcriptional regulation. Lecture topics include an introduction to the general transcriptional machinery, current ideas about activation mechanisms, the relationship of chromatin structure to gene regulation, theoretical aspects of DNA-protein interaction, and methods to identify targets of transcription factors. Descriptions of the techniques taught in the laboratory, as well as descriptions of additional relevant approaches are included in the lectures. An emphasis is placed on the advantages and limitations of each technique, along with the appropriate interpretation of results obtained. The students are encouraged to participate actively in these discussions. From the lectures and discussion, the students learn to design effective experiments, to evaluate their own data, and to critically evaluate the gene expression literature.