The Chromatin, Epigenetics and Gene Expression course is designed for students, postdocs, and principal investigators who have recently ventured into the exciting area of gene regulation. Emphasis will be placed on exposing students to a broad array of methodologies to study gene regulation, chromatin structure and dynamics, including both state-of-the-art and well-developed methods.

Students will perform widely used techniques such as quantitative RT-PCR, reporter assays of enhancer activity, and chromatin immunoprecipitation (ChIP) coupled with sequencing (ChIP-seq). They will generate high-throughput sequencing data to localize Pol II genome-wide, and apply a basic informatics pipeline to analyze the results. Students will also isolate transcription factor complexes and assess their activity in functional assays. They will also use RNAi to knock-down specific factors and evaluate the effects on gene expression.

This course will provide the basic concepts for different methods to analyze the chromatin architecture of the genome. Students will perform Chromosome Conformation Capture (3C) experiments, together with other approaches aimed to interrogate the 3D organization of genomes. Moreover, we will discuss the computational methods required to analyze these data.

Students will learn how to assemble recombinant chromatin and use biophysical methods such as FRET to assay the activity of chromatin remodeling enzymes. They will also learn principles of enzyme kinetics and will apply these to quantify the remodeling reactions.

Given the broad biological roles for DNA-binding transcription factors, and emerging roles of non-coding RNAs in transcription regulation, Electrophoretic Mobility Shift Assays (EMSAs) are again becoming widely used for assessing transcription factor binding to regulatory DNA or RNA elements.  Students will learn how to perform and interpret EMSA experiments, using both microscale thermophoresis and gel-based methods.  Students will also perform in vitro transcription reactions that will allow them to determine whether specific factors (e.g. protein or ncRNA) directly affect transcription.

Experience with basic recombinant DNA techniques is a prerequisite for admission to this course. Lectures by the instructors will cover the current state of the gene expression field, theoretical aspects of the methodology, and broader issues regarding strategies for investigating the regulation of gene expression in eukaryotes. Emphasis will be placed on advantages and limitations of specific techniques, and data interpretation. The students are encouraged and expected to actively participate in these discussions.

Guest lecturers are experts in the field who will discuss contemporary paradigms in eukaryotic gene regulation and technical approaches to interrogate new systems. From the guest lectures and discussions, students will learn to design effective experiments, properly interpret their own data, and critically evaluate the gene expression literature.

Applications from prospective trainees with an interest in cancer-related research are particularly encouraged to apply

Support & Stipends

Major support provided by the National Cancer Institute

Stipends are available to offset tuition costs as follows:

US applicants (National Cancer Institute)
Interdisciplinary Fellowships (transitioning from outside biology)  & Scholarships (transitioning from other biological disciplines) (Helmsley Charitable Trust)
International applicants (Howard Hughes Medical Institute)

Please indicate your eligibility for funding in your stipend request submitted when you apply to the course. Stipend requests do not affect selection decisions made by the instructors.