Regulation of Gene Expression

The control of gene expression is regulated in a highly organized fashion to ensure specific genes are expressed at the appropriate times and levels in response to various genetic and environmental stimuli. In eukaryotes, gene expression is controlled at multiple levels from transcription factor-mediated recruitment of the basal transcription machinery at specific gene promoters to processing and maturation of the RNA transcript. Disruption of these events in humans contributes to many pathologies including cancer, metabolic syndromes, and developmental disorders. Faculty who are investigating the regulation of gene expression are interested in numerous topics including transcriptional regulatory pathways in pro- and eukaryotes, DNA and RNA interactions with proteins, RNA processing and the functions of catalytic RNA, chromatin modification and remodeling, and three-dimensional organization of genes in the nucleus. Research employs a variety of model organisms and utilizes an array of modern techniques in biochemistry and molecular, cellular, and structural biology to elucidate the mechanisms that govern gene expression in pro- and eukaryotes.

Primary Faculty

Peter Freddolino, Ph.D.

Bacterial chromosomal structure and its effect on gene regulation, structure-function relationships in transcriptional regulators, merging experimental and computational data in protein-DNA and protein-RNA binding free energy landscapes

Daniel Goldman, Ph.D.

Identification of signaling pathways, chromatin alterations, and gene expression programs that drive central nervous system regeneration using the retina as a model system

Tom Kerppola, Ph.D.

Protein interactions and modifications in living cells and animals; roles of transcription factor complexes in the control of gene expression

Stephen Ragsdale, Ph.D.

Molecular studies of the human nuclear receptor (Rev-Erb) involved in coupling metabolism to the circadian rhythm; regulation of gene expression by heme, redox poise, and gaseous signaling molecules (CO & NO) 

Kaushik Ragunathan, Ph.D.

Molecular mechanisms that define how histone modifications and the dynamic interactions of histones with histone binding proteins encode stable and heritable patterns of gene expression

Audrey Seasholtz, Ph.D.

Molecular regulation of key mediators of the mammalian stress response: Corticotropin-Releasing Hormone (CRH), CRH receptors and binding protein, and corticosteroid receptors; dysregulation of the stress response in depression, anxiety disorders, and addiction

Raymond Trievel, Ph.D.

Chemical and structural biology of enzymes that covalently modify histones, transcription factors, and other nuclear proteins; current research focuses on elucidating the molecular mechanisms underlying the specificities of histone methyltransferases and demethylases and on developing new assays and reagents to characterize them

David Turner, Ph.D.

Transcriptional and post-transcriptional mechanisms that control neuronal differentiation; regulation of gene expression in the mammalian retina by microRNAs and other small RNAs

Michael Uhler, Ph.D.

Neuronal signaling and gene expression in the context of human neurologic and psychiatric disorders

Anne Vojtek, Ph.D.

Molecular and biochemical analysis of signaling pathways that regulate cell proliferation and neural differentiation

Chase Weidmann, Ph.D.

Integrating massively parallel sequencing and proteomics technologies to measure cell-wide effects of chromatin-associated ribonucleoprotein complexes on gene regulation

Yan Zhang, Ph.D.

Biology, mechanisms, and technological applications of bacterial CRISPR-Cas systems

Secondary Joint Faculty

Renny Franceschi, Ph.D.

Control of gene expression in osteoblasts, the cells that produce and mineralize the extracellular matrix of bone

Roland Kwok, Ph.D.

How protein post-translational modifications, especially acetylation and phosphorylation, alter protein function in cancer cells

Brian Ross, Ph.D.

Molecular imaging of biological processes in living tissue, including noninvasive detection of molecular signaling events to investigate cancer growth and response to therapy

Debra Thompson, Ph.D.

Molecular studies of the function of the mammalian retina, including mechanisms that control signal transduction and tissue-specific gene expression in the retinal pigment epithelium

Nils Walter, Ph.D.

Powerful single molecule studies of mechanistic structure-dynamics-function relationships in RNAs of biomedical and bioanalytical significance; current work ranges from small bacterial riboswitches to RNA-protein complexes involved in human disease