Susan Janicki, Ph.D.

Assistant Professor
Gene Expression and Regulation Program
215-495-6850, Office

Introduction

With the completion of the human genome-sequencing project, it is now more apparent than ever before that we are only at the very beginning stages of understanding the mechanistic complexity required to regulate genomic functions. At the cornerstone are epigenetic mechanisms, which regulate the heritable activation and silencing of specific sets of genes. They function by directly regulating the architecture of chromatin – the packaged form of DNA in the nucleus. Currently, it is not possible to visualize the dynamic interactions of regulatory factors with single-copy endogenous genes in single cells. Insights have been largely gained using methodologies which provide only static images of genes. Therefore, our current understanding of how epigenetic and transcriptional regulatory factors are coordinated and regulated at chromatin is essentially a “black box”.

Research Summary

The Janicki laboratory is using synthetic biology to develop technologies to study transcriptional and epigenetic regulatory mechanisms in single living mammalian cells. In synthetic biology, systems that do not exist in the natural world are engineered for the purpose of simplifying them or designing new functions. Synthetic biology has already been used extensively to study genetic circuitry in yeast and bacteria – typically by measuring protein expression. Application to mammalian systems, however, has been limited by the genomic complexity and restrictive growth conditions of mammalian cells.

For these synthetic biology studies, gene elements are inserted into an inducible transcription unit, which allows DNA, RNA and proteins to be simultaneously and dynamically visualized in single living cells. These constructs are then stably integrated into single genomic sites in mammalian cells as multi-copy arrays. Reporter elements engineered into the transgene allow the productions of both RNA and protein to be directly measured. In this way, it is possible to directly visualize regulatory factor recruitment, RNA synthesis and chromatin decondensation at a molecularly defined transcription site, in real time, in single living mammalian cells.

We have used synthetic biology to investigate mechanisms of transcriptional activation and gene silencing. We are currently expanding our imaging platform and developing new systems to study non-coding RNA, disease-causing mutations, and intron-encoded microRNAs.

It is our long-term goal to use synthetic biology to develop technologies, which will merge molecular biology with high-resolution cellular imaging in order to:

1) Investigate how gene expression mechanisms are coordinated and regulated at chromatin.
2) Discover new transcriptional and epigenetic regulatory mechanisms.
3) Gain insight into how the misregulations of epigenetic and transcriptional mechanisms cause disease.
4) Develop technologies for high-throughput screening to identify and validate disease prevention and treatment therapies.

Selected Publications

Rafalska-Metcalf IU, Powers SL, Joo LM, LeRoy G and Janicki SM. Single cell analysis of transcriptional activation dynamics. PLoS ONE (accepted)

Shav-Tal Y, Darzacq X, Shenoy SM, Fusco D, Janicki SM, Spector DL and Singer RH. Dynamics of Single mRNPs in the Nuclei of Living Cells. (2004) Science 18, 1797-1800.

Janicki SM and SpectorDL. Imaging Gene Expression in Living Cells. (2004) In: Live Cell Imaging: A Laboratory Manual Goldman RD and Spector DL, editors. Cold Spring Harbor Laboratory Press, New York.

Janicki SM, Tsukamoto T, Salghetti SE, Tansey WP, Sachidanandam R, Prasanth KV, Ried T, Shav-Tal Y, Bertrand E, Singer RH and Spector DL. From Silencing to Gene Expression: Real-Time Analysis in Single Cells. (2004) Cell 116, 683-698.

Janicki SM and Spector DL. (2003) Nuclear choreography: interpretations from living cells. Current Opinion in Cell Biology 15, 149-157.

Tsukamoto T, Hashiguchi N, Janicki SM, Tumbar T, Belmont AS, Spector DL. (2000) Visualization of gene activity in living cells. Nature Cell Biology 2, 871-878.