BBS Faculty Member - Stirling Churchman

Stirling Churchman

Department of Genetics

Harvard Medical School
New Research Building, Room 0356
77 Ave. Louis Pasteur
Boston, MA 02115
Tel: 617-432-1917
Fax: 617-367-8346
Email: churchman@genetics.med.harvard.edu
Visit my lab page here.



How do co-transcriptional processes regulate RNA polymerase as it travels along gene bodies? How does this control result in the correct identity and subsequent fate of RNA transcripts? Are these events coordinated across the genome during the execution of gene expression programs? We study the molecular mechanism and functional consequence of transcription elongation within the context of the cell. For this, we investigate the entire system of cellular factors that affect transcription as well as the upstream signaling pathways and the downstream fate of RNA messages.

Transcriptional control is at the heart of developmental, physiological, and disease processes, yet our understanding of transcriptional regulation is primarily limited to events occurring at gene promoters. It is now clear that canonical transcriptional control during initiation is only a portion of the regulation that occurs during gene transcription. Co-transcriptional processes, such as mRNA capping, splicing, chromatin remodeling and the recruitment of RNA binding proteins, must coordinate their action with the progression of RNA polymerase. Many of the regulatory cellular factors ride along with RNA polymerase on its unstructured and dynamically modified C-terminal domain. We seek to understand how these factors precisely coordinate transcription elongation with co-transcriptional processes.

To address these questions, we develop high resolution global strategies to quantitatively observe the density and composition of the RNA polymerase elongation complex. For example, we established a strategy, nascent elongating transcript sequencing (NET-seq), that exploits the extraordinary stability of the DNA-RNA-RNA polymerase ternary complex to capture nascent transcripts directly from live cells (Churchman and Weissman, Nature, 2011). The identity and abundance of the 3’ end of purified transcripts are revealed by deep sequencing thus providing a quantitative, strand-specific measure of RNA polymerase (RNAP) density with single nucleotide precision. NET-seq, by resulting in a non-perturbative measure of transcription initiation, elongation and termination, allows for the in-depth investigation of transcriptional complexities and provides insight into the in vivo dynamics of RNAP that are directly comparable to in vitro biophysical studies. We are applying NET-seq to the nuclear and mitochondrial genomes in human cells and in yeast.

In addition, we are also developing proteomic strategies to study transcription elongation using mass spectroscopy and single molecule fluorescence.



Last Update: 5/28/2013



Publications

For a complete listing of publications click here.

 


 



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