L. Stirling Churchman

Department of Genetics
Harvard Medical School
New Research Building, Room 356
77 Avenue Louis Pasteur, Boston, MA 02115

tel: (617) 432-7663
email: churchman@genetics.med.harvard.edu
web: http://genetics.med.harvard.edu/churchman/

Current Experimental Interests:

Despite the abundance of genomic information, many questions remain about how the cell accesses the information encoded in the genome through RNA polymerase. My goal as an independent researcher is to determine how control of the motor mechanism of RNA polymerase (RNAP) leads to the coordination of transcription with splicing, RNA processing, chromatin remodeling and genome maintenance. I will investigate in both the nucleus and the mitochondria how factors involved in co-transcriptional processes interact with RNAP either directly or indirectly through chromatin to critically alter its transcription rate. My research strategy involves using high resolution approaches that allow the analysis of the molecular mechanism of RNAP.  As a postdoc, I developed a deep sequencing approach that observes RNAP activity in vivo at nucleotide resolution. My data led to conclusions that fundamentally change how the regulation of transcription is viewed within the cell: transcription elongation is punctuated frequently by RNAP pausing and nucleosomes create a significant barrier to elongating RNAP.  As a graduate student, I created in vitro single molecule approaches that exceed fundamental resolution limits of fluorescence microscopy which I applied to elucidate the processivity mechanism of unconventional myosins.  My lab is uniquely situated to combine single molecule in vitro approaches with genomic approaches to reveal how control of the transcriptional process results in the exquisitely choreographed transcriptome we observe.

Regulation of the RNA Polymerase Motor Mechanism In Vivo

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 at promoters is only a portion of the regulation that occurs during normal transcription and that the abnormal regulation of gene expression through changes in post-initiation events is likely to mediate a significant part of the dysregulation of cell growth and function in diseases.  Furthermore, the control of transcriptional elongation is not only essential for coordinating gene expression, but it is also involved in recruitment of chromatin modifiers that adjust chromatin structure, set histone marks and repair DNA damage.

In vitro studies have thoroughly documented the natural propensity for RNAP pause during elongation, but it is largely unknown how the cell exploits this property to control gene expression and to coordinate co-transcriptional processes6. My NET-seq data showed that RNAP II pauses frequently at defined locations throughout gene bodies which depends on elongation factors and chromatin structure.  I propose that pausing is a central component of the transcription process allowing the coordination of co-transcriptional processes such as splicing, termination, chromatin remodeling and the assembly of mRNA-protein complexes.  As these pauses are likely to be altered during the regulation of gene expression, it is essential to understand their role in the transcription process, so that post-initiation control of transcription after stimuli and during development can be appreciated and, in the longer term, the design of pharmacological perturbations can be pursued.

The long-term goals of my work are to determine how the motor mechanism of RNA polymerase is manipulated by cellular factors to integrate cellular and organismal signaling processes in order to produce correct transcriptomes and precise genetic and epigenetic states and how disruption of these mechanisms can lead to disease.


Selected Publications:

Churchman, L.S. and Weissman, J.S. (2011)  Nascent transcript sequencing visualizes transcription at nucleotide resolution. Nature 469, 368-373.

Mortensen*, K., Churchman*, L.S., Spudich, J.A., and Flyvbjerg, H.  (2010)  Optimized localization analysis for single-molecule tracking and super-resolution microscopy. Nature Methods 7, 377-381.  *equal authorship

Churchman, L.S., and Spudich, J.A.  (2007)  Colocalization of fluorescent probes: Accurate and precise registration with nanometer resolution. In Single-Molecule Techniques: A Laboratory Manual, P. Selvin and T. Ha, editors. Cold Spring Harbor Laboratory Press, 73-84.

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