Daniel R. Larson, Ph.D.
Daniel R. Larson, Ph.D.
Investigator
Head, Systems Biology of Gene Expression
NIH Stadtman Investigator

The primary goal of Dan Larson's laboratory is to understand gene expression in eukaryotic cells, starting from the mechanistic behavior of individual macromolecules and proceeding to their regulation in cells and tissue. The laboratory utilizes a battery of biophysical and molecular approaches, including single-molecule microscopy, fluorescence fluctuation analysis, RNA visualization in fixed and living cells, and computational modeling of gene regulation. Dr. Larson helped pioneer in vivo single molecule studies of transcription and splicing. The view that has emerged from these studies is that gene regulation is a dynamic process resulting in stochastic variation within populations. This 'noise' in gene expression influences phenotype selection and disease progression.

Areas of Expertise
1) transcription, 2) splicing, 3) single-molecule microscopy, 4) RNA, 5) stochastic gene expression, 6) non-coding RNA

Contact Info

Daniel R. Larson, Ph.D.
Center for Cancer Research
National Cancer Institute
Building 41, Room B201
Bethesda, MD 20892
Ph: 301-496-0986
dan.larson@nih.gov

Gene expression refers to the sum of processes that enable cells to control their complement of RNA, and the study of gene expression has been spurred by genome-wide techniques such as microarrays and chromatin immunoprecipitation. Placing these data within a cellular context to reveal the underlying mechanisms of gene regulation has been a central challenge in the field of systems biology. In recent years, through parallel advances in microscopy, fluorescent probe development, and computational modeling, it has become possible to describe gene expression in a fundamentally different way: one can now directly observe single molecules of RNA in living and fixed cells using the fluorescence microscope. This direct measurement of the first steps of gene expression provides an exquisite picture of gene regulation in intact cells. Genetic networks can be viewed in their native context, with spatial resolution on the order of nanometers and time resolution on the order of milliseconds. The view that has emerged from these studies is that gene regulation is an extremely dynamic process where the random behavior of individual molecules plays an important role in determining how a cell controls expression levels. In a range of organisms it is now becoming clear that stochastic effects- 'noise' in gene expression - influences phenotype selection and disease progression. For example, we demonstrated how yeast uses multiple kinetic modes of transcription to establish cellular mRNA levels with tunable variability.

We further demonstrated how transcription factors search throughout the nucleus to find their binding sites, and we described how this mechanism results in a system which is finely balanced for efficiency and dynamic control. The mechanisms of genetic control in higher eukaryotes, where cells are specialized for particular expression programs, are more complicated than in single-celled organisms, and future work is aimed at developing a holistic understanding of the interplay between genetic elements, nuclear structure, epigenetic factors, and dynamics in controlling mRNA levels. Our goal is to achieve a quantitative understanding of the factors which control the levels of mRNA in the cell. In addition to elucidating the mechanisms of mRNA regulation, we also seek to understand the cellular role of non-coding RNAs in modulating gene expression. This general class of RNAs, identified through sequencing, is largely uncharacterized, necessitating in vivo mechanistic studies where these RNAs can be observed functioning in their native context. Finally, we aim to utilize these studies of gene regulation to create genes which can be manipulated with spatial and temporal precision: we have created 'caged' promoters which can be turned on with photons in the living cell.

Thus, the projects in the laboratory are loosely divided into several areas including: 1) deciphering the role of transcription factor dynamics in controlling transcription in vivo; 2) developing computational models of gene expression for single genes and networks; 3) understanding the role of nuclear structure in modulating gene expression; 4) developing optogenetic methods for controlling single genes in situ; and 5) reconstituting in vitro transcription which quantitatively recapitulates in vivo behavior.

Scientific Focus Areas:
Biomedical Engineering and Biophysics, Cell Biology, Chromosome Biology, Systems Biology
  1. Lenstra TL, Coulon A, Chow CC, Larson DR.
    Mol Cell. 60: 597-610, 2015. [ Journal Article ]
  2. Coulon A, Ferguson ML, de Turris V, Palangat M, Chow CC, Larson DR.
    eLife. 3: 10.7554/eLife.03939, 2014. [ Journal Article ]
  3. Larson D, Zenklusen D, Wu B, Chao J, Singer R.
    Science. 332: 475-8, 2011. [ Journal Article ]
  4. Trcek T, Larson DR, Moldón A, Query CC, Singer RH.
    Cell. 147: 1484-97, 2011. [ Journal Article ]
  5. Zenklusen D, Larson DR, Singer RH.
    Nat. Struct. Mol. Biol. 15: 1263-71, 2008. [ Journal Article ]

The primary goal of Dan Larson's laboratory is to understand gene expression in eukaryotic cells, starting from the mechanistic behavior of individual macromolecules and proceeding to their regulation in cells and tissue. The laboratory utilizes a battery of biophysical and molecular approaches, including single-molecule microscopy, multiphoton microscopy, fluorescence fluctuation analysis, RNA visualization in fixed and living cells, and computational modeling of dynamic gene regulation. Dr. Larson was trained in biophysics, receiving a B.S. in physics from The Ohio State University and then a Ph. D in biophysics from Cornell University working in the laboratory of Watt W. Webb. During this time, he developed a range of optical methods for interrogating macromolecular interactions in living cells. As a joint postdoctoral fellow in the laboratories of Robert Singer and John Condeelis, he helped pioneer in vivo single molecule studies of transcription. Currently, the lab focuses on the regulation and function of RNA in a cell-biological context, including transcription, splicing, post-transcriptional processing, and decay. The large and ever-growing catalog of cellular RNAs and their multiple roles in gene regulation and disease progression makes this field an exciting and dynamic area of research.

Name Position
Huimin Chen Ph.D. Postdoctoral Fellow (CRTA)
Tineke Lenstra Ph.D. Postdoctoral Fellow (Visiting)
Murali Palangat Ph.D. Research Biologist
Simona Patange B.S. Predoctoral Fellow (IRTA)
Joseph Rodriguez Ph.D. Postdoctoral Fellow (CRTA)
Yihan Wan Ph.D. Postdoctoral Fellow (Visiting)
Matthew Ferguson, Ph.D.
Postdoctoral Fellow
2011 - 2013

Assistant Professor, Department of Physics
Boise State University
Boise, ID

Dr. Ferguson's current research focuses on understanding the physical basis of transcriptional regulation and splcing of RNA in eukaryotes by single molecule live cell fluorescence microscropy. View Dr. Ferguson's profile.


 

Antoine Coulon, Ph.D.
Postdoctoral Fellow
2011 - 2015

Institute Curie, Group Leader, CNRS
Paris, France

View Dr. Coulon's profile.


 

Research

Gene expression refers to the sum of processes that enable cells to control their complement of RNA, and the study of gene expression has been spurred by genome-wide techniques such as microarrays and chromatin immunoprecipitation. Placing these data within a cellular context to reveal the underlying mechanisms of gene regulation has been a central challenge in the field of systems biology. In recent years, through parallel advances in microscopy, fluorescent probe development, and computational modeling, it has become possible to describe gene expression in a fundamentally different way: one can now directly observe single molecules of RNA in living and fixed cells using the fluorescence microscope. This direct measurement of the first steps of gene expression provides an exquisite picture of gene regulation in intact cells. Genetic networks can be viewed in their native context, with spatial resolution on the order of nanometers and time resolution on the order of milliseconds. The view that has emerged from these studies is that gene regulation is an extremely dynamic process where the random behavior of individual molecules plays an important role in determining how a cell controls expression levels. In a range of organisms it is now becoming clear that stochastic effects- 'noise' in gene expression - influences phenotype selection and disease progression. For example, we demonstrated how yeast uses multiple kinetic modes of transcription to establish cellular mRNA levels with tunable variability.

We further demonstrated how transcription factors search throughout the nucleus to find their binding sites, and we described how this mechanism results in a system which is finely balanced for efficiency and dynamic control. The mechanisms of genetic control in higher eukaryotes, where cells are specialized for particular expression programs, are more complicated than in single-celled organisms, and future work is aimed at developing a holistic understanding of the interplay between genetic elements, nuclear structure, epigenetic factors, and dynamics in controlling mRNA levels. Our goal is to achieve a quantitative understanding of the factors which control the levels of mRNA in the cell. In addition to elucidating the mechanisms of mRNA regulation, we also seek to understand the cellular role of non-coding RNAs in modulating gene expression. This general class of RNAs, identified through sequencing, is largely uncharacterized, necessitating in vivo mechanistic studies where these RNAs can be observed functioning in their native context. Finally, we aim to utilize these studies of gene regulation to create genes which can be manipulated with spatial and temporal precision: we have created 'caged' promoters which can be turned on with photons in the living cell.

Thus, the projects in the laboratory are loosely divided into several areas including: 1) deciphering the role of transcription factor dynamics in controlling transcription in vivo; 2) developing computational models of gene expression for single genes and networks; 3) understanding the role of nuclear structure in modulating gene expression; 4) developing optogenetic methods for controlling single genes in situ; and 5) reconstituting in vitro transcription which quantitatively recapitulates in vivo behavior.

Scientific Focus Areas:
Biomedical Engineering and Biophysics, Cell Biology, Chromosome Biology, Systems Biology

Publications

  1. Lenstra TL, Coulon A, Chow CC, Larson DR.
    Mol Cell. 60: 597-610, 2015. [ Journal Article ]
  2. Coulon A, Ferguson ML, de Turris V, Palangat M, Chow CC, Larson DR.
    eLife. 3: 10.7554/eLife.03939, 2014. [ Journal Article ]
  3. Larson D, Zenklusen D, Wu B, Chao J, Singer R.
    Science. 332: 475-8, 2011. [ Journal Article ]
  4. Trcek T, Larson DR, Moldón A, Query CC, Singer RH.
    Cell. 147: 1484-97, 2011. [ Journal Article ]
  5. Zenklusen D, Larson DR, Singer RH.
    Nat. Struct. Mol. Biol. 15: 1263-71, 2008. [ Journal Article ]

Biography

The primary goal of Dan Larson's laboratory is to understand gene expression in eukaryotic cells, starting from the mechanistic behavior of individual macromolecules and proceeding to their regulation in cells and tissue. The laboratory utilizes a battery of biophysical and molecular approaches, including single-molecule microscopy, multiphoton microscopy, fluorescence fluctuation analysis, RNA visualization in fixed and living cells, and computational modeling of dynamic gene regulation. Dr. Larson was trained in biophysics, receiving a B.S. in physics from The Ohio State University and then a Ph. D in biophysics from Cornell University working in the laboratory of Watt W. Webb. During this time, he developed a range of optical methods for interrogating macromolecular interactions in living cells. As a joint postdoctoral fellow in the laboratories of Robert Singer and John Condeelis, he helped pioneer in vivo single molecule studies of transcription. Currently, the lab focuses on the regulation and function of RNA in a cell-biological context, including transcription, splicing, post-transcriptional processing, and decay. The large and ever-growing catalog of cellular RNAs and their multiple roles in gene regulation and disease progression makes this field an exciting and dynamic area of research.

Team

Name Position
Huimin Chen Ph.D. Postdoctoral Fellow (CRTA)
Tineke Lenstra Ph.D. Postdoctoral Fellow (Visiting)
Murali Palangat Ph.D. Research Biologist
Simona Patange B.S. Predoctoral Fellow (IRTA)
Joseph Rodriguez Ph.D. Postdoctoral Fellow (CRTA)
Yihan Wan Ph.D. Postdoctoral Fellow (Visiting)

Alumni

Matthew Ferguson, Ph.D.
Postdoctoral Fellow
2011 - 2013

Assistant Professor, Department of Physics
Boise State University
Boise, ID

Dr. Ferguson's current research focuses on understanding the physical basis of transcriptional regulation and splcing of RNA in eukaryotes by single molecule live cell fluorescence microscropy. View Dr. Ferguson's profile.


 

Antoine Coulon, Ph.D.
Postdoctoral Fellow
2011 - 2015

Institute Curie, Group Leader, CNRS
Paris, France

View Dr. Coulon's profile.


 

Software