Adam Corrigan | University College London (original) (raw)
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Papers by Adam Corrigan
Development (Cambridge, England), Jan 24, 2015
Much of development and disease concerns the generation of gene expression differences between re... more Much of development and disease concerns the generation of gene expression differences between related cells sharing similar niches. However most analyses of gene expression only assess population and time-averaged levels of steady-state transcription. The mechanisms driving differentiation are buried within snapshots of the average cell, lacking dynamic information and the diverse regulatory history experienced by individual cells. Here we use a quantitative imaging platform with large time series data sets to determine the regulation of developmental gene expression by cell cycle, lineage, motility and environment. We apply this technology to the regulation of the pluripotency gene Nanog, in mouse embryonic stem cells (ESCs). Our data reveal the diversity of cell and population-level interactions with Nanog dynamics and heterogeneity, and how this regulation responds to triggers of pluripotency. Cell cycles are highly heterogeneous and cycle time increases with Nanog reporter expr...
Methods in cell biology, 2015
In a wide range of organisms the kinetics of transcription have been found to be noisy, with &quo... more In a wide range of organisms the kinetics of transcription have been found to be noisy, with "bursts" or "pulses" of transcription interspersed with irregular periods of inactivity. The in vivo analysis of transcription dynamics can be most directly monitored using RNA stem loop motifs derived from MS2 and other bacteriophages. Here we describe the implementation of the MS2 RNA detection system and the steps required for precise measurement of transcription dynamics in highly motile cells. Automated image processing techniques are used to track large numbers of cells and measure transcription in a systematic and unbiased manner. We discuss popular methods for automatic image segmentation and frame-to-frame tracking of cells, and the considerations required to make measurements as quantitatively as possible.
Langmuir, 2009
Particle tracking microrheology (PTM) has been used to study the sol-gel transition in solvent-in... more Particle tracking microrheology (PTM) has been used to study the sol-gel transition in solvent-induced fibrillar beta-lactoglobulin gels at room temperature and pH 7. The passive nature of microrheology allowed measurements to be made around and below the critical gelation concentration. The method of superposition introduced by Larsen and Furst (Larsen, T. H.; Furst, E. M. Phys. Rev. Lett. 2008, 100, 146001) was applied to the one-particle mean square displacement (MSD), yielding a critical relaxation exponent of n = 0.58 at concentrations close to the measured critical concentration of 4% (w/v). At a higher concentration of 12% (w/v), n was observed to decrease. The pregel and gel master curves were used to find the viscoelastic moduli over 8 decades of frequency. Combined with the measured shift factors, this allowed cure curves at 1 Hz to be constructed for direct comparison with results from bulk rheology. Time-independent modulus superposition was found for all concentrations. Good agreement for concentration scaling was found between the traditional methods for characterizing gels and the recently described microrheological determination of the gel time and critical behavior.
The European Physical Journal E, 2009
Current Biology, 2014
Transcription is highly stochastic, occurring in irregular bursts. For temporal and spatial preci... more Transcription is highly stochastic, occurring in irregular bursts. For temporal and spatial precision of gene expression, cells must somehow deal with this noisy behavior. To address how this is achieved, we investigated how transcriptional bursting is entrained by a naturally oscillating signal, by direct measurement of transcription together with signal dynamics in living cells. We identify a Dictyostelium gene showing rapid transcriptional oscillations with the same period as extracellular cAMP signaling waves. Bursting approaches antiphase to cAMP waves, with accelerating transcription cycles during differentiation. Although coupling between signal and transcription oscillations was clear at the population level, single-cell transcriptional bursts retained considerable heterogeneity, indicating that transcription is not governed solely by signaling frequency. Previous studies implied that burst heterogeneity reflects distinct chromatin states. Here we show that heterogeneity is determined by multiple intrinsic and extrinsic cues and is maintained by a transcriptional persistence. Unusually for a persistent transcriptional behavior, the lifetime was only 20 min, with rapid randomization of transcriptional state by the response to oscillatory signaling. Linking transcription to rapid signaling oscillations allows reduction of gene expression heterogeneity by temporal averaging, providing a mechanism to generate precision in cell choices during development.
Development (Cambridge, England), Jan 24, 2015
Much of development and disease concerns the generation of gene expression differences between re... more Much of development and disease concerns the generation of gene expression differences between related cells sharing similar niches. However most analyses of gene expression only assess population and time-averaged levels of steady-state transcription. The mechanisms driving differentiation are buried within snapshots of the average cell, lacking dynamic information and the diverse regulatory history experienced by individual cells. Here we use a quantitative imaging platform with large time series data sets to determine the regulation of developmental gene expression by cell cycle, lineage, motility and environment. We apply this technology to the regulation of the pluripotency gene Nanog, in mouse embryonic stem cells (ESCs). Our data reveal the diversity of cell and population-level interactions with Nanog dynamics and heterogeneity, and how this regulation responds to triggers of pluripotency. Cell cycles are highly heterogeneous and cycle time increases with Nanog reporter expr...
Methods in cell biology, 2015
In a wide range of organisms the kinetics of transcription have been found to be noisy, with &quo... more In a wide range of organisms the kinetics of transcription have been found to be noisy, with "bursts" or "pulses" of transcription interspersed with irregular periods of inactivity. The in vivo analysis of transcription dynamics can be most directly monitored using RNA stem loop motifs derived from MS2 and other bacteriophages. Here we describe the implementation of the MS2 RNA detection system and the steps required for precise measurement of transcription dynamics in highly motile cells. Automated image processing techniques are used to track large numbers of cells and measure transcription in a systematic and unbiased manner. We discuss popular methods for automatic image segmentation and frame-to-frame tracking of cells, and the considerations required to make measurements as quantitatively as possible.
Langmuir, 2009
Particle tracking microrheology (PTM) has been used to study the sol-gel transition in solvent-in... more Particle tracking microrheology (PTM) has been used to study the sol-gel transition in solvent-induced fibrillar beta-lactoglobulin gels at room temperature and pH 7. The passive nature of microrheology allowed measurements to be made around and below the critical gelation concentration. The method of superposition introduced by Larsen and Furst (Larsen, T. H.; Furst, E. M. Phys. Rev. Lett. 2008, 100, 146001) was applied to the one-particle mean square displacement (MSD), yielding a critical relaxation exponent of n = 0.58 at concentrations close to the measured critical concentration of 4% (w/v). At a higher concentration of 12% (w/v), n was observed to decrease. The pregel and gel master curves were used to find the viscoelastic moduli over 8 decades of frequency. Combined with the measured shift factors, this allowed cure curves at 1 Hz to be constructed for direct comparison with results from bulk rheology. Time-independent modulus superposition was found for all concentrations. Good agreement for concentration scaling was found between the traditional methods for characterizing gels and the recently described microrheological determination of the gel time and critical behavior.
The European Physical Journal E, 2009
Current Biology, 2014
Transcription is highly stochastic, occurring in irregular bursts. For temporal and spatial preci... more Transcription is highly stochastic, occurring in irregular bursts. For temporal and spatial precision of gene expression, cells must somehow deal with this noisy behavior. To address how this is achieved, we investigated how transcriptional bursting is entrained by a naturally oscillating signal, by direct measurement of transcription together with signal dynamics in living cells. We identify a Dictyostelium gene showing rapid transcriptional oscillations with the same period as extracellular cAMP signaling waves. Bursting approaches antiphase to cAMP waves, with accelerating transcription cycles during differentiation. Although coupling between signal and transcription oscillations was clear at the population level, single-cell transcriptional bursts retained considerable heterogeneity, indicating that transcription is not governed solely by signaling frequency. Previous studies implied that burst heterogeneity reflects distinct chromatin states. Here we show that heterogeneity is determined by multiple intrinsic and extrinsic cues and is maintained by a transcriptional persistence. Unusually for a persistent transcriptional behavior, the lifetime was only 20 min, with rapid randomization of transcriptional state by the response to oscillatory signaling. Linking transcription to rapid signaling oscillations allows reduction of gene expression heterogeneity by temporal averaging, providing a mechanism to generate precision in cell choices during development.