Single-cell Transcription Research Articles

Kv3.3b expression defines the shape of the complex spike in the Purkinje cell

The complex spike (CS) in cerebellar Purkinje Cells (PC) is not an all-or-nothing phenomena as originally proposed, but shows variability depending on the spiking behavior of the Inferior Olive and intrinsic variability in the number and shape of spikelets. The potassium channel Kv3.3b, which has been proposed to undergo developmental changes during the postnatal PC maturation, has been shown to be crucial for the repolarization of the spikelets in the CS. We address here the regulation of the intrinsic CS variability by the expression of inactivating Kv3.3 channels in PCs by combining patch-clamp recordings and single-cell PCR methods on the same neurons, using a technique that we recently optimized to correlate single cell transcription levels with membrane ion channel electrophysiology. We show that while the inactivating TEA sensitive Kv3.3 current peak intensity increases with postnatal age, the channel density does not, arguing against postnatal developmental changes of Kv3.3b expression. Real time PCR of Kv3.3b showed a high variability from cell to cell, correlated with the Kv3.3 current density, and suggesting that there are no mechanisms regulating these currents beyond the mRNA pool. We show a significant correlation between normalized quantity of Kv3.3b mRNA and both the number of CS spikelets and their rate of voltage fluctuation, linking the intrinsic CS shape directly to the Kv3.3b mRNA pool. Comparing the observed cell-to-cell variance with studies on transcriptional noise suggests that fluctuations of the Kv3.3b mRNA pool are possibly not regulated but represent merely transcriptional noise, resulting in intrinsic variability of the CS.

Quantitative, Non-Disruptive Monitoring of Transcription in Single Cells with a Broad-Host Range GFP-luxCDABE Dual Reporter System

A dual promoter probe system based on a tandem bi-cistronic GFP-luxCDABE reporter cassette is described and implemented. This system is assembled in two synthetic, modular, broad-host range plasmids based on pBBR1 and RK2 origins of replication, allowing its utilization in an extensive number of gram-negative bacteria. We analyze the performance of this dual cassette in two hosts, Escherichia coli and Pseudomonas putida, by examining the induction properties of the lacIq-Ptrc expression system in the first host and the Pb promoter of the benzoate degradation pathway in the second host. By quantifying the bioluminescence signal produced through the expression of the lux genes, we explore the dynamic range of induction for the two systems (Ptrc-based and Pb-based) in response to the two inducers. In addition, by quantifying the fluorescence signals produced by GFP expression, we were able to monitor the single-cell expression profile and to explore stochasticity of the same two promoters by flow cytometry. The results provided here demonstrate the power of the dual GFP-luxCDABE cassette as a new, single-step tool to assess promoter properties at both the population and single-cell levels in gram-negative bacteria.

Neuronal Classification and Marker Gene Identification via Single-Cell Expression Profiling of Brainstem Vestibular Neurons Subserving Cerebellar Learning

Identification of marker genes expressed in specific cell types is essential for the genetic dissection of neural circuits. Here we report a new strategy for classifying heterogeneous populations of neurons into functionally distinct types and for identifying associated marker genes. Quantitative single-cell expression profiling of genes related to neurotransmitters and ion channels enables functional classification of neurons; transcript profiles for marker gene candidates identify molecular handles for manipulating each cell type. We apply this strategy to the mouse medial vestibular nucleus (MVN), which comprises several types of neurons subserving cerebellar-dependent learning in the vestibulo-ocular reflex. Ion channel gene expression differed both qualitatively and quantitatively across cell types and could distinguish subtle differences in intrinsic electrophysiology. Single-cell transcript profiling of MVN neurons established six functionally distinct cell types and associated marker genes. This strategy is applicable throughout the nervous system and could facilitate the use of molecular genetic tools to examine the behavioral roles of distinct neuronal populations.

Massively Parallel Single-Molecule and Single-Cell Emulsion Reverse Transcription Polymerase Chain Reaction Using Agarose Droplet Microfluidics

A microfluidic device for performing single copy, emulsion Reverse Transcription Polymerase Chain Reaction (RT-PCR) within agarose droplets is presented. A two-aqueous-inlet emulsion droplet generator was designed and fabricated to produce highly uniform monodisperse picoliter agarose emulsion droplets with RT-PCR reagents in carrier oil. Template RNA or cells were delivered from one inlet with RT-PCR reagents/cell lysis buffer delivered separately from the other. Efficient RNA/cell encapsulation and RT-PCR at the single copy level was achieved in agarose-in-oil droplets, which, after amplification, can be solidified into agarose beads for further analysis. A simple and efficient method to graft primer to the polymer matrix using 5'-acrydite primer was developed to ensure highly efficient trapping of RT-PCR products in agarose. High-throughput single RNA molecule/cell RT-PCR was demonstrated in stochastically diluted solutions. Our results indicate that single-molecule RT-PCR can be efficiently carried out in agarose matrix. Single-cell RT-PCR was successfully performed which showed a clear difference in gene expression level of EpCAM, a cancer biomarker gene, at the single-cell level between different types of cancer cells. This work clearly demonstrates for the first time, single-copy RT-PCR in agarose droplets. We believe this will open up new possibilities for viral RNA detection and single-cell transcription analysis.

“Mix of Mics”- Phenotypic and Biological Heterogeneity of “Multipotent” Muscle Interstitial Cells (MICs)

The capacity of adult skeletal muscle for regeneration appears to be limited, with progressive impairment in repair efficiency of injured muscles observed in chronic muscular disorders and during aging. While satellite cells, the committed adult muscle stem cells, are the main direct cell source supporting the regenerative potential of adult skeletal muscles, the characterization of the cell types and signals that constitute the functional "niche" of satellite cells is currently the object of intense investigation. Recent studies have identified a functional relationship between satellite cells and various cell types located in key anatomical position, such as the interstitium of skeletal muscles. This heterogeneous population of muscle interstitial cells (MICs) appears to retain an intrinsic multipotency within the mesodermal lineage, and their direct or indirect contribution to myofiber turnover, repair and degeneration has been suggested by many studies that will be reviewed here. Given the existing gap of knowledge on lineage identity and functional properties of MICs, their detailed characterization at the single cell level holds the promise to provide key insight into the composition of this heterogeneous population and the dynamic transition through distinct sub-populations in healthy, diseased and aging muscles. This review provides an overview of the results of various studies describing the phenotype and the function of cells isolated from skeletal muscle interstitium, and discusses the importance of single cell transcription profiling in order to decipher the functional and phenotypical heterogeneity of muscle interstitial cells (MICs).

Cholinergic circuits integrate neighboring visual signals in a Drosophila motion detection pathway.

Detecting motion is a feature of all advanced visual systems [1], nowhere more so than in flying animals, like insects [2,3]. In flies, an influential autocorrelation model for motion detection, the elementary motion detector circuit (EMD; [4,5]), compares visual signals from neighboring photoreceptors to derive information on motion direction and velocity. This information is fed by two types of interneuron, L1 and L2, in the first optic neuropile, or lamina, to downstream local motion detectors in columns of the second neuropile, the medulla. Despite receiving carefully matched photoreceptor inputs, L1 and L2 drive distinct, separable pathways responding preferentially to moving "on" and "off" edges, respectively [6, 7]. Our serial electron microscopy (EM) identifies two types of transmedulla (Tm) target neurons, Tm1 and Tm2, that receive apparently matched synaptic inputs from L2. Tm2 neurons also receive inputs from two retinotopically posterior neighboring columns via L4, a third type of lamina neuron. Light microscopy reveals that the connections in these L2/L4/Tm2 circuits are highly determinate. Single-cell transcript profiling suggests that nicotinic acetylcholine receptors mediate transmission within the L2/L4/Tm2 circuits, whereas L1 is apparently glutamatergic. We propose that Tm2 integrates sign-conserving inputs from neighboring columns to mediate the detection of front-to-back motion generated during forward motion.

Controlling gene expression in response to stress

Acute stress puts cells at risk, and rapid adaptation is crucial for maximizing cell survival. Cellular adaptation mechanisms include modification of certain aspects of cell physiology, such as the induction of efficient changes in the gene expression programmes by intracellular signalling networks. Recent studies using genome-wide approaches as well as single-cell transcription measurements, in combination with classical genetics, have shown that rapid and specific activation of gene expression can be accomplished by several different strategies. This article discusses how organisms can achieve generic and specific responses to different stresses by regulating gene expression at multiple stages of mRNA biogenesis from chromatin structure to transcription, mRNA stability and translation.

High-throughput microfluidic single-cell RT-qPCR

A long-sought milestone in microfluidics research has been the development of integrated technology for scalable analysis of transcription in single cells. Here we present a fully integrated microfluidic device capable of performing high-precision RT-qPCR measurements of gene expression from hundreds of single cells per run. Our device executes all steps of single-cell processing, including cell capture, cell lysis, reverse transcription, and quantitative PCR. In addition to higher throughput and reduced cost, we show that nanoliter volume processing reduced measurement noise, increased sensitivity, and provided single nucleotide specificity. We apply this technology to 3,300 single-cell measurements of (i) miRNA expression in K562 cells, (ii) coregulation of a miRNA and one of its target transcripts during differentiation in embryonic stem cells, and (iii) single nucleotide variant detection in primary lobular breast cancer cells. The core functionality established here provides the foundation from which a variety of on-chip single-cell transcription analyses will be developed.

Measurement and Modulation of Nuclear Receptor-Mediated Transcription in Single Cells Using Light

Nuclear receptors coordinate a diverse range of responses in higher eukaryotes and are involved in a wide range of human diseases. The ligand-dependent nature of these transcription factors makes them appealing targets for therapeutic interventions, necessitating both a mechanistic molecular understanding of interactions between ligand and receptor and a quantitative understanding of how receptors control output from target genes. Here, we utilize single molecule observation of mRNA in living and fixed cells to develop a stochastic model of nuclear-receptor mediated gene activation, and we develop a new light-activation technology to turn on a single gene and follow dynamic synthesis of RNA from the active locus. We determined that nuclear-receptors control mRNA synthesis by frequency modulation of the active state. This mechanism reproduces the classic Hill dose response that has been observed for nuclear-receptor mediated transcription and also explains the variation or ‘noise’ in expression which we measure for our reporter gene. To quantitatively control this transcription with high temporal and spatial resolution, we developed a class of photolyzable reagents (“caged” ligands) which repress transcription in the caged form and activate transcription in the uncaged form. Using light-activation of the cage, we are able to turn on the transcription of single cells in confluent tissue culture. We expect that the ability to measure and modulate transcription at the single molecule level with light will be critical in understanding the function of nuclear-receptor mediated signaling in tissue and eventually in whole animals.

RNA-Seq and find: entering the RNA deep field

Initial high-throughput RNA sequencing (RNA-Seq) experiments have revealed a complex and dynamic transcriptome, but because it samples transcripts in proportion to their abundances, assessing the extent and nature of low-level transcription using this technique has been difficult. A new assay, RNA CaptureSeq, addresses this limitation of RNA-Seq by enriching for low-level transcripts with cDNA tiling arrays prior to high-throughput sequencing. This approach reveals a plethora of transcripts that have been previously dismissed as 'noise', and hints at single-cell transcription fingerprints that may be crucial in defining cellular function in normal and disease states.

Retraction Notice to: Population-Level Transcription Cycles Derive from Stochastic Timing of Single-Cell Transcription

(Cell 138, 498–501; August 7, 2009)In this paper, we used computational approaches to show that transcriptional cycling, i.e., periodic assembly of transcription factors and their cofactors and the resulting cyclical accumulation of mRNA, may stem from stochastic timing and sequential activation of transcription in individual cells. We also presented experimental results in support of the model. We have recently uncovered instances in several figures where experimental data points were altered or selectively included in or excluded from the analyses; these manipulations do not affect the computational modeling. The first author has acknowledged responsibility for the manipulations. We have now reanalyzed the experimental data and find that they no longer provide statistically significant support for our claim of population-level transcription cycling. We are therefore retracting the paper. We sincerely apologize for any inconvenience this might cause.

The Medial Amygdalar Nucleus: A Novel Glucose-Sensing Region That Modulates the Counterregulatory Response to Hypoglycemia

OBJECTIVETo determine whether the medial amygdalar nucleus (MAN) represents a novel brain glucose-sensing region involved in the detection of hypoglycemia and generation of a counterregulatory hormone response.RESEARCH DESIGN AND METHODSFura-2 calcium imaging was used to assess glucose responsivity in neurons isolated from the MAN and single-cell real-time reverse transcription PCR used to examine gene expression within glucose-responsive neurons. In vivo studies with local MAN perfusion of the glucoprivic agent, 2-deoxyglucose (2-DG), under normal and hypoglycemic conditions and also after MAN lesioning with ibotenic acid, were used to examine the functional role of MAN glucose sensors. In addition, retrograde neuronal tracer studies were used to examine reciprocal pathways between the MAN and the ventromedial hypothalamus (VMH).RESULTSThe MAN contains a population of glucose-sensing neurons (13.5%), which express glucokinase, and the selective urocortin 3 (UCN3) receptor CRH-R2, but not UCN3 itself. Lesioning the MAN suppressed, whereas 2-DG infusion amplified, the counterregulatory response to hyperinsulinemic hypoglycemia in vivo. However, 2-DG infusion to the MAN or VMH under normoglycemic conditions had no systemic effect. The VMH is innervated by UCN3 neurons that arise mainly from the MAN, and ∼1/3 of MAN UCN3 neurons are active during mild hypoglycemia.CONCLUSIONSThe MAN represents a novel limbic glucose-sensing region that contains characteristic glucokinase-expressing glucose-sensing neurons that respond directly to manipulations of glucose availability both in vitro and in vivo. Moreover, UCN3 neurons may provide feedback inhibitory regulation of the counterregulatory response through actions within the VMH and the MAN.

ATM-Dependent Chromatin Changes Silence Transcription In cis to DNA Double-Strand Breaks

DNA double-strand breaks (DSBs) initiate extensive local and global alterations in chromatin structure, many of which depend on the ATM kinase. Histone H2A ubiquitylation (uH2A) on chromatin surrounding DSBs is one example, thought to be important for recruitment of repair proteins. uH2A is also implicated in transcriptional repression; an intriguing yet untested hypothesis is that this function is conserved in the context of DSBs. Using a novel reporter that allows for visualization of repair protein recruitment and local transcription in single cells, we describe an ATM-dependent transcriptional silencing program in cis to DSBs. ATM prevents RNA polymerase II elongation-dependent chromatin decondensation at regions distal to DSBs. Silencing is partially dependent on E3 ubiquitin ligases RNF8 and RNF168, whereas reversal of silencing relies on the uH2A deubiquitylating enzyme USP16. These findings give insight into the role of posttranslational modifications in mediating crosstalk between diverse processes occurring on chromatin.

ATM Creates a Veil of Transcriptional Silence

The ATM kinase orchestrates diverse responses to DNA damage. By simultaneously monitoring transcription and DNA-damage responses in single cells, Shanbhag et al. (2010) now uncover a role of ATM in preventing transcription near DNA double-strand breaks.

Correlated Levels of mRNA and Soma Size in Single Identified Neurons: Evidence for Compartment-specific Regulation of Gene Expression

In addition to the overall complexity of transcriptional regulation, cells also must take into account the subcellular distribution of these gene products. This is particularly challenging for morphologically complex cells such as neurons. Yet the interaction between cellular morphology and gene expression is poorly understood. Here we provide some of the first evidence for a relationship between neuronal compartment size and maintenance of mRNA levels in neurons. We find that single-cell transcript levels of 18S rRNA, GAPDH, and EF1-alpha, all gene products with primary functions in the cell soma, are strongly correlated to soma size in multiple distinct neuronal types. Levels of mRNA for the K+ channel shal, which is localized exclusively to the soma, are negatively correlated with soma size, suggesting that gene expression does not simply track positively with compartment size. Conversely, levels of beta-actin and beta-tubulin mRNA, which are major cytoskeletal proteins of neuronal processes, do not correlate with soma size, but are strongly correlated with one another. Additionally, actin/tubulin expression levels correlate with voltage-gated ion channels that are uniquely localized to axons. These results suggest that steady-state transcript levels are differentially regulated based on the subcellular compartment within which a given gene product primarily acts.

Smoking of crack cocaine as a risk factor for HIV infection among people who use injection drugs

Little is known about the possible role that smoking crack cocaine has on the incidence of HIV infection. Given the increasing use of crack cocaine, we sought to examine whether use of this illicit drug has become a risk factor for HIV infection. We included data from people participating in the Vancouver Injection Drug Users Study who reported injecting illicit drugs at least once in the month before enrolment, lived in the greater Vancouver area, were HIV-negative at enrolment and completed at least 1 follow-up study visit. To determine whether the risk of HIV seroconversion among daily smokers of crack cocaine changed over time, we used Cox proportional hazards regression and divided the study into 3 periods: May 1, 1996-Nov. 30, 1999 (period 1), Dec. 1, 1999-Nov. 30, 2002 (period 2), and Dec. 1, 2002-Dec. 30, 2005 (period 3). Overall, 1048 eligible injection drug users were included in our study. Of these, 137 acquired HIV infection during follow-up. The mean proportion of participants who reported daily smoking of crack cocaine increased from 11.6% in period 1 to 39.7% in period 3. After adjusting for potential confounders, we found that the risk of HIV seroconversion among participants who were daily smokers of crack cocaine increased over time (period 1: hazard ratio [HR] 1.03, 95% confidence interval [CI] 0.57-1.85; period 2: HR 1.68, 95% CI 1.01-2.80; and period 3: HR 2.74, 95% CI 1.06-7.11). Smoking of crack cocaine was found to be an independent risk factor for HIV seroconversion among people who were injection drug users. This finding points to the urgent need for evidence-based public health initiatives targeted at people who smoke crack cocaine.

Population-Level Transcription Cycles Derive from Stochastic Timing of Single-Cell Transcription

Population-Level Transcription Cycles Derive from Stochastic Timing of Single-Cell Transcription

Population-Level Transcription Cycles Derive from Stochastic Timing of Single-Cell Transcription

Population-Level Transcription Cycles Derive from Stochastic Timing of Single-Cell Transcription

RETRACTED: Population-Level Transcription Cycles Derive from Stochastic Timing of Single-Cell Transcription

Eukaryotic transcription is a dynamic process relying on a large number of proteins. By measuring the cycling expression of the pyruvate dehydrogenase kinase 4 gene in human cells, we constructed a detailed stochastic model for single-gene transcription at the molecular level using realistic kinetics for diffusion and protein complex dynamics. We observed that gene induction caused an approximate 60 min periodicity of several transcription related processes: first, the covalent histone modifications and presence of many regulatory proteins at the transcription start site; second, RNA polymerase II activity; third, chromatin loop formation; and fourth, mRNA accumulation. Our model can predict the precise timing of single-gene activity leading to transcriptional cycling on the cell population level when we take into account the sequential and irreversible multistep nature of transcriptional initiation. We propose that the cyclic nature of population gene expression is primarily based on the intrinsic periodicity of the transcription process itself.

Single-cell transcript analysis of human embryonic stem cells

We demonstrate the qualitative and quantitative power of single-cell transcript analysis to characterize transcriptome dynamics in human embryonic stem cells (hESC's). Single-cell analysis can systematically determine unique cellular profiles for use in cell sorting and identification, show the potential to augment standing models of cellular differentiation, and elucidate the behavior of stem cells exiting pluripotency. Using single-cell analysis of H9 hESC's differentiating under three culture conditions, we revealed transient expression of mesendodermal markers in all three protocols, followed by increasingly stable expression of embryonic endoderm and extra-embryonic endoderm markers. Our single-cell profiles reveal mixed populations of cell types, with both transcriptional and temporal heterogeneity marking differentiation under all conditions. Interestingly, we also observe extensive and prolonged co-expression of markers regulating both pluripotency and lineage differentiation in all culture conditions, and we find that pluripotency marker transcripts remain detectable in the majority of cells for many days. Finally, we show that cells derived from undifferentiated hESC colonies display consistent gene expression profiles characterized by three cohorts of transcripts: uniform, absent and sporadically detected messages, and that a striking correlation exists between genes' membership in these cohorts and their hESC promoter chromatin state, with bivalent promoters dominating the sporadic transcripts.