65 research outputs found
Analysis of circadian pattern reveals tissue-specific alternative transcription in leptin signaling pathway
*Background*
It has been previously reported that most mammalian genes display a circadian oscillation in their baseline expression. Consequently, the phase and amplitude of each component of a signal transduction cascade has downstream consequences. 

*Results*
We report our analysis of alternative transcripts in the leptin signaling pathway which is responsible for the systemic regulation of macronutrient storage and energy balance. We focused on the circadian expression pattern of a critical component of the leptin signaling system, suppressor of cytokine signaling 3 (SOCS3). On an Affymetrix GeneChip 430A2 microarray, this gene is represented by three probe sets targeting different regions within the 3’ end of the last exon. We demonstrate that in murine brown adipose tissue two downstream 3’ probe sets experience circadian baseline oscillation in counter-phase to the upstream probe set. Such differences in expression patterns are a telltale sign of alternative splicing within the last exon of SOCS3. In contrast, all three probe sets oscillated in a common phase in murine liver and white adipose tissue. This suggests that the regulation of SOCS3 expression in brown fat is tissue specific. Another component of the signaling pathway, Janus kinase (JAK), is directly regulated by SOCS and has alternative transcript probe sets oscillating in counter-phase in a white adipose tissue specific manner.
 
*Conclusion*
We hypothesize that differential oscillation of alternative transcripts may provide a mechanism to maintain steady levels of expression in spite of circadian baseline variation
Spatio-Temporal Dynamics of Yeast Mitochondrial Biogenesis: Transcriptional and Post-Transcriptional mRNA Oscillatory Modules
Examples of metabolic rhythms have recently emerged from studies of budding
yeast. High density microarray analyses have produced a remarkably detailed
picture of cycling gene expression that could be clustered according to
metabolic functions. We developed a model-based approach for the decomposition
of expression to analyze these data and to identify functional modules which,
expressed sequentially and periodically, contribute to the complex and intricate
mitochondrial architecture. This approach revealed that mitochondrial
spatio-temporal modules are expressed during periodic spikes and specific
cellular localizations, which cover the entire oscillatory period. For instance,
assembly factors (32 genes) and translation regulators (47 genes) are expressed
earlier than the components of the amino-acid synthesis pathways (31 genes). In
addition, we could correlate the expression modules identified with particular
post-transcriptional properties. Thus, mRNAs of modules expressed
“early” are mostly translated in the vicinity of
mitochondria under the control of the Puf3p mRNA-binding protein. This last
spatio-temporal module concerns mostly mRNAs coding for basic elements of
mitochondrial construction: assembly and regulatory factors. Prediction that
unknown genes from this module code for important elements of mitochondrial
biogenesis is supported by experimental evidence. More generally, these
observations underscore the importance of post-transcriptional processes in
mitochondrial biogenesis, highlighting close connections between nuclear
transcription and cytoplasmic site-specific translation
Will systems biology offer new holistic paradigms to life sciences?
A biological system, like any complex system, blends stochastic and deterministic features, displaying properties of both. In a certain sense, this blend is exactly what we perceive as the “essence of complexity” given we tend to consider as non-complex both an ideal gas (fully stochastic and understandable at the statistical level in the thermodynamic limit of a huge number of particles) and a frictionless pendulum (fully deterministic relative to its motion). In this commentary we make the statement that systems biology will have a relevant impact on nowadays biology if (and only if) will be able to capture the essential character of this blend that in our opinion is the generation of globally ordered collective modes supported by locally stochastic atomisms
Behavior of a Metabolic Cycling Population at the Single Cell Level as Visualized by Fluorescent Gene Expression Reporters
BACKGROUND: During continuous growth in specific chemostat cultures, budding yeast undergo robust oscillations in oxygen consumption that are accompanied by highly periodic changes in transcript abundance of a majority of genes, in a phenomenon called the Yeast Metabolic Cycle (YMC). This study uses fluorescent reporters of genes specific to different YMC phases in order to visualize this phenomenon and understand the temporal regulation of gene expression at the level of individual cells within the cycling population. METHODOLOGY: Fluorescent gene expression reporters for different phases of the YMC were constructed and stably integrated into the yeast genome. Subsequently, these reporter-expressing yeast were used to visualize YMC dynamics at the individual cell level in cultures grown in a chemostat or in a microfluidics platform under varying glucose concentrations, using fluorescence microscopy and quantitative Western blots. CONCLUSIONS: The behavior of single cells within a metabolic cycling population was visualized using phase-specific fluorescent reporters. The reporters largely recapitulated genome-specified mRNA expression profiles. A significant fraction of the cell population appeared to exhibit basal expression of the reporters, supporting the hypothesis that there are at least two distinct subpopulations of cells within the cycling population. Although approximately half of the cycling population initiated cell division in each permissive window of the YMC, metabolic synchrony of the population was maintained. Using a microfluidics platform we observed that low glucose concentrations appear to be necessary for metabolic cycling. Lastly, we propose that there is a temporal window in the oxidative growth phase of the YMC where the cycling population segregates into at least two subpopulations, one which will enter the cell cycle and one which does not
Time warping of evolutionary distant temporal gene expression data based on noise suppression
<p>Abstract</p> <p>Background</p> <p>Comparative analysis of genome wide temporal gene expression data has a broad potential area of application, including evolutionary biology, developmental biology, and medicine. However, at large evolutionary distances, the construction of global alignments and the consequent comparison of the time-series data are difficult. The main reason is the accumulation of variability in expression profiles of orthologous genes, in the course of evolution.</p> <p>Results</p> <p>We applied Pearson distance matrices, in combination with other noise-suppression techniques and data filtering to improve alignments. This novel framework enhanced the capacity to capture the similarities between the temporal gene expression datasets separated by large evolutionary distances. We aligned and compared the temporal gene expression data in budding (<it>Saccharomyces cerevisiae</it>) and fission (<it>Schizosaccharomyces pombe</it>) yeast, which are separated by more then ~400 myr of evolution. We found that the global alignment (time warping) properly matched the duration of cell cycle phases in these distant organisms, which was measured in prior studies. At the same time, when applied to individual ortholog pairs, this alignment procedure revealed groups of genes with distinct alignments, different from the global alignment.</p> <p>Conclusion</p> <p>Our alignment-based predictions of differences in the cell cycle phases between the two yeast species were in a good agreement with the existing data, thus supporting the computational strategy adopted in this study. We propose that the existence of the alternative alignments, specific to distinct groups of genes, suggests presence of different synchronization modes between the two organisms and possible functional decoupling of particular physiological gene networks in the course of evolution.</p
Collective Dynamics of Gene Expression in Cell Populations
The phenotypic state of the cell is commonly thought to be determined by the set of expressed genes. However, given the apparent complexity of genetic networks, it remains open what processes stabilize a particular phenotypic state. Moreover, it is not clear how unique is the mapping between the vector of expressed genes and the cell's phenotypic state. To gain insight on these issues, we study here the expression dynamics of metabolically essential genes in twin cell populations. We show that two yeast cell populations derived from a single steady-state mother population and exhibiting a similar growth phenotype in response to an environmental challenge, displayed diverse expression patterns of essential genes. The observed diversity in the mean expression between populations could not result from stochastic cell-to-cell variability, which would be averaged out in our large cell populations. Remarkably, within a population, sets of expressed genes exhibited coherent dynamics over many generations. Thus, the emerging gene expression patterns resulted from collective population dynamics. It suggests that in a wide range of biological contexts, gene expression reflects a self-organization process coupled to population-environment dynamics
Phenotypic Signatures Arising from Unbalanced Bacterial Growth
Fluctuations in the growth rate of a bacterial culture during unbalanced growth are generally considered undesirable in quantitative studies of bacterial physiology. Under well-controlled experimental conditions, however, these fluctuations are not random but instead reflect the interplay between intra-cellular networks underlying bacterial growth and the growth environment. Therefore, these fluctuations could be considered quantitative phenotypes of the bacteria under a specific growth condition. Here, we present a method to identify “phenotypic signatures” by time-frequency analysis of unbalanced growth curves measured with high temporal resolution. The signatures are then applied to differentiate amongst different bacterial strains or the same strain under different growth conditions, and to identify the essential architecture of the gene network underlying the observed growth dynamics. Our method has implications for both basic understanding of bacterial physiology and for the classification of bacterial strains
An Increase in Mitochondrial DNA Promotes Nuclear DNA Replication in Yeast
Coordination between cellular metabolism and DNA replication determines when cells initiate division. It has been assumed that metabolism only plays a permissive role in cell division. While blocking metabolism arrests cell division, it is not known whether an up-regulation of metabolic reactions accelerates cell cycle transitions. Here, we show that increasing the amount of mitochondrial DNA accelerates overall cell proliferation and promotes nuclear DNA replication, in a nutrient-dependent manner. The Sir2p NAD+-dependent de-acetylase antagonizes this mitochondrial role. We found that cells with increased mitochondrial DNA have reduced Sir2p levels bound at origins of DNA replication in the nucleus, accompanied with increased levels of K9, K14-acetylated histone H3 at those origins. Our results demonstrate an active role of mitochondrial processes in the control of cell division. They also suggest that cellular metabolism may impact on chromatin modifications to regulate the activity of origins of DNA replication
Predicting Cellular Growth from Gene Expression Signatures
Maintaining balanced growth in a changing environment is a fundamental
systems-level challenge for cellular physiology, particularly in microorganisms.
While the complete set of regulatory and functional pathways supporting growth
and cellular proliferation are not yet known, portions of them are well
understood. In particular, cellular proliferation is governed by mechanisms that
are highly conserved from unicellular to multicellular organisms, and the
disruption of these processes in metazoans is a major factor in the development
of cancer. In this paper, we develop statistical methodology to identify
quantitative aspects of the regulatory mechanisms underlying cellular
proliferation in Saccharomyces cerevisiae. We find that the
expression levels of a small set of genes can be exploited to predict the
instantaneous growth rate of any cellular culture with high accuracy. The
predictions obtained in this fashion are robust to changing biological
conditions, experimental methods, and technological platforms. The proposed
model is also effective in predicting growth rates for the related yeast
Saccharomyces bayanus and the highly diverged yeast
Schizosaccharomyces pombe, suggesting that the underlying
regulatory signature is conserved across a wide range of unicellular evolution.
We investigate the biological significance of the gene expression signature that
the predictions are based upon from multiple perspectives: by perturbing the
regulatory network through the Ras/PKA pathway, observing strong upregulation of
growth rate even in the absence of appropriate nutrients, and discovering
putative transcription factor binding sites, observing enrichment in
growth-correlated genes. More broadly, the proposed methodology enables
biological insights about growth at an instantaneous time scale, inaccessible by
direct experimental methods. Data and tools enabling others to apply our methods
are available at http://function.princeton.edu/growthrate
Synchronized ATP oscillations have a critical role in prechondrogenic condensation during chondrogenesis
The skeletal elements of embryonic limb are prefigured by prechondrogenic condensation in which secreted molecules such as adhesion molecules and extracellular matrix have crucial roles. However, how the secreted molecules are controlled to organize the condensation remains unclear. In this study, we examined metabolic regulation of secretion in prechondrogenic condensation, using bioluminescent monitoring systems. We here report on ATP oscillations in the early step of chondrogenesis. The ATP oscillations depended on both glycolysis and mitochondrial respiration, and their synchronization among cells were achieved via gap junctions. In addition, the ATP oscillations were driven by Ca2+ oscillations and led to oscillatory secretion in chondrogenesis. Blockade of the ATP oscillations prevented cellular condensation. Furthermore, the degree of cellular condensation increased with the frequency of ATP oscillations. We conclude that ATP oscillations have a critical role in prechondrogenic condensation by inducing oscillatory secretion
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