Raymond E. Chen

Cell-Type Specific Features of Circular RNA Expression

Thousands of loci in the human and mouse genomes give rise to circular RNA transcripts; at many of these loci, the predominant RNA isoform is a circle. Using an improved computational approach for circular RNA identification, we found widespread circular RNA expression in Drosophila melanogaster and estimate that in humans, circular RNA may account for 1% as many molecules as poly(A) RNA. Analysis of data from the ENCODE consortium revealed that the repertoire of genes expressing circular RNA, the ratio of circular to linear transcripts for each gene, and even the pattern of splice isoforms of circular RNAs from each gene were cell-type specific. These results suggest that biogenesis of circular RNA is an integral, conserved, and regulated feature of the gene expression program.

Stress resistance and signal fidelity independent of nuclear MAPK function

Elevated external solute stimulates a conserved MAPK cascade that elicits responses that maintain osmotic balance. The yeast high-osmolarity glycerol (HOG) pathway activates Hog1 MAPK (mammalian ortholog p38α/SAPKα), which enters the nucleus and induces expression of >50 genes, implying that transcriptional up-regulation is necessary to cope with hyperosmotic stress. Contrary to this expectation, we show here that cells lacking the karyopherin required for Hog1 nuclear import or in which Hog1 is anchored at the plasma membrane (or both) can withstand long-term hyperosmotic challenge by ionic and nonionic solutes without exhibiting the normal change in transcriptional program (comparable with hog1Δ cells), as judged by mRNA hybridization and microarray analysis. For such cells to survive hyperosmotic stress, systematic genetic analysis ruled out the need for any Hog1-dependent transcription factor, the Hog1-activated MAPKAP kinases, or ion, glycerol, and water channels. By contrast, enzymes needed for glycerol production were essential for viability. Thus, control of intracellular glycerol formation by Hog1 is critical for maintenance of osmotic balance but not transcriptional induction of any gene.

Dynamic localization of Fus3 mitogen-activated protein kinase is necessary to evoke appropriate responses and avoid cytotoxic effects.

ABSTRACT Cellular responses to many external stimuli are mediated by mitogen-activated protein kinases (MAPKs). We investigated whether dynamic intracellular movement contributes to the spatial and temporal characteristics of the responses elicited by a prototypic MAPK, Fus3, in the mating pheromone response pathway in budding yeast (Saccharomyces cerevisiae). Confining Fus3 in the nucleus, via fusion to a histone H2B, reduced MAPK activation and diminished all responses (pheromone-induced gene expression, cell cycle arrest, projection formation, and mating). Elimination of MAPK phosphatases restored more robust outputs for all responses, indicating that nuclear sequestration impedes full MAPK activation but does not abrogate its functional competence. Restricting Fus3 to the plasma membrane, via fusion to a lipid-modified CCaaX motif, led to MAPK hyperactivation yet severely impaired all response outputs. Fus3-CCaaX also caused aberrant cell morphology and a proliferation defect. Unlike similar phenotypes induced by pathway hyperactivation via upstream components, these deleterious effects were independent of the downstream transcription factor Ste12. Thus, appropriate cellular responses require free subcellular MAPK transit to disseminate MAPK activity optimally because preventing dynamic MAPK movement either markedly impaired signal-dependent activation and/or resulted in improper biological outputs.

Systematic Epistasis Analysis of the Contributions of Protein Kinase A- and Mitogen-Activated Protein Kinase-Dependent Signaling to Nutrient Limitation-Evoked Responses in the Yeast Saccharomyces cerevisiae

Cellular responses to environmental stimuli require conserved signal transduction pathways. In budding yeast (Saccharomyces cerevisiae), nutrient limitation induces morphological changes that depend on the protein kinase A (PKA) pathway and the Kss1 mitogen-activated protein kinase (MAPK) pathway. It was unclear to what extent and at what level there is synergy between these two distinct signaling modalities. We took a systematic genetic approach to clarify the relationship between these inputs. We performed comprehensive epistasis analysis of mutants lacking different combinations of all relevant pathway components. We found that these two pathways contribute additively to nutrient limitation-induced haploid invasive growth. Moreover, full derepression of either pathway rendered it individually sufficient for invasive growth and thus, normally, both are required only because neither is maximally active. Furthermore, in haploids, the MAPK pathway contributes more strongly than the PKA pathway to cell elongation and adhesion, whereas nutrient limitation-induced unipolar budding is independent of both pathways. In contrast, in diploids, upon nutrient limitation the MAPK pathway regulates cell elongation, the PKA pathway regulates unipolar budding, and both regulate cell adhesion. Thus, although there are similarities between haploids and diploids, cell type-specific differences clearly alter the balance of the signaling inputs required to elicit the various nutrient limitation-evoked cellular behaviors.

Systems biology approaches in cell signaling research

The use of methods for global and quantitative analysis of cells is providing new systems-level insights into signal transduction processes. Recent studies reveal important information about the rates of signal transmission and propagation, help establish some general regulatory characteristics of multi-tiered signaling cascades, and illuminate the combinatorial nature of signaling specificity in cell differentiation.

Power Allocation with Outage Probability Constraints in Lognormal Fading Wireless Channels: A Relaxation Approach

This paper concerns stochastic power allocation in lognormal fading wireless channels. We consider an outage-based quality of service (QoS) specification which requires that, for each transmitter/receiver pair, the outage probability is kept below a given level. We show that the problem of finding a minimal power allocation to achieve this QoS goal over log-normal fading wireless channels (with statistically independent fadings) can be relaxed as a posynomial program, which can be furthered solved by the very efficient interior-point method.

Design and Analysis of CMOS-Controlled Tunable Photodetectors for Multiwavelength Discrimination

In this paper, a metal-semiconductor-metal (MSM) based photodetector for multiple wavelength discrimination is fully introduced and analyzed. Its spectral response is programmable electrically through a set of low-voltage binary patterns that can be generated from CMOS circuits. Consequently, the wavelength reconfiguration time of the detector is set primarily by the electronics switching time, which is on the order of nanoseconds. Additionally, the spectral response of the detector can be arbitrarily shaped for any specific system need based on algorithms we introduce here. The nanosecond wavelength reconfigurability feature of the detector offers flexibility for designing high-efficiency wavelength reconfigurable optical networks.

Spectral shaping of electrically controlled MSM-based tunable photodetectors

Spectral shaping of electrically controlled metal-semiconductor-metal-based tunable photodetectors is experimentally demonstrated in the telecommunication C-band. By illuminating the device with more interference patterns, we can shape and design the spectral response of the detector for various system applications. The experimental results are in excellent agreement with the mathematical models.

Linear electro-optic conversion of sampled voltage signals using a low-temperature-grown GaAs MSM and a multiple quantum well modulator

We present the hybrid integration of a low-temperature-grown GaAs metal-semiconductor-metal photoconductive switch with a GaAs SEED optical modulator, for sampling input voltages with potentially >40-GHz bandwidth and performing linear electro-optic conversion at a rate >500 megasamples/sec.