Gene choice in cancer cells is exclusive in ion transport but concurrent in DNA replication.

Cancers share common cellular and physiological features. Little is known about whether distinctive gene expression patterns can be displayed at the single-cell level by gene families in cancer cells. The expression of gene homologs within a family can exhibit concurrence and exclusivity.

Polysome propensity and tunable thresholds in coding sequence length enable differential mRNA stability.

The half-life of mRNAs, as well as their translation, increases in proportion to the optimal codons, indicating a tight coupling of codon-dependent differential translation and degradation. Little is known about the regulation of this coupling. We found that the mRNA stability gain in yeast depends on the mRNA coding sequence length.

The life and death of RNA across temperatures.

Temperature is an environmental condition that has a pervasive effect on cells along with all the molecules and reactions in them. The mechanisms by which prototypical RNA molecules sense and withstand heat have been identified mostly in bacteria and archaea. The relevance of these phenomena is, however, broader, and similar mechanisms have been recently found throughout the tree of life, from sex determination in reptiles to adaptation of viral RNA polymerases, to genetic disorders in humans.

Determinants of the temperature adaptation of mRNA degradation.

The rate of chemical reactions increases proportionally with temperature, but the interplay of biochemical reactions permits deviations from this relation and adaptation. The degradation of individual mRNAs in yeast increased to varying degrees with temperature. We examined how these variations are influenced by the translation and codon composition of mRNAs.

Gene Families With Stochastic Exclusive Gene Choice Underlie Cell Adhesion in Mammalian Cells.

Exclusive stochastic gene choice combines precision with diversity. This regulation enables most T-cells to express exactly one T-cell receptor isoform chosen from a large repertoire, and to react precisely against diverse antigens. Some cells express two receptor isoforms, revealing the stochastic nature of this process.

Tuning up Transcription Factors for Therapy.

The recent developments in the delivery and design of transcription factors put their therapeutic applications within reach, exemplified by cell replacement, cancer differentiation and T-cell based cancer therapies. The success of such applications depends on the efficacy and precision in the action of transcription factors. The biophysical and genetic characterization of the paradigmatic prokaryotic repressors, LacI and TetR and the designer transcription factors, transcription activator-like effector (TALE) and CRISPR-dCas9 revealed common principles behind their efficacy, which can aid the optimization of transcriptional activators and repressors.

Contribution of RNA Degradation to Intrinsic and Extrinsic Noise in Gene Expression.

Genetically identical cells contain variable numbers of molecules, even if the cells share the same environment. This stochastic variability is prominent when molecules have low abundance, which is the case for mRNA noise. Most studies focused on how transcription affects mRNA noise, and little is known about the role of RNA degradation.

Synthetic Transcription Factors Switch from Local to Long-Range Control during Cell Differentiation.

Genes, including promoters and enhancers, are regulated by short- and long-range interactions in higher eukaryotes. It is unclear how mammalian gene expression subject to such a combinatorial regulation can be controlled by synthetic transcription factors (TF). Here, we studied how synthetic TALE transcriptional activators and repressors affect the expression of genes in a gene array during cellular differentiation.

Stochastic Gene Choice during Cellular Differentiation.

Genes in higher eukaryotes are regulated by long-range interactions, which can determine what combination of genes is expressed in a chromosomal segment. The choice of the genes can display exclusivity, independence, or co-occurrence. We introduced a simple measure to quantify this interdependence in gene expression and differentiated mouse embryonic stem cells to neurons to measure the single-cell expression of the gene isoforms in the protocadherin (Pcdh) cluster, a key component of neuronal diversity.

Impact of Methods on the Measurement of mRNA Turnover.

The turnover of the RNA molecules is determined by the rates of transcription and RNA degradation. Several methods have been developed to study RNA turnover since the beginnings of molecular biology. Here we summarize the main methods to measure RNA half-life: transcription inhibition, gene control, and metabolic labelling.

Multiplexed gene control reveals rapid mRNA turnover.

The rates of mRNA synthesis and decay determine the mRNA expression level. The two processes are under coordinated control, which makes the measurements of these rates challenging, as evidenced by the low correlation among the methods of measurement of RNA half-lives. We developed a minimally invasive method, multiplexed gene control, to shut off expression of genes with controllable synthetic promoters.

Measurement of In Vivo Protein Binding Affinities in a Signaling Network with Mass Spectrometry.

Protein interaction networks play a key role in signal processing. Despite the progress in identifying the interactions, the quantification of their strengths lags behind. Here we present an approach to quantify the in vivo binding of proteins to their binding partners in signaling-transcriptional networks, by the pairwise genetic isolation of each interaction and by varying the concentration of the interacting components over time.

Measurement of bistability in a multidimensional parameter space.

Bistability plays an important role to generate two stable states for alternative cell fates, or to promote cellular diversity and cell cycle oscillations. Positive feedback loops are necessary for the existence of bistability and ultrasensitive reactions in the loops broaden the parameter range of bistability. The broader parameter range a system's bistability covers, the more robust the two states are.

An open-loop approach to calculate noise-induced transitions.

Bistability permits the co-existence of two distinct cell fates in a population of genetically identical cells. Noise induced transitions between two fates of a bistable system are difficult to calculate due to the intricate interplay between nonlinear dynamics and noise in bistable positive feedback loops. Here we opened multivariable feedback loops at the slowest variable to obtain the open-loop function and the fluctuations in the open-loop output.

Contribution of Bistability and Noise to Cell Fate Transitions Determined by Feedback Opening.

Alternative cell fates represent a form of non-genetic diversity, which can promote adaptation and functional specialization. It is difficult to predict the rate of the transition between two cell fates due to the strong effect of noise on feedback loops and missing parameters. We opened synthetic positive feedback loops experimentally to obtain open-loop functions.

Protein Dimerization Generates Bistability in Positive Feedback Loops.

Bistability plays an important role in cellular memory and cell-fate determination. A positive feedback loop can generate bistability if it contains ultrasensitive molecular reactions. It is often difficult to detect bistability based on such molecular mechanisms due to its intricate interaction with cellular growth.

Identification of optimal parameter combinations for the emergence of bistability.

Bistability underlies cellular memory and maintains alternative differentiation states. Bistability can emerge only if its parameter range is either physically realizable or can be enlarged to become realizable. We derived a general rule and showed that the bistable range of a reaction parameter is maximized by a pair of other parameters in any gene regulatory network provided they satisfy a general condition.

Quantification of pre-mRNA escape rate and synergy in splicing.

Splicing reactions generally combine high speed with accuracy. However, some of the pre-mRNAs escape the nucleus with a retained intron. Intron retention can control gene expression and increase proteome diversity.

Myoblasts inhibit prostate cancer growth by paracrine secretion of tumor necrosis factor-α.

Purpose: Myoblasts can form muscle fibers after transplantation. Therefore, they are envisioned as a treatment for urinary incontinence after radical prostatectomy. However, to our knowledge the safety of this treatment and the interaction of myoblasts with any remaining neighboring cancer are unknown.

Stochastic signalling rewires the interaction map of a multiple feedback network during yeast evolution.

During evolution, genetic networks are rewired through strengthening or weakening their interactions to develop new regulatory schemes. In the galactose network, the GAL1/GAL3 paralogues and the GAL2 gene enhance their own expression mediated by the Gal4p transcriptional activator. The wiring strength in these feedback loops is set by the number of Gal4p binding sites.

Modeling of chromosomal epigenetic silencing processes.

Silenced genes in eukaryotes are packaged into heterochromatin. In addition to establishing a passive storage site for inactive genes in differentiated cells, silencing can play an active role in promoting cellular differentiation. Here, we describe quantitative modeling of silencing processes.

Construction of cis-regulatory input functions of yeast promoters.

Promoters contain a large number of binding sites for transcriptional factors transmitting signals from a variety of cellular pathways. The promoter processes these input signals and sets the level of gene expression, the output of the gene. Here, we describe how to design genetic constructs and measure gene expression to deliver data suitable for quantitative analysis.

Spatial epigenetic control of mono- and bistable gene expression.

Bistability in signaling networks is frequently employed to promote stochastic switch-like transitions between cellular differentiation states. Differentiation can also be triggered by antagonism of activators and repressors mediated by epigenetic processes that constitute regulatory circuits anchored to the chromosome. Their regulatory logic has remained unclear.