Specificity factors in cytoplasmic polyadenylation

Poly(A) tail elongation after export of an messenger RNA (mRNA) to the cytoplasm is called cytoplasmic polyadenylation. It was first discovered in oocytes and embryos, where it has roles in meiosis and development. In recent years, however, has been implicated in many other processes, including synaptic plasticity and mitosis. This review aims to introduce cytoplasmic polyadenylation with an emphasis on the factors and elements mediating this process for different mRNAs and in different animal species. We will discuss the RNA sequence elements mediating cytoplasmic polyadenylation in the 3′ untranslated regions of mRNAs, including the CPE, MBE, TCS, eCPE, and C-CPE. In addition to describing the role of general polyadenylation factors, we discuss the specific RNA binding protein families associated with cytoplasmic polyadenylation elements, including CPEB (CPEB1, CPEB2, CPEB3, and CPEB4), Pumilio (PUM2), Musashi (MSI1, MSI2), zygote arrest (ZAR2), ELAV like proteins (ELAVL1, HuR), poly(C) binding proteins (PCBP2, αCP2, hnRNP-E2), and Bicaudal C (BICC1). Some emerging themes in cytoplasmic polyadenylation will be highlighted. To facilitate understanding for those working in different organisms and fields, particularly those who are analyzing high throughput data, HUGO gene nomenclature for the human orthologs is used throughout. Where human orthologs have not been clearly identified, reference is made to protein families identified in man

CPEB4 function in macrophages

[eng] As innate immune cells, macrophages sense endogenous and exogenous danger signals and respond orchestrating inflammatory processes. For the rapid induction and efficient resolution of inflammatory responses, macrophages induce the expression of pro- inflammatory and anti-inflammatory mediators, which cross-regulate each other through feedback loops. This process requires tightly controlled gene expression at multiple levels. Recently, the regulation of mRNA deadenylation has emerged as a key regulator of the strength and, critically, the duration of transient inflammatory responses. Cytoplasmic Polyadenylation Element Binding (CPEB1-4) family of RNA-binding proteins target mRNAs containing Cytoplasmic Polyadenylation Elements (CPEs) in their 3’UTR. CPEBs orchestrate the assembly of two types of ribonucleoprotein complexes (mRNPs) which can repress or stimulate the translation of target mRNAs by modulating the length of poly(A) tail. Several inflammatory mediators harbour CPEs in their 3’UTRs and are potential CPEB targets. Thus, we hypothesized that CPEBs could be an additional checkpoint to control inflammatory responses. We find that CPEB4 is a novel player in macrophage response to LPS. Upon LPS treatment, CPEB4 is upregulated and its polyadenylation function is activated, a process mediated by the MAPK p38α and ERK1/2 and two AU Rich Element Binding Proteins (ARE-BPs). Interestingly, the pattern of CPEB4 expression and activity suggests that it participates in late LPS-response, when the resolution of inflammation occurs. Indeed, myeloid-specific Cpeb4KO mice display increased sensitivity to LPS-induced endotoxic shock. We identify CPEB4 target mRNAs by RNA-Immunoprecipitation and Sequencing (RIP-Seq), uncovering that CPEB4 regulates the expression of negative regulators of MAPK signalling, thus creating the negative feedback loop needed the resolution of inflammation. Moreover, we also describe how the interplay between CPEB4, HuR and TTP defines mRNA behaviour during the different temporal windows of inflammatory responses.[spa] Como células del sistema inmune innato, los macrófagos detectan señales de peligro endógenas y exógenas y responden desencadenando procesos inflamatorios. Estas respuestas inflamatorias tienen que ser inducidas rápidamente pero a su vez, deben ser eficientemente resueltas. Para ello, los macrófagos inducen la expresión de mediadores pro- y anti- inflamatorios que controlan la expresión unos de otros mediante complejos circuitos regulatorios. Estos procesos requieren un estricto control de la expresión génica a distintos niveles. En los últimos años, se ha descrito que la regulación de los mRNAs por deadenilación es un elemento crucial para regular intensidad y sobretodo la duración de las respuestas inflamatorias. La família de proteínas de unión al RNA CPEBs (Cytoplasmic Polyadenylation Element Binding, CPEB1-4), unen mRNAs que contienen CPEs (Cytoplasmic Polyadenylation Elements) en su 3’UTR. Las CPEBs pueden reclutar dos tipos de complejos en los mRNAs que unen. Estos complejos modulan la longitud de la cola poly(A) y, por tanto, pueden reprimir o estimular su traducción. Los mRNAs de múltiples mediadores inflamatorios y son susceptibles de ser regulados por las CPEBs ya que contienen CPEs en sus 3’UTRs. Por tanto, las CPEBs podrían ser un nuevo mecanismo regulador del desarrollo de las respuestas inflamatorias. En este trabajo hemos descubierto que CPEB4 participa en la respuesta de los macrófagos frente a LPS. El tratamiento con LPS provoca un incremento en los niveles de CPEB4 y promueve que su función sea de polyadenylación. Este proceso es mediado por las MAPK p38α y ERK1/2 y dos proteínas que regulan mRNAs mediante la unión a AREs. El patrón de expresión de CPEB4 sugiere que esta proteína participa en la fase tardía de la respuesta a LPS, cuándo la respuesta inflamatoria es resuelta. Apoyando esta hipótesis, ratones KO para CPEB4 en las células mieloides son más sensibles al shock séptico inducido por LPS. Identificando los mRNAs que CPEB4 regula en este contexto, hemos descrito que CPEB4 regula la expresión de inhibidores de la señalización de la vía MAPK. De este modo, CPEB4 es necesaria para la resolución de la inflamación en respuesta a LPS. Además, hemos descrito como la regulación de mRNAs por CPEB4, HuR y TTP define diferentes patrones temporales de expresión durante el desarrollo de respuestas inflamatorias

A Model of the Roles of Essential Kinases in the Induction and Expression of Late Long-Term Potentiation

The induction of late long-term potentiation (L-LTP) involves complex interactions among second messenger cascades. To gain insights into these interactions, a mathematical model was developed for L-LTP induction in the CA1 region of the hippocampus. The differential equation-based model represents actions of protein kinase A (PKA), MAP kinase (MAPK), and CaM kinase II (CAMKII) in the vicinity of the synapse, and activation of transcription by CaM kinase IV (CAMKIV) and MAPK. L-LTP is represented by increases in a synaptic weight. Simulations suggest that steep, supralinear stimulus-response relationships between stimuli (elevations in [Ca2+]) and kinase activation are essential for translating brief stimuli into long-lasting gene activation and synaptic weight increases. Convergence of multiple kinase activities to induce L-LTP helps to generate a threshold whereby the amount of L-LTP varies steeply with the number of tetanic electrical stimuli. The model simulates tetanic, theta-burst, pairing-induced, and chemical L-LTP, as well as L-LTP due to synaptic tagging. The model also simulates inhibition of L-LTP by inhibition of MAPK, CAMKII, PKA, or CAMKIV. The model predicts results of experiments to delineate mechanisms underlying L-LTP induction and expression. For example, the cAMP antagonist RpcAMPs, which inhibits L-LTP induction, is predicted to inhibit ERK activation. The model also appears useful to clarify similarities and differences between hippocampal L-LTP and long-term synaptic strengthening in other systems.Comment: Accepted to Biophysical Journal. Single PDF, 7 figs include

IST Austria Thesis

The aim of this thesis was the development of new strategies for optical and optogenetic control of proliferative and pro-survival signaling, and characterizing them from the molecular mechanism up to cellular effects. These new light-based methods have unique features, such as red light as an activator, or the avoidance of gene delivery, which enable to overcome current limitations, such as light delivery to target tissues and feasibility as therapeutic approach. A special focus was placed on implementing these new light-based approaches in pancreatic β-cells, as β-cells are the key players in diabetes and especially their loss in number negatively affects disease progression. Currently no treatment options are available to compensate the lack of functional β-cells in diabetic patients. In a first approach, red-light-activated growth factor receptors, in particular receptor tyrosine kinases were engineered and characterized. Receptor activation with light allows spatio-temporal control compared to ligand-based activation, and especially red light exhibits deeper tissue penetration than other wavelengths of the visible spectrum. Red-light-activated receptor tyrosine kinases robustly activated major growth factor related signaling pathways with a high temporal resolution. Moreover, the remote activation of the proliferative MAPK/Erk pathway by red-light-activated receptor tyrosine kinases in a pancreatic β-cell line was also achieved, through one centimeter thick mouse tissue. Although red-light-activated receptor tyrosine kinases are particularly attractive for applications in animal models due to the deep tissue penetration of red light, a drawback, especially with regard to translation into humans, is the requirement of gene therapy. In a second approach an endogenous light-sensitive mechanism was identified and its potential to promote proliferative and pro-survival signals was explored, towards light-based tissue regeneration without the need for gene transfer. Blue-green light illumination was found to be sufficient for the activation of proliferation and survival promoting signaling pathways in primary pancreatic murine and human islets. Blue-green light also led to an increase in proliferation of primary islet cells, an effect which was shown to be mostly β-cell specific in human islets. Moreover, it was demonstrated that this approach of pancreatic β-cell expansion did not have any negative effect on the β-cell function, in particular on their insulin secretion capacity. In contrast, a trend for enhanced insulin secretion under high glucose conditions after illumination was detected. In order to unravel the detailed characteristics of this endogenous light-sensitive mechanism, the precise light requirements were determined. In addition, the expression of light sensing proteins, OPN3 and rhodopsin, was detected. The observed effects were found to be independent of handling effects such as temperature differences and cytochrome c oxidase dependent ATP increase, but they were found to be enhanced through the knockout of OPN3. The exact mechanism of how islets cells sense light and the identity of the photoreceptor remains unknown. Summarized two new light-based systems with unique features were established that enable the activation of proliferative and pro-survival signaling pathways. While red-light-activated receptor tyrosine kinases open a new avenue for optogenetics research, by allowing non-invasive control of signaling in vivo, the identified endogenous light-sensitive mechanism has the potential to be the basis of a gene therapy-free therapeutical approach for light-based β-cell expansion

Dynamical Models of biological networks

In der Molekularbiologie sind mathematische Modelle von regulatorischen und metabolischen Netzwerken essentiell, um von einer Betrachtung isolierter Komponenten und Interaktionen zu einer systemischen Betrachtungsweise zu kommen. Genregulatorische Systeme eignen sich besonders gut zur Modellierung, da sie experimentell leicht zugänglich und manipulierbar sind. In dieser Arbeit werden verschiedene genregulatorische Netzwerke unter Zuhilfenahme von mathematischen Modellen analysiert. Weiteres wird ein Modell einer in silico Zelle vorgestellt und diskutiert. Zunächst werden zwei zyklische genregulatorische Netzwerke - der klassische Repressilator und ein Repressilator mit zusätzlicher Autoaktivierung – im Detail mit analytischen Methoden untersucht. Um den Einfluß zufällig schwankender Molekülzahlen auf die Dynamik der beiden Systeme zu untersuchen, werden stochastische Modelle erstellt und die beiden oszillierenden Systeme verglichen. Weiteres werden mögliche Auswirkungen von Genduplikationen auf ein einfaches genregulatorisches Netzwerk untersucht. Dazu wird zunächst ein kleines Netzwerk von GATA Transkriptionsfaktoren, das eine zentrale Rolle in der Regulation des Stickstoffmetabolismus in Hefe spielt, modelliert und das Modell mit experimentellen Daten verglichen, um Parameterregionen einschränken zu können. Außerdem werden potentielle Topologien genregulatorischer Netzwerke von GATA Transkriptionsfaktoren in verwandten Fungi mittels sequenzbasierender Methoden gesucht und verglichen. Im letzten Teil der Arbeit wird MiniCellSim vorgestellt, ein Modell einer selbständigen in silico Zelle. Es erlaubt ein dynamisches System, das eine Protozelle mit einem genregulatorischen Netzwerk, einem einfachen Metabolismus und einer Zellmembran beschreibt, aus einer Sequenz abzuleiten. Nachdem alle Parameter, die zur Berechnung des dynamischen Systems benötigt werden, ohne zusätzliche Eingabe nur aus der Sequenzinformation abgeleitet werden, kann das Modell für Studien zur Evolution von genregulatorischen Netzwerken verwendet werden.In this thesis different types of gene regulatory networks are analysed using mathematical models. Further a computational framework of a novel, self-contained in silico cell model is described and discussed. At first the behaviour of two cyclic gene regulatory systems - the classical repressilator and a repressilator with additional auto-activation - are inspected in detail using analytical bifurcation analysis. To examine the behaviour under random fluctuations, stochastic versions of the systems are created. Using the analytical results sustained oscillations in the stochastic versions are obtained, and the two oscillating systems compared. In the second part of the thesis possible implications of gene duplication on a simple gene regulatory system are inspected. A model of a small network formed by GATA-type transcription factors, central in nitrogen catabolite repression in yeast, is created and validated against experimental data to obtain approximate parameter values. Further, topologies of potential gene regulatory networks and modules consisting of GATA-type transcription factors in other fungi are derived using sequence-based approaches and compared. The last part describes MiniCellSim, a model of a self-contained in silico cell. In this framework a dynamical system describing a protocell with a gene regulatory network, a simple metabolism, and a cell membrane is derived from a string representing a genome. All the relevant parameters required to compute the time evolution of the dynamical system are calculated from within the model, allowing the system to be used in studies of evolution of gene regulatory and metabolic networks