Cellular Regulatory Systems Research Articles

Biochemical and cellular basis of oxidative stress: Implications for disease onset.

Cellular oxidation-reduction (redox) systems, which encompass pro- and antioxidant molecules, are integral components of a plethora of essential cellular processes. Any dysregulation of these systems can cause molecular imbalances between the pro- and antioxidant moieties, leading to a state of oxidative stress. Long-lasting oxidative stress can manifest clinically as a variety of chronic illnesses including cancers, neurodegenerative disorders, cardiovascular disease, and metabolic diseases like diabetes. As such, this review investigates the impact of oxidative stress on the human body with emphasis on the underlying oxidants, mechanisms, and pathways. It also discusses the available antioxidant defense mechanisms. The cellular monitoring and regulatory systems that ensure a balanced oxidative cellular environment are detailed. We critically discuss the notion of oxidants as a double-edged sword, being signaling messengers at low physiological concentrations but causative agents of oxidative stress when overproduced. In this regard, the review also presents strategies employed by oxidants including redox signaling and activation of transcriptional programs such as those mediated by the Nrf2/Keap1 and NFk signaling. Likewise, redox molecular switches of peroxiredoxin and DJ-1 and the proteins they regulate are presented. The review concludes that a thorough comprehension of cellular redox systems is essential to develop the evolving field of redox medicine.

Post-Covid Syndrome: Pathophysiology of Systemic Disregulations

The main processes that characterize the post-COVID syndrome are analyzed as a version of the “prolonged” pathology of acute COVID-19. Considering the variety of manifestations of post-covid pathology, the main blocks of systemic, cellular and molecular dysregulations are distinguished. As the main reasons, the following are considered: the consequences of systemic and organ damage in the acute phase of COVID-19, the persistent activity of “hidden” pathogens and the altered status of the patient’s protective immune systems. Long-term pathology, as a multisystem syndrome, reflects disturbances in the main cellular and molecular regulatory systems: stochastic disorganization of immune responses, vascular endothelial dysfunction, cellular inflammation, imbalance of coagulation and antithrombosis systems, deviations in autoimmune processes, etc. These findings orient new cellular and biochemical targets for timely therapy. The varied nature of the symptoms suggests a selective use of therapeutic approaches.

Pleiotropic Effects of Icariside II on the Cardiovascular System: Novel Applications of Ethnopharmacology in Targeting Vascular Remodeling.

Pleiotropic Effects of Icariside II on the Cardiovascular System: Novel Applications of Ethnopharmacology in Targeting Vascular Remodeling.

Lysine Acetylation, Cancer Hallmarks and Emerging Onco-Therapeutic Opportunities.

Simple SummarySeveral histone deacetylase inhibitors have been approved by FDA for cancer treatment. Intensive efforts have been devoted to enhancing its anti-cancer efficacy by combining it with various other agents. Yet, no guideline is available to assist in the choice of candidate drugs for combination towards optimal solutions for different clinical problems. Thus, it is imperative to characterize the primary cancer hallmarks that lysine acetylation is associated with and gain knowledge on the key cancer features that each combinatorial onco-therapeutic modality targets to aid in the combinatorial onco-therapeutic design. Cold atmospheric plasma represents an emerging anti-cancer modality via manipulating cellular redox level and has been demonstrated to selectively target several cancer hallmarks. This review aims to delineate the intrinsic connections between lysine acetylation and cancer properties, and forecast opportunities histone deacetylase inhibitors may have when combined with cold atmospheric plasma as novel precision onco-therapies.Acetylation, a reversible epigenetic process, is implicated in many critical cellular regulatory systems including transcriptional regulation, protein structure, activity, stability, and localization. Lysine acetylation is the most prevalent and intensively investigated among the diverse acetylation forms. Owing to the intrinsic connections of acetylation with cell metabolism, acetylation has been associated with metabolic disorders including cancers. Yet, relatively little has been reported on the features of acetylation against the cancer hallmarks, even though this knowledge may help identify appropriate therapeutic strategies or combinatorial modalities for the effective treatment and resolution of malignancies. By examining the available data related to the efficacy of lysine acetylation against tumor cells and elaborating the primary cancer hallmarks and the associated mechanisms to target the specific hallmarks, this review identifies the intrinsic connections between lysine acetylation and cancer hallmarks and proposes novel modalities that can be combined with HDAC inhibitors for cancer treatment with higher efficacy and minimum adverse effects.

Ventricular transmural decremental conduction explains short t-peak-t-end interval in “in silico” ECG reconstruction model

Abstract Introduction In chronic hepatic cirrhosis (CHC), T-wave peak to T-wave end interval (TPTE) has shown prognostic value for survival and liver transplantation. Altered cellular ionic regulatory systems may produce decremental conduction in ventricular endocardial to epicardial activation wavefront propagation and ECG waveforms, particularly the T-wave. It was investigated whether ventricular transmural activation wavefront conduction may affect T-wave shape and impact TPTE duration, using “in silico” ECG reconstruction. Methods Mammalian-derived ventricular endocardial to epicardial AP waveforms (APW) were simulated and deployed in 10 discrete layers in homogeneous impedance ventricular wedge-like model. A uniform conduction model was employed to mimic normal heart, in which the speed of propagation of the activation wavefront was nonzero and constant in all layers. In CHC heart, a decremental conduction model was employed, in which the speed of propagation of the activation wavefront was maximal at the endocardial layer and exponentially decayed to greater than zero speed at the epicardial layer. ECG was computed as the sum of dipoles weighted by the inverse of the squared distance to an observation electrode arbitrarily located outside the wedge. One dipole was one layer thick, and its charge was assumed as the time-integral of the current generated by the difference of potential between adjacent APW, from endocardial to epicardial layers. ECG was reconstructed in one axis. Results Two-dimensional transmural APW distribution and respective reconstructed ECGs are presented in Figures 1 and 2. In uniform endocardial to epicardial transmural conduction model, QRS complex was taller and shorter as well as TPTE was larger (Fig. 1) than respective counterparts in decremental conduction model (Fig. 2). Additionally, peak-amplitude of the T-wave as well as the maximal slope of the TPTE were lower in decremental as compared to uniform conduction model. Conclusion Using “in silico” ECG reconstruction, decrementally conducted model of epicardial to endocardial ventricular transmural activation wavefront propagation yields wider and lower amplitude QRS complex as well as shorter TPTE, as compared to respective counterparts in uniformly conducted activation wavefront model. Ventricular transmural decremental conduction model offers an insight into electrophysiological background of ECG findings in CHC. (NCT01433848) Transmural APW distribution vs ECG Funding Acknowledgement Type of funding source: Public Institution(s). Main funding source(s): Universidade do Estado do Rio de Janeiro; Rio de Janeiro, RJ - Brazil

The phosphoinositide regulatory network in Trypanosoma brucei: Implications for cell-wide regulation in eukaryotes.

The unicellular eukaryote Trypanosoma brucei undergoes extensive cellular and developmental changes during its life cycle. These include regulation of mammalian stage surface antigen variation and surface composition changes between life stages; switching between glycolysis and oxidative phosphorylation; differential mRNA editing; and changes in posttranscriptional gene expression, protein trafficking, organellar function, and cell morphology. These diverse events are coordinated and controlled throughout parasite development, maintained in homeostasis at each life stage, and are essential for parasite survival in both the host and insect vector. Described herein are the enzymes and metabolites of the phosphatidylinositol (PI) cellular regulatory network, its integration with other cellular regulatory systems that collectively control and coordinate these numerous cellular processes, including cell development and differentiation and the many associated complex processes in multiple subcellular compartments. We conclude that this regulation is the product of the organization of these enzymes within the cellular architecture, their activities, metabolite fluxes, and responses to environmental changes via signal transduction and other processes. We describe a paradigm for how these enzymes and metabolites could function to control and coordinate multiple cellular functions. The significance of the PI system’s regulatory functions in single-celled eukaryotes to metazoans and their potential as chemotherapeutic targets are indicated.

Reduction by, ligand exchange among, and covalent binding to glutathione and cellular thiols link metabolism and disposition of dietary arsenic species with toxicity

Arsenic (As) is a common contaminant in the earth’s crust and widely distributed in food and drinking water. As exposures have been associated with human disease, including cancer, diabetes, lung and cardiovascular disorders, and there is accumulating evidence that early life exposures are important in the etiology. Mode-of-action analysis includes a critical role for metabolic activation of As species to reactive trivalent intermediates that disrupt cellular regulatory systems by covalent binding to thiol groups. The central role of glutathione (GSH) in the chemical reactions of metabolism and disposition of arsenic species was investigated here. The chemical kinetics were measured for reactions in which GSH is a ligand for trivalent As complex formation, a reductant for pentavalent As species, and a participant in ligand exchange reactions with other biological As-thiol complexes. The diverse reactions of GSH with As species demonstrate prominent roles in: (1) metabolic activation via reduction; (2) transport from tissues that are the primary sources of reactive trivalent As intermediates following ingestion (intestine and liver) to downstream target organs (e.g., lung, kidney, and bladder); and (3) oxidation to the terminal metabolite, dimethylarsinic acid (DMAV), which is excreted. Studies of As metabolism and disposition emphasize the link between metabolic activation vs. excretion of As (i.e., internal dosimetry of reactive species) and the disruption of critical cellular thiol-based regulatory processes that define the dose-response characteristics of disease in human epidemiological studies and animal models and underpin risk assessment.

Integrated Metabolomics and Phytochemical Genomics Approaches for Studies on St. John’s Wort

Metabolomics is widely applied for investigation of the correlation between metabolites and genes responsible for the synthesis of the particular sets of metabolites. In this review, we discuss metabolomics research on Hypericum perforatum (St. John’s Wort) to elucidate the overall regulation of the metabolism related to the mechanisms of natural variations and environmental stresses such as fungal infections, light stresses, and chemical elicitors. We also focus on phytochemical genomics and genomic information. St. John’s Wort is a medicinal plant with high potential of producing hypericin used for mild depression remedy, so knowledge on the biosynthetic pathway of unique metabolites is fundamental for their biotechnological commercial production. These metabolites have often complex biosynthetic pathway and it is challenging to identify all of the catalyzing enzymes. The development of metabolic systems biology could open new channels for high-speed construction and evaluation of hypotheses for cellular regulatory systems.

Cyclic di-GMP-Mediated Regulation of Gene Transfer and Motility in Rhodobacter capsulatus.

Gene transfer agents (GTAs) are bacteriophage-like particles produced by several bacterial and archaeal lineages that contain small pieces of the producing cells' genomes that can be transferred to other cells in a process similar to transduction. One well-studied GTA is RcGTA, produced by the alphaproteobacterium Rhodobacter capsulatus RcGTA gene expression is regulated by several cellular regulatory systems, including the CckA-ChpT-CtrA phosphorelay. The transcription of multiple other regulator-encoding genes is affected by the response regulator CtrA, including genes encoding putative enzymes involved in the synthesis and hydrolysis of the second messenger bis-(3'-5')-cyclic dimeric GMP (c-di-GMP). To investigate whether c-di-GMP signaling plays a role in RcGTA production, we disrupted the CtrA-affected genes potentially involved in this process. We found that disruption of four of these genes affected RcGTA gene expression and production. We performed site-directed mutagenesis of key catalytic residues in the GGDEF and EAL domains responsible for diguanylate cyclase (DGC) and c-di-GMP phosphodiesterase (PDE) activities and analyzed the functions of the wild-type and mutant proteins. We also measured RcGTA production in R. capsulatus strains where intracellular levels of c-di-GMP were altered by the expression of either a heterologous DGC or a heterologous PDE. This adds c-di-GMP signaling to the collection of cellular regulatory systems controlling gene transfer in this bacterium. Furthermore, the heterologous gene expression and the four gene disruptions had similar effects on R. capsulatus flagellar motility as found for gene transfer, and we conclude that c-di-GMP inhibits both RcGTA production and flagellar motility in R. capsulatusIMPORTANCE Gene transfer agents (GTAs) are virus-like particles that move cellular DNA between cells. In the alphaproteobacterium Rhodobacter capsulatus, GTA production is affected by the activities of multiple cellular regulatory systems, to which we have now added signaling via the second messenger dinucleotide molecule bis-(3'-5')-cyclic dimeric GMP (c-di-GMP). Similar to the CtrA phosphorelay, c-di-GMP also affects R. capsulatus flagellar motility in addition to GTA production, with lower levels of intracellular c-di-GMP favoring increased flagellar motility and gene transfer. These findings further illustrate the interconnection of GTA production with global systems of regulation in R. capsulatus, providing additional support for the notion that the production of GTAs has been maintained in this and related bacteria because it provides a benefit to the producing organisms.

Hijacking of host cellular components as proviral factors by plant-infecting viruses.

Plant viruses are important pathogens that cause serious crop losses worldwide. They are obligate intracellular parasites that commandeer a wide array of proteins, as well as metabolic resources, from infected host cells. In the past two decades, our knowledge of plant-virus interactions at the molecular level has exploded, which provides insights into how plant-infecting viruses co-opt host cellular machineries to accomplish their infection. Here, we review recent advances in our understanding of how plant viruses divert cellular components from their original roles to proviral functions. One emerging theme is that plant viruses have versatile strategies that integrate a host factor that is normally engaged in plant defense against invading pathogens into a viral protein complex that facilitates viral infection. We also highlight viral manipulation of cellular key regulatory systems for successful virus infection: posttranslational protein modifications for fine control of viral and cellular protein dynamics; glycolysis and fermentation pathways to usurp host resources, and ion homeostasis to create a cellular environment that is beneficial for viral genome replication. A deeper understanding of viral-infection strategies will pave the way for the development of novel antiviral strategies.

Metabolism and disposition of arsenic species from controlled dosing with sodium arsenite in adult and neonatal rhesus monkeys. VI. Toxicokinetic studies following oral administration

Arsenic is a common toxic contaminant in food and drinking water. Metabolic activation of arsenic species produces reactive trivalent intermediates that can disrupt cellular regulatory systems by covalent binding to thiol groups. Arsenic exposures have been associated with human diseases including cancer, diabetes, lung and cardiovascular disorders and there is accumulating evidence that early life exposures are important in the etiology. Previous toxicokinetic studies of arsenite ingestion in neonatal CD-1 mice showed consistent evidence for metabolic and physiologic immaturity that led to elevated internal exposures to trivalent arsenic species in the youngest mice, relative to adults. The current study in rhesus monkeys showed that metabolism and binding of trivalent intermediates after arsenite ingestion were similar between adult monkeys and CD-1 mice. Unlike neonatal mice, monkeys from the age of 5–70 days showed similar metabolism and binding profiles, which were also similar to those in adults. The absence of evidence for metabolic immaturity in monkeys suggests that toxicological effects observed in mice from early postnatal exposures to arsenic could over-predict those possible in primates, based on significantly higher internal exposures.

Genome-Wide Identification of Putative MicroRNAs in Cassava (Manihot esculenta Crantz) and Their Functional Landscape in Cellular Regulation.

MicroRNAs are small noncoding RNAs, involved in the regulation of many cellular processes in plants. Hundreds of miRNAs have been identified in cassava by various techniques, yet these identifications were constrained by a lack of miRNA templates and the narrow range of conditions in transcriptome study. In this research, we conducted genome-wide analysis identification, whereby miRNAs from cassava genome were thoroughly screened using bioinformatics approach independent of predefined templates and studied conditions. Our work provided a catalog of putative mature miRNAs and explored the landscape of miRNAome in cassava. These putative miRNAs were validated using statistical analysis as well as available cassava expression data. We showed that the crowded locations of cassava miRNAs are consistent with other plants and animals and hypothesized to have the same evolutionary origin. At least 10 conserved miRNAs were identified in cassava based on the comparative study of miRNA conservation. Finally, investigation of miRNAs and target gene relationships enabled us to envisage the complexities of cellular regulatory systems modulated at posttranscriptional level.

Overview of the BioCreative VI Precision Medicine Track: mining protein interactions and mutations for precision medicine.

The Precision Medicine Initiative is a multicenter effort aiming at formulating personalized treatments leveraging on individual patient data (clinical, genome sequence and functional genomic data) together with the information in large knowledge bases (KBs) that integrate genome annotation, disease association studies, electronic health records and other data types. The biomedical literature provides a rich foundation for populating these KBs, reporting genetic and molecular interactions that provide the scaffold for the cellular regulatory systems and detailing the influence of genetic variants in these interactions. The goal of BioCreative VI Precision Medicine Track was to extract this particular type of information and was organized in two tasks: (i) document triage task, focused on identifying scientific literature containing experimentally verified protein–protein interactions (PPIs) affected by genetic mutations and (ii) relation extraction task, focused on extracting the affected interactions (protein pairs). To assist system developers and task participants, a large-scale corpus of PubMed documents was manually annotated for this task. Ten teams worldwide contributed 22 distinct text-mining models for the document triage task, and six teams worldwide contributed 14 different text-mining systems for the relation extraction task. When comparing the text-mining system predictions with human annotations, for the triage task, the best F-score was 69.06%, the best precision was 62.89%, the best recall was 98.0% and the best average precision was 72.5%. For the relation extraction task, when taking homologous genes into account, the best F-score was 37.73%, the best precision was 46.5% and the best recall was 54.1%. Submitted systems explored a wide range of methods, from traditional rule-based, statistical and machine learning systems to state-of-the-art deep learning methods. Given the level of participation and the individual team results we find the precision medicine track to be successful in engaging the text-mining research community. In the meantime, the track produced a manually annotated corpus of 5509 PubMed documents developed by BioGRID curators and relevant for precision medicine. The data set is freely available to the community, and the specific interactions have been integrated into the BioGRID data set. In addition, this challenge provided the first results of automatically identifying PubMed articles that describe PPI affected by mutations, as well as extracting the affected relations from those articles. Still, much progress is needed for computer-assisted precision medicine text mining to become mainstream. Future work should focus on addressing the remaining technical challenges and incorporating the practical benefits of text-mining tools into real-world precision medicine information-related curation.

Integrative landscape of dysregulated signaling pathways of clinically distinct pancreatic cancer subtypes

Despite modern therapeutic advances, the survival prospects of pancreatic cancer patients have remained poor. Besides being highly metastatic, pancreatic cancer is challenging to treat because it is caused by a heterogeneous array of somatic mutations that impact a variety of signaling pathways and cellular regulatory systems. Here we use publicly available transcriptomic, copy number alteration and mutation profiling datasets from pancreatic cancer patients together with data on disease outcomes to show that the three major pancreatic cancer subtypes each display distinctive aberrations in cell signaling and metabolic pathways. Importantly, patients afflicted with these different pancreatic cancer subtypes also exhibit distinctive survival profiles. Within these patients, we find that dysregulation of the phosphoinositide 3-kinase and mitogen-activated protein kinase pathways, and p53 mediated disruptions of cell cycle processes are apparently drivers of disease. Further, we identify for the first time the molecular perturbations of signalling networks that are likely the primary causes of oncogenesis in each of the three pancreatic cancer subtypes.

Keeping the home fires burning: AMP-activated protein kinase.

Living cells obtain energy either by oxidizing reduced compounds of organic or mineral origin or by absorbing light. Whichever energy source is used, some of the energy released is conserved by converting adenosine diphosphate (ADP) to adenosine triphosphate (ATP), which are analogous to the chemicals in a rechargeable battery. The energy released by the conversion of ATP back to ADP is used to drive most energy-requiring processes, including cell growth, cell division, communication and movement. It is clearly essential to life that the production and consumption of ATP are always maintained in balance, and the AMP-activated protein kinase (AMPK) is one of the key cellular regulatory systems that ensures this. In eukaryotic cells (cells with nuclei and other internal membrane-bound structures, including human cells), most ATP is produced in mitochondria, which are thought to have been derived by the engulfment of oxidative bacteria by a host cell not previously able to use molecular oxygen. AMPK is activated by increasing AMP or ADP (AMP being generated from ADP whenever ADP rises) coupled with falling ATP. Relatives of AMPK are found in essentially all eukaryotes, and it may have evolved to allow the host cell to monitor the output of the newly acquired mitochondria and step their ATP production up or down according to the demand. Structural studies have illuminated how AMPK achieves the task of detecting small changes in AMP and ADP, despite the presence of much higher concentrations of ATP. Recently, it has been shown that AMPK can also sense the availability of glucose, the primary carbon source for most eukaryotic cells, via a mechanism independent of changes in AMP or ADP. Once activated by energy imbalance or glucose lack, AMPK modifies many target proteins by transferring phosphate groups to them from ATP. By this means, numerous ATP-producing processes are switched on (including the production of new mitochondria) and ATP-consuming processes are switched off, thus restoring energy homeostasis. Drugs that modulate AMPK have great potential in the treatment of metabolic disorders such as obesity and Type 2 diabetes, and even cancer. Indeed, some existing drugs such as metformin and aspirin, which were derived from traditional herbal remedies, appear to work, in part, by activating AMPK.

A survey of the approaches for identifying differential methylation using bisulfite sequencing data.

DNA methylation is an important epigenetic mechanism that plays a crucial role in cellular regulatory systems. Recent advancements in sequencing technologies now enable us to generate high-throughput methylation data and to measure methylation up to single-base resolution. This wealth of data does not come without challenges, and one of the key challenges in DNA methylation studies is to identify the significant differences in the methylation levels of the base pairs across distinct biological conditions. Several computational methods have been developed to identify differential methylation using bisulfite sequencing data; however, there is no clear consensus among existing approaches. A comprehensive survey of these approaches would be of great benefit to potential users and researchers to get a complete picture of the available resources. In this article, we present a detailed survey of 22 such approaches focusing on their underlying statistical models, primary features, key advantages and major limitations. Importantly, the intrinsic drawbacks of the approaches pointed out in this survey could potentially be addressed by future research.

Bivalent kinetic binding model to surface plasmon resonance studies of antigen-antibody displacement reactions

Molecular and functional analysis of small molecule binding to protein can provoke insights into cellular signaling and regulatory systems as well as facilitate pharmaceutical drug discovery. In label free small molecule detection the displacement assay format can be applied. This is beneficial because displacement of high molecular weight receptors is detected instead of low molecular weight ligand as in classical binding analysis. Thus, detection limit is potentially lowered.Using the influenza haemagglutinin (HA) peptide binding to mono or bivalent anti-haemagglutinin peptide antibody displacement assay formats could be established. The exact time resolved analysis of binding and dissolution of ligand HA and anti-Haemagglutinin peptide antibody was achieved with surface plasmon resonance (SPR) spectroscopy.Mathematical models could be developed from kinetic equations of ligand binding to mono or bivalent antibodies. With this, an accurate simulation of the SPR results was reached. The simulation plot had to be exactly adjusted to the SPR results to determine all kinetic rate constants defining ligand and receptor binding kinetics. Large variations in receptor concentration gave almost identical rate constants in binding. It became obvious that rebinding is in any case not necessary to understand the binding kinetics of our model system HA/anti-HA. Maximum decline of SPR response could be used to determine ligand concentrations in analyte.

The Tumorigenic Roles of the Cellular REDOX Regulatory Systems.

The cellular REDOX regulatory systems play a central role in maintaining REDOX homeostasis that is crucial for cell integrity, survival, and proliferation. To date, a substantial amount of data has demonstrated that cancer cells typically undergo increasing oxidative stress as the tumor develops, upregulating these important antioxidant systems in order to survive, proliferate, and metastasize under these extreme oxidative stress conditions. Since a large number of chemotherapeutic agents currently used in the clinic rely on the induction of ROS overload or change of ROS quality to kill the tumor, the cancer cell REDOX adaptation represents a significant obstacle to conventional chemotherapy. In this review we will first examine the different factors that contribute to the enhanced oxidative stress generally observed within the tumor microenvironment. We will then make a comprehensive assessment of the current literature regarding the main antioxidant proteins and systems that have been shown to be positively associated with tumor progression and chemoresistance. Finally we will make an analysis of commonly used chemotherapeutic drugs that induce ROS. The current knowledge of cancer cell REDOX adaptation raises the issue of developing novel and more effective therapies for these tumors that are usually resistant to conventional ROS inducing chemotherapy.

Experimental detection of short regulatory motifs in eukaryotic proteins: tips for good practice as well as for bad.

It has become clear in outline though not yet in detail how cellular regulatory and signalling systems are constructed. The essential machines are protein complexes that effect regulatory decisions by undergoing internal changes of state. Subcomponents of these cellular complexes are assembled into molecular switches. Many of these switches employ one or more short peptide motifs as toggles that can move between one or more sites within the switch system, the simplest being on-off switches. Paradoxically, these motif modules (termed short linear motifs or SLiMs) are both hugely abundant but difficult to research. So despite the many successes in identifying short regulatory protein motifs, it is thought that only the “tip of the iceberg” has been exposed. Experimental and bioinformatic motif discovery remain challenging and error prone. The advice presented in this article is aimed at helping researchers to uncover genuine protein motifs, whilst avoiding the pitfalls that lead to reports of false discovery.Electronic supplementary materialThe online version of this article (doi:10.1186/s12964-015-0121-y) contains supplementary material, which is available to authorized users.

Regulatory Divergence of Transcript Isoforms in a Mammalian Model System.

Phenotypic differences between species are driven by changes in gene expression and, by extension, by modifications in the regulation of the transcriptome. Investigation of mammalian transcriptome divergence has been restricted to analysis of bulk gene expression levels and gene-internal splicing. Using allele-specific expression analysis in inter-strain hybrids of Mus musculus, we determined the contribution of multiple cellular regulatory systems to transcriptome divergence, including: alternative promoter usage, transcription start site selection, cassette exon usage, alternative last exon usage, and alternative polyadenylation site choice. Between mouse strains, a fifth of genes have variations in isoform usage that contribute to transcriptomic changes, half of which alter encoded amino acid sequence. Virtually all divergence in isoform usage altered the post-transcriptional regulatory instructions in gene UTRs. Furthermore, most genes with isoform differences between strains contain changes originating from multiple regulatory systems. This result indicates widespread cross-talk and coordination exists among different regulatory systems. Overall, isoform usage diverges in parallel with and independently to gene expression evolution, and the cis and trans regulatory contribution to each differs significantly.