SEARCH · Search bioRxiv

Results for “Physiology”

Search indexed bioRxiv preprints in genomics, neuroscience, cell biology and bioinformatics. Read source abstracts and check manuscript versions; preprints are not peer reviewed.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,225 records · Page 68Linked to original sources

bioRxiv2018

Single-cell transcriptome analysis reveals estrogen signaling augments the mitochondrial folate pathway to coordinately fuel purine and polyamine synthesis in breast cancer cells

Estrogen regulates diverse physiological effects and drives breast tumor progression by directly activating estrogen receptor (ER). However, due to the stochastic nature of gene transcription and the resulting heterogeneous cellular response, it is important to investigate estrogen-stimulated gene expression profiles at the single-cell level in order to fully understand how ER regulates transcription in breast cancer cells. In this study, we performed single-cell transcriptome analysis on ER-positive breast cancer cell lines following 17{beta}-estradiol stimulation. Overall, we observed robust gene expression diversity between individual cells. Moreover, we found over two thirds of the genes in breast cancer cells displayed a bimodal expression pattern, which caused averaging artifacts and masked the identification of potential estrogen-regulated genes. We overcame this issue by reconstructing a dynamic estrogen-responsive transcriptional network from discrete time points into a pseudotemporal continuum. Pathway analysis of the differentially expressed genes derived from the pseudotemporal analysis showed an estrogen-stimulated metabolic switch that favored biosynthesis and cell proliferation but reduced estrogen degradation. In addition, we identified folate-mediated one-carbon metabolism as a novel estrogen-regulated pathway in breast cancer cells. Notably, estrogen stimulation reprogramed this pathway through the mitochondrial folate pathway to coordinately fuel polyamine and de novo purine synthesis. Finally, we showed AZIN1 and PPAT, key regulators in the above pathways, are direct ER target genes and essential for breast cancer cell survival and growth. In summary, our single-cell study illustrated a dynamic transcriptional heterogeneity in ER-positive breast cancer cells in response to estrogen stimulation and uncovered a novel mechanism of an estrogen-mediated metabolic switch.

genomics↗

bioRxiv2018

Modulation of slow and fast oscillations by direct current stimulation in the cerebral cortex in vitro

Non-invasive brain stimulation techniques, such as transcranial direct current stimulation (tDCS), play a growing role in the treatment of neurological disorders. However, the mechanisms by which electric fields modulate cortical network activity are only partially understood. To explore the spatiotemporal modulation of cortical activity by electric fields (DC fields), we exposed neocortical slices to constant fields of varying intensity and direction and we measured their effect on the low (<1 Hz) and high frequencies (beta 15-30 Hz and gamma 30-90 Hz) of spontaneously generated cortical oscillations. Slow oscillations consist of Up (active) and Down (silent) states. We found that DC fields ranging from -6 to +6 V/m induced an exponential increase in the frequency of slow oscillations through the regulation of the excitability and duration of Down states, while hardly affecting Up states duration. A computational model based on the mean-field theory of attractor dynamics provided a mechanistic and quantitative description of the network dynamics underlying such precise modulation of slow oscillatory frequency. The modulation of high frequencies by DC fields was less consistent, the high frequency power varying with the intensity of the fields only in a fraction of slices. Interestingly, negative DC fields of increasing intensities progressively and effectively reversed the increase in high frequency power induced by kainate application. Our findings have implications for the understanding of cortical oscillations and the mechanisms by which they are modulated by DC fields and may contribute to the future development of tools with an accurate spatiotemporal control of cortical activity.\n\nSignificance statementActing on the brain through electrical stimulation in order to correct dysfunctions or to induce functional recovery is a relatively common technique nowadays used in the clinical realm. In spite of the existence of previous studies on the effect of electric fields on neuronal and network physiology, questions regarding the mechanisms underlying exogenous electrical modulation of cortical dynamics still remain open. We demonstrate that continuous electric fields between -6 and +6 V/m induce a precise modulation of slow and fast cortical rhythms. Based on both experimental evidence and theoretical analysis, we describe some of the mechanistic underpinnings at play and provide useful information for the development of tools with better spatiotemporal control of cortical activity.

neuroscience↗

bioRxiv2018

Structural and functional influences of urban and rural childhoods on the medial prefrontal cortex

Global increases in urbanization have brought dramatic economic, environmental and social changes. However, less is understood about how these may influence disease-related brain mechanisms underlying epidemiological observations that urban birth and childhoods may increase the risk for neuropsychiatric disorders, including increased social stress and depression. In a genetically homogeneous Han Chinese adult population with divergent urban and rural birth and childhoods, we examined the structural and functional MRI neural correlates of childhood urbanicity, focusing on behavioral traits responding to social status threats, and polygenic risk for depression. Subjects with divergent rural and urban childhoods were similar in adult socioeconomic status and were genetically homogeneous. Urban childhoods, however, were associated with higher trait anxiety-depression. On structural MRI, urban childhoods were associated with relatively reduced medial prefrontal gray matter volumes. Functional medial prefrontal engagement under social status threat during working memory correlated with trait anxiety-depression in subjects with urban childhoods, to a significantly greater extent than in their rural counterparts, implicating an exaggerated physiological response to the threat context. Stress-associated medial prefrontal engagement also interacted with polygenic risk for depression, significantly predicting a differential response in individuals with urban but not rural childhoods. Developmental urbanicity thus differentially influenced medial prefrontal structure and function, at least in part through mechanisms associated with the neural processing of social status threat, trait anxiety, and genetic risk for depression, which may be factors in the association of urbanicity with adult psychopathology.\n\nSignificance StatementUrban living has been associated with social inequalities and stress. However, less is understood about the neural underpinnings by which these stressors affect disease risk, and in particular, genetic risk for depression. Leveraging urbanization in China, we studied adults with diverse urban and rural upbringings, who were genetically homogeneous and with similar current socioeconomic status, to isolate the effects of childhood urbanicity. At medial prefrontal cortex, a region critical for processing emotional stressors and social status, genetic risk for depression resulted in more deleterious function under stress in individuals with urban, but not rural childhoods. This implicates medial prefrontal cortexs critical role in brain development, integrating genetic mechanisms of stress and depression with the childhood environment.

neuroscience↗

bioRxiv2018

Engineering of a Polydisperse Small Heat-Shock Protein Reveals Conserved Motifs of Oligomer Plasticity

Small heat-shock proteins (sHSP) are molecular chaperones that bind and sequester partially and globally unfolded states of their client proteins. Of paramount importance to their physiological roles is the assembly into large oligomers, which for mammalian sHSP are polydisperse and undergo subunit exchange. The flexibility and dynamic nature of these oligomers mediates functional regulation by phosphorylation and underpins the deleterious effects of disease-linked mutations. Previously, we discovered that the archaeal Hsp16.5, which natively forms ordered and symmetric 24-subunit oligomers, can be engineered to transition to an ordered and symmetric 48-subunit oligomer by insertion of a peptide from human HspB1 (Hsp27) at the junction of the N-terminal and -crystallin domains. Here, we carried out a detailed analysis of the determinants of Hsp16.5 oligomeric plasticity by altering the sequence and length of the inserted peptide. Utilizing light scattering, blue native gel electrophoresis, native mass spectrometry and electron microscopy, we uncovered the existence of an array of oligomeric states (30 to 38 subunits) that can be populated as a consequence of different insertions. These oligomers are intermediate states on the assembly pathway of the 48-subunit oligomer as two of the variants can concurrently form 24-subunit or 30-38 subunit polydisperse oligomers. Polydisperse Hsp16.5 oligomers displayed higher affinity to a model client protein consistent with a general mechanism for recognition and binding that involves increased access of the hydrophobic N-terminal region. Our findings, which integrate structural and functional analyses from evolutionarily-distant sHSP, support a model wherein the modular architecture of these proteins encodes motifs of oligomer polydispersity, dissociation and expansion to achieve functional diversity and regulation.

biochemistry↗

bioRxiv2018

Messenger RNA biomarker signatures for forensic body fluid identification revealed by targeted RNA sequencing

The recovery of a DNA profile from the perpetrator or victim in criminal investigations can provide valuable source level information for investigators. However, a DNA profile does not reveal the circumstances by which biological material was transferred. Some contextual information can be obtained by a determination of the tissue or fluid source of origin of the biological material as it is potentially indicative of some behavioral activity on behalf of the individual that resulted in its transfer from the body. Here, we sought to improve upon established RNA based methods for body fluid identification by developing a targeted multiplexed next generation mRNA sequencing assay comprising a panel of approximately equal sized gene amplicons. The multiplexed biomarker panel includes several highly specific gene targets with the necessary specificity to definitively identify most forensically relevant biological fluids and tissues (blood, semen, saliva, vaginal secretions, menstrual blood and skin). In developing the biomarker panel we evaluated 66 gene targets, with a progressive iteration of testing target combinations that exhibited optimal sensitivity and specificity using a training set of forensically relevant body fluid samples. The current assay comprises 33 targets: 6 blood, 6 semen, 6 saliva, 4 vaginal secretions, 5 menstrual blood and 6 skin markers. We demonstrate the sensitivity and specificity of the assay and the ability to identify body fluids in single source and admixed stains. A 16 sample blind test was carried out by one lab with samples provided by the other participating lab. The blinded lab correctly identified the body fluids present in 15 of the samples with the major component identified in the 16th. Various classification methods are being investigated to permit inference of the body fluid/tissue in dried physiological stains. These include the percentage of reads in a sample that are due to each of the 6 tissues/body fluids tested and inter-sample differential gene expression revealed by agglomerative hierarchical clustering.

genomics↗

bioRxiv2018

FANCM-family branchpoint translocases remove co-transcriptional R-loops

Co-transcriptional R-loops arise from physiological or aberrant stalling of RNA polymerase, leading to formation of stable DNA:RNA hybrids. Unresolved R-loops can promote genome instability. Here, we show that the Fanconi anemia- and breast cancer-associated FANCM protein can directly unwind DNA-RNA hybrids from co-transcriptional R-loops in vitro. FANCM processively unwinds both short and long R-loops, irrespective of sequence, topology or coating by replication protein A. R-loops can also be unwound in the same assay by the yeast and bacterial orthologs of FANCM, Mph1 and RecG, indicating an evolutionary conserved function. Consistent with this biochemical activity of FANCM, we show that FANCM deficient cells are sensitive to drugs that stabilize R-loop formation. Our work reveals a mechanistic basis for R-loop metabolism that is critical for genome stability.

biochemistry↗

bioRxiv2018

Caenorhabditis elegans locomotion dynamics is affected by internally localized magnetic fields

C. elegans nematodes are a model organism used broadly to investigate the impact of environmental factors on physiology and behavior. Here, C. elegans with internalized paramagnetic nanoparticles were placed inside magnetic field to explore effects on locomotion. We hypothesize that internalized paramagnetic nanoparticles combined with external magnetic field affect C. elegans locomotion machinery. To test our hypothesis, we used young adult C. elegans fed on bacteria mixed with paramagnetic nanoparticles of 1 m, 100 nm and 40 nm diameter. The presence of nanoparticles inside the worms body (alimentary canal, body muscle) was verified by fluorescent and electron microscopy. A custom-made software was used to track freely moving C. elegans in the absence or presence of magnetic field sequentially for 200+200 sec. We used established metrics to quantify locomotion-related parameters, including posture, motion and path features. Key features of C. elegans locomotion (increased body bends and stay ratio, decreased range, forward movement, and speed along the magnetic field) were affected in worms with internalized nanoparticles of 100 nm and 1 m in the presence of magnetic field, in contrast to untreated worms. Our work contributes on clarifying the effect of internalized paramagnetic nanoparticles, combined with magnetic field, on C. elegans locomotion. Summary StatementC. elegans with internalized paramagnetic nanoparticles are placed inside magnetic field to explore effects on locomotion. Results support the potential of C. elegans to investigate the impact of the above environmental factors on behavior.

biophysics↗

bioRxiv2018

Timing of Cyclic Estradiol Treatment Differentially Affects Cognition in Aged Female Rhesus Monkeys

Some evidence suggests that there may be a limited \"window of opportunity\" for beneficial effects of hormone therapy on physiology after menopause in women. We tested, in aged, surgically menopausal (ovariectomized) rhesus monkeys, whether the timing of cyclic estradiol (E2) treatment impacted its effect on cognitive function. Monkeys were assigned to one of four treatment conditions after ovariectomy: either vehicle or E2 treatment for the duration of the protocol, vehicle for the first 2 years of the protocol followed by E2 for the remainder (delayed treatment), or E2 for the first year of the protocol followed by vehicle for the remainder (withdrawn treatment). Delayed treatment addressed the hypothesis that E2 treatment initiated more than 2 years after ovariectomy would have a reduced effect on cognitive function. Withdrawn treatment mirrors current clinical advice to women to use hormone therapy in the initial post-menopausal period then discontinue it. Two periods of cognitive testing assessed treatment effects on cognition over time. E2 treatment predominantly affected a prefrontal cortex-dependent test of spatiotemporal working memory (delayed response). Monkeys with delayed E2 treatment improved in delayed response performance over time, whereas vehicle-treated monkeys declined. Monkeys with withdrawn E2 treatment maintained their performance across assessments, as did monkeys treated with E2 across the entire protocol. These findings suggest that a \"window of opportunity\" for hormone treatment after cessation of ovarian function, if present in nonhuman primates, lasts longer than 2 years. It also supports the notion that beneficial effects of hormone therapy may persist after discontinuation of treatment.

neuroscience↗

bioRxiv2018

Diverse spatial organization of photosynthetic membranes among purple nonsulfur bacteria

In diverse bacteria, proper cellular physiology requires the utilization of protein- or membrane-bound compartments that afford specific metabolic capabilities. One such compartment is the light-harvesting intracytoplasmic membrane (ICM) of purple nonsulfur bacteria (PNSB). Here we reveal that ICMs are subject to differential spatial organization among PNSB. We visualized ICMs in live cells of fourteen PNSB species by exploiting the natural autofluorescence of the photosynthetic machinery. We then quantitatively characterized ICM localization using automated computational analysis of autofluorescence patterns within single cells across the population. Our studies revealed that ICMs are localized in distinct subcellular patterns that differ between species; some PNSB elaborate ICMs throughout the cell, while others spatially restrict ICM to varying degrees. The most highly-restricted ICMs were localized in a specific pattern corresponding to progression of cell growth and division. An identical pattern of ICM restriction was conserved across at least two genera. Phylogenetic and phenotypic comparisons established that ICM localization and ICM architecture are not strictly interdependent and that neither trait fully correlates with the evolutionary relatedness of the species. This discovery of new diversity in bacterial cell organization has implications for understanding both the mechanisms underpinning spatial arrangement of bacterial compartments and the potential benefits of adopting different spatiotemporal patterns.

microbiology↗

bioRxiv2018

Substrate deformations induce directed keratinocyte migration

Cell migration is an essential part of many (patho)physiological processes in the body, including keratinocyte re-epithelialization of healing wounds. Recent interest in the mechanobiology of tissues suggests that physical forces and mechanical cues from the wound bed (in addition to biochemical signals) may also play an important role in the healing process. Previously, we explored this possibility and found that polyacrylamide (PA) gel stiffness affected primary human keratinocyte behavior and that mechanical deformations in soft (~1.2 kPA) PA gels produced by neighboring cells appeared to influence the process of de novo epithelial sheet formation. In order to clearly demonstrate that keratinocytes do respond to such deformations, we conducted a series of experiments where we observed the response of single keratinocytes to a prescribed local substrate deformation that mimicked a neighboring cell or evolving multicellular aggregate via a servo-controlled microneedle. We also examined the effect of adding either Y27632, a rho kinase inhibitor, or blebbistatin, a non-muscle myosin II inhibitor, on the response of the cells to PA gel deformations. The results of this study indicate that keratinocytes do sense and respond to mechanical signals comparable to those that originate from substrate displacements imposed by neighboring cells, a finding that could have important implications for the process of keratinocyte re-epithelialization that takes place during normal and pathologic wound healing. Furthermore, the Rho/ROCK pathway and the engagement of NM II are both essential to the observed process of substrate deformation-directed keratinocyte migration.

biophysics↗

bioRxiv2018

Electrical Excitability of the Endoplasmic Reticulum Membrane Drives Electrical Bursting and the Pulsatile Secretion of Insulin in a Pancreatic Beta Cell Model

Pancreatic {beta}-cells secrete insulin, the hormone that controls glucose homeostasis in vertebrates. When activated by glucose, {beta}-cells display a biphasic electrical response. An initial phase, in which the cell fires action potentials continuously, is followed by a phase with a characteristic firing pattern, known as electrical bursting, that consists on brief pulses of action potentials separated by intervals of rest. Electrical bursting is believed to mediate the pulsatile secretion of insulin. The electrical response of {beta}-cells has been extensively studied at experimental and theoretical level. However, there is still no consensus on the cellular mechanisms that underlie each of the phases of the response. In this paper, I propose the hypothesis that the pattern of the plasma membrane (PM) response of stimulated {beta}-cells is generated by the electrical activity of the endoplasmic reticulum (ER) membrane. In this hypothesis, the interaction of the two excitable membranes, PM and ER membrane, each operating at a different time scale, generates both, the initial continuous phase and the periodic bursting phase. A mathematical model based on the hypothesis is presented. The behavior of the model {beta}-cell replicates the main features of the physiological response of pancreatic {beta}-cells to nutrients and to neuro-endocrine regulatory factors. The model cell displays a biphasic response to the simulated elevation of glucose. It generates electrical bursting with frequencies comparable to those observed in live cells. The simulation of the action of regulatory factors mimics the actual effect of the factors on the frequency of bursting. Finally, the model shows that a cell with a defective ER response behaves like a dysfunctional {beta}-cell from individuals with type 2 diabetes mellitus, a result that suggests that the electrical malfunction of the ER membrane may represent one of the primary causes of type 2 diabetes. Dynamic analysis of the ER behavior has revealed that, depending on the transport rates of Ca2+ in and out of the ER, the system has three possible dynamic states. They consist on the hyperpolarization of the ER membrane, periodic oscillations of the electric potential across the membrane, and the depolarization of the membrane. Each of these states determines a different functional program in the cell. The hyperpolarized state maintains the cell at rest, in a non-secreting state. Periodic oscillations of the ER membrane cause electrical bursting in the PM and the consequent pulsatile secretion of insulin. Finally, the depolarized state causes continuous firing and an acute secretory activity, the hyperactive conditions of the initial phase of the {beta}-cell response to glucose. The dynamic states of the ER are also associated with different long-term effects. So, conditions that induce the hyperactive depolarized state in {beta}-cells also potentiate apoptosis. The induction of the oscillatory state by glucose and neuro-endocrine factors seems to activate also cell proliferation. In extreme conditions though, such as the chronic treatment of T2DM with incretin analogs, the activation of the oscillatory state may lead to the appearance of cancer. The mathematical model presented here is an illustration of how, even in a extremely simplified system, the nonlinearity or excitability of the ER membrane can produce a repertoire of dynamic states that are able to generate a complex response comparable to the response observed experimentally in pancreatic {beta}-cells. In actual cells, with a much higher number of parameters susceptible to be modified by environmental and genetic factors, the ER membrane is likely to have a significantly bigger set of dynamic states each capable to direct the cell in a particular functional or developmental direction. The potential role of the electrical activity of the ER membrane in cellular processes such as fertilization, cell proliferation and differentiation, and cell death, as well as in the development of diverse pathological conditions is analyzed in the discussion.

cell biology↗

bioRxiv2018

Affective bonding explains post-traumatic behavioral development in adult mice

In human post-traumatic stress disorder (PTSD), a major psychiatry challenge is how diverse stress reactions emerge after a protracted symptom-free period. Here, we study the behavioral development in mice isolated after observing an aggressive encounter inflicted upon their pair-housed partners and compared the results with those in multiple control paradigms. Compared with mice plainly isolated, mice isolated following the acute witnessing social stress gradually developed a wide range of long-term differences of their physiological conditions, spontaneous behaviors, and social interactions, including paradoxical results if interpreted in traditional ways. To address this developmental diversity, we applied fine-scale behavioral analysis to standard behavioral tests and showed that the seemingly sudden emergent behavioral differences developed gradually. Mice showed different developmental patterns in different zones of a behavior testing apparatus. However, the results of the fine-scale analysis together with state-space behavioral characterization allow a consistent interpretation of the seemingly conflicting observations among multiple tests. Interestingly, these behavioral differences were not observed if the aggressive encounter happened to a stranger mouse. Additionally, traumatized mice showed rebound responses to their partners after the long separation. In contrast, mice pair-housed with their attacked partners after the aggressive encounters still showed a difference in social interactions, while a difference in spontaneous behaviors did not occur. Accordingly, we propose that social relationship is the single common factor underlying the otherwise independent development of behavioral differences in this mouse paradigm and that the gained insights could have parallels in human PTSD development.

neuroscience↗

bioRxiv2018

Endotoxin Tolerance Induced by Different TLR Ligands

Endotoxin tolerance is a long-recognised property of macrophages that leads to an altered response to repeated or chronic exposure to Toll-like receptor (TLR) ligands. The physiological role of tolerance is to limit the potential damage to host tissue that may otherwise result from prolonged production of pro-inflammatory cytokines. Endotoxin tolerance is induced by all TLRs tested to date, however, tolerance induced by the TLR4 ligand lipopolysaccharide (LPS) is by far the best studied. LPS tolerance involves a global transcriptional shift from a pro-inflammatory response toward one characterised by the expression of anti-inflammatory and pro-resolution factors. Although largely reversible, LPS-tolerance leads to a hybrid macrophage activation state that is pro-inflammatory in nature but possesses distinct regulatory anti-inflammatory features. Remarkably, a comparative transcriptomic analysis of tolerance induced by different TLR ligands has not previously been reported. Here we describe the transcriptomic profiles of mouse macrophages tolerised with ligands for TLR2, TLR3, TLR4 and TLR 9. While we identified TLR-specific transcriptional profiles in macrophages tolerised with each ligand, tolerance induced by TLR4 was the most comprehensive state, such that each gene tolerised by any of the TLRs tested was also found to be tolerised by TLR4. Pro-inflammatory cytokines are not universally supressed in all tolerant cells but distinct patterns of cytokine expression distinguished TLR-specific tolerance. Analysis of gene regulatory regions revealed specific DNA sequence motifs associated with distinct states of TLR tolerance, implicating previously identified as well as novel transcriptional regulators of tolerance in macrophages. These data provide a basis for the future exploitation of TLR-specific tolerant states to achieve therapeutic re-programming of the innate immune response.

immunology↗

bioRxiv2018

Differential Antiviral Activities of RSV Inhibitors in Human Airway Epithelium

We report the use of reconstituted 3D-human airway epithelium cells of bronchial origin (HuAEC) in an air-liquid interface to study respiratory syncytial virus (RSV) infection and to assess the efficacy of RSV inhibitors in (pre-)clinical development. RSV-A replicates efficiently in HuAEC and viral RNA is shed for weeks after infection. RSV infection reduces the ciliary beat frequency of the ciliated cells as of 4 days post infection, with complete ciliary dyskinesia observed by day 10. Treatment with RSV fusion inhibitors resulted in an antiviral effect only when added at the time of infection. In contrast, the use of replication inhibitors (both nucleoside and non-nucleosides) elicited a marked antiviral effect even when start of treatment was delayed until one or even three days after infection. Levels of the inflammation marker RANTES (mRNA) increased [~]200-fold in infected-untreated cultures (at three weeks post infection), but levels were comparable to those of uninfected cultures in the presence of PC-876, a RSV-replication inhibitor, demonstrating that an efficient antiviral treatment inhibits virus induced inflammation in this model. Overall, HuAEC offer a robust and physiologically relevant model to study RSV replication and to assess the efficacy of antiviral compounds.

microbiology↗

bioRxiv2018

HIF-2α is essential for carotid body development and function

Mammalian adaptation to oxygen flux occurs at many levels, from shifts in cellular metabolism to physiological adaptations facilitated by the sympathetic nervous system and carotid body (CB). Interactions between differing forms of adaptive response to hypoxia, including transcriptional responses orchestrated by the Hypoxia Inducible transcription Factors (HIFs), are complex and clearly synergistic. We show here that there is an absolute developmental requirement for HIF-2a, one of the HIF isoforms, for growth and survival of oxygen sensitive glomus cells of the carotid body. The loss of these cells renders mice incapable of ventilatory responses to hypoxia, and this has striking effects on processes as diverse as arterial pressure regulation, exercise performance, and glucose homeostasis. We show that the expansion of the glomus cells is correlated with mTORC1 activation, and is functionally inhibited by rapamycin treatment. These findings demonstrate the central role played by HIF-2a in carotid body development, growth and function.

bioinformatics↗

bioRxiv2018

Functional repurposing of regulatory element activity during mammalian evolution

The spatiotemporal control of gene expression exerted by promoters and enhancers is central for organismal development, physiology and behaviour. These two types of regulatory elements have long been distinguished from each other based on their function, but recent work highlighted common architectural and functional features. It also suggested that inheritable alterations in the epigenetic and sequence context of regulatory elements might underlie evolutionary changes of their principal activity, which could result in changes in the transcriptional profile of genes under their control or even facilitate the birth of new genes. Here, based on integrated cross-mammalian analyses of DNase hypersensitivity, chromatin modification and transcriptional data, we provide support for this hypothesis by detecting 449 regulatory elements with signatures of activity turnover in sister species from the primate and rodent lineages (termed \"P/E\" elements). Through the comparison with outgroup species, we defined the directionality of turnover events, which revealed that most instances represent transformations of ancestral enhancers into promoters, leading to the emergence of species-specific transcribed loci or 5 exons. Notably, P/E elements have distinct GC sequence compositions and stabilizing 5 splicing (U1) regulatory motif patterns, which may predispose them to functional repurposing during evolution. Moreover, we trace changes in the U1 and polyadenylation signal densities and distributions that accompanied and likely drove the evolutionary activity switches. Overall, our work suggests rather widespread evolutionary remodelling of regulatory element functions. Functional repurposing thus represents a notable mechanism that likely facilitated regulatory innovation and the origination of new genes and exons during mammalian evolution.

genomics↗

bioRxiv2018

The universal mechanism of intermediate filament transport

Intermediate filaments (IFs) are a major component of the cytoskeleton that regulates a wide range of physiological properties in eukaryotic cells. In motile cells, the IF network has to adapt to constant changes of cell shape and tension. In this study, we used two cell lines that express vimentin and keratins 8/18 to study the dynamic behavior of these IFs. We demonstrated that both IF types undergo extensive transport along microtubules. This was an unexpected result as keratin filament remodeling has been described to depend on actin dynamics. We established the role of kinesin-1 in vimentin and keratin IF transport by knocking out KIF5B, the ubiquitous isoform of kinesin-1. Futhermore, we demonstrated that unlike typical membrane cargoes, transport of both types of IFs does not involve kinesin light chains, but requires the presence of the same region of the kinesin-1 tail, suggesting a unified mechanism of IF transport.

cell biology↗

bioRxiv2018

Higher transcriptome stability during aging in long-lived giant mole-rats compared to short-lived rats

Many aging-associated physiological changes are known to come up in short- and long-lived species with a different trajectory and emerging evidence suggests that large parts of life history trait differences between species are based on inter-species variation in gene expression. Little information is yet available, however, about transcriptome changes during aging when comparing mammals with different lifespans. For this reason, we studied the transcriptomes of five tissues and two age cohorts in two similar sized rodent species with very different lifespans: rat (Rattus norvegicus) and giant mole-rat (Fukomys mechowii) with maximum lifespans of 3.8 and >20 years, respectively. Our results show that giant mole-rats exhibit higher transcriptome stability during aging than the rat. While well-known aging signatures (e.g. up-regulation of pro-inflammatory genes) were detected in all rat tissues, they showed up only in one giant mole-rat tissue. Furthermore, many differentially expressed genes that were found in both species, were regulated in opposite directions during aging. This suggests that expression changes that cause aging in short-lived species are counteracted in long-lived species. Taken together, transcriptome stability may be one key causal factor of the long life- and healthspan of giant mole-rats and maybe of African mole-rats in general.

systems biology↗