RNA polymerase II pausing regulates chromatin organization in erythrocytes.

Chicken erythrocytes are nucleated cells often considered to be transcriptionally inactive, although the epigenetic changes and chromatin remodeling that would mediate transcriptional repression and the extent of gene silencing during avian terminal erythroid differentiation are not fully understood. Here, we characterize the changes in gene expression, chromatin accessibility, genome organization and chromatin nuclear disposition during the terminal stages of erythropoiesis in chicken and uncover complex chromatin reorganization at different genomic scales. We observe a robust decrease in transcription in erythrocytes, but a set of genes maintains their expression, including genes involved in RNA polymerase II (Pol II) promoter-proximal pausing. Erythrocytes exhibit a reoriented nuclear architecture, with accessible chromatin positioned towards the nuclear periphery together with the paused RNA Pol II. In erythrocytes, chromatin domains are partially lost genome-wide, except at minidomains retained around paused promoters. Our results suggest that promoter-proximal pausing of RNA Pol II contributes to the transcriptional regulation of the erythroid genome and highlight the role of RNA polymerase in the maintenance of local chromatin organization.

Heterochromatin as an Important Driver of Genome Organization.

Heterochromatin is a constituent of eukaryotic genomes with functions spanning from gene expression silencing to constraining DNA replication and repair. Inside the nucleus, heterochromatin segregates spatially from euchromatin and is localized preferentially toward the nuclear periphery and surrounding the nucleolus. Despite being an abundant nuclear compartment, little is known about how heterochromatin regulates and participates in the mechanisms driving genome organization. Here, we review pioneer and recent evidence that explores the functional role of heterochromatin in the formation of distinct chromatin compartments and how failure of the molecular mechanisms forming heterochromatin leads to disarray of genome conformation and disease.

Early Post-stroke Activation of Vascular Endothelial Growth Factor Receptor 2 Hinders the Receptor 1-Dependent Neuroprotection Afforded by the Endogenous Ligand.

Vascular endothelial growth factor (VEGF) has long been connected to the development of tissue lesion following ischemic stroke. Contradictory findings either situate VEGF as a promoter of large infarct volumes or as a potential attenuator of damage due to its well documented neuroprotective capability. The core of this discrepancy mostly lies on the substantial number of pleiotropic functions driven by VEGF. Mechanistically, these effects are activated through several VEGF receptors for which various closely related ligands exist. Here, we tested in an experimental model of stroke how the differential activation of VEGF receptors 1 and 2 would modify functional and histological outcomes in the acute phase post-ischemia. We also assessed whether VEGF-mediated responses would involve the modulation of inflammatory mechanisms and how this trophic factor acted specifically on neuronal receptors. We produced ischemic infarcts in adult rats by transiently occluding the middle cerebral artery and induced the pharmacological inhibition of VEGF receptors by i.c.v. administration of the specific VEGFR2 inhibitor SU1498 and the pan-VEGFR blocker Axitinib. We evaluated the neurological performance of animals at 24 h following stroke and the occurrence of brain infarctions analyzed at the gross metabolic and neuronal viability levels. We also assessed the induction of peripheral pro- and anti-inflammatory cytokines in the cerebrospinal fluid and blood and assessed the polarization of activated microglia. Finally, we studied the direct involvement of cortical neuronal receptors for VEGF with in vitro assays of excitotoxic damage. Preferential VEGFR1 activation by the endogenous ligand promotes neuronal protection and prevents the presentation of large volume infarcts that highly correlate with neurological performance, while the concomitant activation of VEGFR2 reduces this effect, even in the presence of exogenous ligand. This process partially involves the polarization of microglia to the state M2. At the cellular level, neurons also responded better to the preferential activation of VEGFR1 when challenged to N-methyl-D-aspartate-induced excitotoxicity. Endogenous activation of VEGFR2 hinders the neuroprotective mechanisms mediated by the activation of VEGFR1. The selective modulation of these concurrent processes might enable the development of therapeutic approaches that target specific VEGFR1-mediated signaling during the acute phase post-stroke.

Endogenous recovery after brain damage: molecular mechanisms that balance neuronal life/death fate.

Neuronal survival depends on multiple factors that comprise a well-fueled energy metabolism, trophic input, clearance of toxic substances, appropriate redox environment, integrity of blood-brain barrier, suppression of programmed cell death pathways and cell cycle arrest. Disturbances of brain homeostasis lead to acute or chronic alterations that might ultimately cause neuronal death with consequent impairment of neurological function. Although we understand most of these processes well when they occur independently from one another, we still lack a clear grasp of the concerted cellular and molecular mechanisms activated upon neuronal damage that intervene in protecting damaged neurons from death. In this review, we summarize a handful of endogenously activated mechanisms that balance molecular cues so as to determine whether neurons recover from injury or die. We center our discussion on mechanisms that have been identified to participate in stroke, although we consider different scenarios of chronic neurodegeneration as well. We discuss two central processes that are involved in endogenous repair and that, when not regulated, could lead to tissue damage, namely, trophic support and neuroinflammation. We emphasize the need to construct integrated models of neuronal degeneration and survival that, in the end, converge in neuronal fate after injury. Under neurodegenerative conditions, endogenously activated mechanisms balance out molecular cues that determine whether neurons contend toxicity or die. Many processes involved in endogenous repair may as well lead to tissue damage depending on the strength of stimuli. Signaling mediated by trophic factors and neuroinflammation are examples of these processes as they regulate different mechanisms that mediate neuronal demise including necrosis, apoptosis, necroptosis, pyroptosis and autophagy. In this review, we discuss recent findings on balanced regulation and their involvement in neuronal death.