Tunable intervalence charge transfer in ruthenium Prussian blue analogue enables stable and efficient biocompatible artificial synapses

Emerging concepts for neuromorphic computing, bioelectronics, and brain-computer interfacing inspire new research avenues aimed at understanding the relationship between oxidation state and conductivity in unexplored materials. Here, we present ruthenium Prussian blue analogue (RuPBA), a mixed valence coordination compound with an open framework structure and ability to conduct both ionic and electronic charge, for flexible artificial synapses that reversibly switch conductance by more than four orders of magnitude based on electrochemically tunable oxidation state. Retention of programmed states is improved by nearly two orders of magnitude compared to the extensively studied organic polymers, thus reducing the frequency, complexity and energy costs associated with error correction schemes. We demonstrate dopamine detection using RuPBA synapses and biocompatibility with neuronal cells, evoking prospective application for brain-computer interfacing. By application of electron transfer theory to in-situ spectroscopic probing of intervalence charge transfer, we elucidate a switching mechanism whereby the degree of mixed valency between N-coordinated Ru sites controls the carrier concentration and mobility, as supported by DFT

Regulation Of Chromatin Structre And Transcription By Poly(Adp-Ribose) Polymerase -1

The process of transcription, which is a vital step in the cellular response to physiological and environmental stimuli, is highly regulated at multiple levels. Many proteins are involved in orchestrating transcriptional responses, including proteins that modulate the physiological template for transcription, chromatin. One such protein is the highly abundant nuclear enzyme Poly(ADP-ribose) Polymerase-1 , or PARP-1. Although PARP-1 has classically been studied with relation to its role in the detection and repair of DNA damage, recent work has uncovered physiological functions of PARP-1 in regulating transcription. PARP-1 has been shown to have a range of functions in transcriptional regulating, including acting as a co-activator and as a modulator of chromatin structure. Although there are increasing numbers of studies revealing roles for PARP-1 in many processes, the molecular mechanisms of PARP-1 action in most pathways is largely unknown. In this study, I have investigated transcriptional regulation by PARP-1 in vivo, using both genomic and gene-specific analyses in breast cancer cells and human cardiomyocytes. Using chromatin immunoprecipitation coupled with DNA microarrays (ChIPchip), I show that PARP-1 binds to active promoters in MCF-7 breast cancer cells, and that at genes that are positively-regulated by PARP-1, it acts to exclude the binding of linker histone H1. Further analysis revealed that exclusion of H1 from promoters allows for a favorable chromatin structure which in turn permits the binding of RNA Polymerase II at target genes. This open chromatin conformation also requires methylated histones, which PARP-1 maintains by PARylating and preventing recruitment of the demethylase KDM5B, a pathway which is also utilized by signaldependent transcription. Besides breast cancer, PARP-1 plays a prominent role in other pathologies, one of which is the progression of cardiovascular disease (CVD). I use a human cardiomyocyte cell line to show that TNF-alpha can drastically increase the binding of the transcription factor NF-kappa-B to chromatin, and that this causes changes in the gene expression profile of these cells. PARP-1 is known to cooperate with NF-kappa-B at target genes. I show that in human cardiomyocytes, PARP-1 is required for NF-kappa-B upregulated genes, but not for down-regulated genes, confirming its role as an activator of NF-kappa-B-dependent transcription. Interestingly, I see that the majority of NF-kappa-B binding in the presence of TNF-alpha is not to canonical NF-kappa-B binding sites, suggesting the the majority of the NF-kappa-B response is intricately dependent on other transcription factors, and I show that one of these factors, ATF2, is vital for recruiting NF-kappa-B to promoters and regulating transcription. It will be interesting to further investigate how PARP-1 and ATF2 may be collaborating at target genes. Together, these data demonstrate a conserved binding pattern of PARP-1 on chromatin across cell types, and establish novel connections between PARP-1, signaling pathways, chromatin and gene expression

Epigenetics of cellular reprogramming

Cells are constantly changing their state of equilibrium in response to internal and external stimuli. These changes in cell identity are driven by highly coordinated modulation of gene expression. This coordinated regulation is achieved in large part due to changes in the structure and composition of the chromatin, driven by epigenetic modulators. Recent discoveries in cellular and genomic reprogramming have highlighted the importance of chromatin modifications to reach and uphold the fidelity of target cell states. In this review, we focus on the latest work addressing the mechanisms surrounding the epigenetic regulation of various types of reprogramming, including somatic cell nuclear transfer (SCNT), cell fusion and transcription factor-induced and microRNA-induced pluripotency. The studies covered herein showcase the interplay between these epigenetic pathways, and highlight the importance of furthering our understanding of these connections to form a clearer picture of the mechanisms underlying stable cell fate transitions

Expression of Alternative Ago2 Isoform Associated with Loss of microRNA-Driven Translational Repression in Mouse Oocytes

Mouse oocyte maturation, fertilization, and reprogramming occur in the absence of transcription, and thus, changes in mRNA levels and translation rate are regulated through post-transcriptional mechanisms [1]. Surprisingly, microRNA function, which is a major form of post-transcriptional regulation, is absent during this critical period of mammalian development [2, 3]. Here, we investigated the mechanisms underlying the global suppression of microRNA activity. In both mouse and frogs, microRNA function was active in growing oocytes but then absent during oocyte maturation. RNA sequencing (RNA-seq) of mouse oocytes uncovered that the microRNA effector protein AGO2 is predominantly expressed as an alternative isoform that encodes a truncated protein lacking all of the known essential domains. Full-length Ago2 as well as the related Argonautes (Ago1, Ago3, and Ago4) were lowly expressed in maturing mouse oocytes. Reintroduction of full-length AGO2 together with an exogenous microRNA in either mouse or frog oocytes restored translational repression of a target reporter. However, levels of endogenous transcripts remained unchanged. Consistent with a lack of microRNA activity, analysis of transcripts with alternative polyadenylation sites showed increased stability of transcripts with a longer 3' UTR during oocyte maturation. Redundant mechanisms protecting endogenous transcripts and the conserved loss of microRNA activity suggest a strong selection for suppressing microRNA function in vertebrate oocytes

GRHL2-Dependent Enhancer Switching Maintains a Pluripotent Stem Cell Transcriptional Subnetwork after Exit from Naive Pluripotency

The enhancer landscape of pluripotent stem cells undergoes extensive reorganization during early mammalian development. The functions and mechanisms behind such reorganization, however, are unclear. Here, we show that the transcription factor GRHL2 is necessary and sufficient to activate an epithelial subset of enhancers as naive embryonic stem cells (ESCs) transition into formative epiblast-like cells (EpiLCs). Surprisingly, many GRHL2 target genes do not change in expression during the ESC-EpiLC transition. Instead, enhancers regulating these genes in ESCs diminish in activity in EpiLCs while GRHL2-dependent alternative enhancers become activated to maintain transcription. GRHL2 therefore assumes control over a subset of the naive network via enhancer switching to maintain expression of epithelial genes upon exit from naive pluripotency. These data evoke a model where the naive pluripotency network becomes partitioned into smaller, independent networks regulated by EpiLC-specific transcription factors, thereby priming cells for lineage specification

Two miRNA clusters reveal alternative paths in late-stage reprogramming.

Ectopic expression of specific factors such as Oct4, Sox2, and Klf4 (OSK) is sufficient to reprogram somatic cells into induced pluripotent stem cells (iPSCs). In this study, we examine the paths taken by cells during the reprogramming process by following the transcriptional activation of two pluripotent miRNA clusters (mir-290 and mir-302) in individual cells in vivo and in vitro with knockin reporters. During embryonic development and embryonic stem cell differentiation, all cells sequentially expressed mir-290 and mir-302. In contrast, during OSK-induced reprogramming, cells activated the miRNA loci in a stochastic, nonordered manner. However, the addition of Sall4 to the OSK cocktail led to a consistent reverse sequence of locus activation (mir-302 then mir-290) and increased reprogramming efficiency. These results demonstrate that cells can follow multiple paths during the late stages of reprogramming, and that the trajectory of any individual cell is strongly influenced by the combination of factors introduced