bluuebunny/crossref_metadata_2025_split huggingface dataset:
Loss of the Pioneer Factor FOXA1 Results in Genome-wide Epigenetic Reprogramming and activation of Interferon-Response Genes includingCD274/PD-L1
Authors: Hu Wenhuo , Yamashita Hironobu , Craig Jenna , Walter Vonn , Warrick Joshua I. , Al-Ahmadie Hikmat , DeGraff David J. 
Published: September 2020

AbstractForkhead Box A1 (FOXA1) is a pioneer transcription factor critical in epigenetic regulation of chromatin and cell fate determination. Reduced FOXA1 expression is an independent predictor of poor overall survival in bladder cancer patients. However, the impact ofFOXA1loss on chromatin epigenetics in bladder cancer is unknown. Therefore, we determined the impact ofFOXA1knock out (KO) on epigenetic modification of chromatin and associated gene expression. We identified 8,230 differentially expressed genes followingFOXA1KO. Surprisingly, Gene Set Enrichment Analysis (GSEA) identified IFNɑ/ɣ gene expression signatures as enriched followingFOXA1KO.FOXA1KO induced both increased and decreased numbers of histone 3 lysine 27 acetylation (H3K27ac) sites throughout the genome. As expected, the majority of differences in H3K27ac across genomic areas inFOXA1KO cells is mapped to intergenic and intronic regions where enhancers reside. In addition, a subset of differential H3K27ac levels were also mapped to proximal promoters and within gene bodies. Integrated analysis of RNA/ChIP-seq data shows changes in gene expression that are mirrored by differences in H3K27ac. Motif analysis of DNA sequence enriched for H3K27ac identified significant increases in transcription factor binding motifs including the interferon sensitive response element (ISRE) and interferon response factors such as IRF1. Moreover, we identified increased H3K27ac of regulatory elements as being associated with several upregulated interferon sensitive genes (ISGs) inFOXA1KO cells, includingCD274/PD-L1. Western blotting and Q-RT-PCR confirmed upregulation ofCD274/PD-L1 followingFOXA1KO. Analysis of TCGA data confirmed an inverse relationship betweenFOXA1andCD274in bladder cancer, as well as in other cancers. In summary, we provide evidence of widespread epigenetic reprogramming afterFOXA1KO in bladder cancer cells. Additionally, we provide evidence thatFOXA1KO-induced epigenetic changes contribute to activation of a global interferon-dominant expression signature, including the immune checkpoint targetCD274/PD-L1 in a cancer cell-intrinsic manner.
RNA sequence and structure determinants of Pol III transcriptional termination in human cells
Authors: Verosloff Matthew S. , Corcoran William K. , Dolberg Taylor B. , Leonard Joshua N. , Lucks Julius B. 
Published: September 2020

AbstractThe precise mechanism of transcription termination of the eukaryotic RNA polymerase III (Pol III) has been a subject of considerable debate. Although previous studies have clearly shown that at the end of RNA transcripts, tracts comprised of multiple uracils are required for Pol III termination, whether upstream RNA secondary structure in the nascent transcript is necessary for robust transcriptional termination is still subject to debate. We sought to address this directly through the development of anin celluloPol III transcription termination assay using a synthetic biology approach. Specifically, we utilized the recently developed Tornado expression system and a stabilized Corn RNA aptamer to create a Pol III-transcribed RNA that produces a detectable fluorescent signal when transcribed in human cells. To study the effects of RNA sequence and structure on Pol III termination, we systematically varied the sequence context upstream of the aptamer and identified sequence characteristics that enhance or diminish termination. We found that in the absence of predicted secondary structure, only poly-U tracts longer than then the average length found in the human genome (4–5 nucleotides), efficiently terminate Pol III transcription. We found that shorter poly-U tracts could induce termination when placed in proximity to secondary structural elements, while secondary structure by itself was not sufficient to induce termination. These findings demonstrate a key role for sequence and structural elements within Pol III-transcribed nascent RNA for efficient transcription termination, and demonstrate a generalizable assay for characterizing Pol III transcription in human cells.
A long-range chromatin interaction regulates SATB homeobox 1 gene expression in trophoblast stem cells
Authors: Yu Wei , Chakravarthi V. Praveen , Borosha Shaon , Ratri Anamika , Dalal Khyati , Wolfe Michael W. , Starks Rebekah R. , Tuteja Geetu , Rumi M.A. Karim 
Published: September 2020

ABSTRACTSATB homeobox proteins are important regulators of developmental gene expression. Among the stem cell lineages determined during early embryonic development, trophoblast stem (TS) cells exhibit robust SATB expression. Both SATB1 and SATB2 act to maintain trophoblast stem-state. However, the molecular mechanisms that regulate TS-specificSatbexpression are not yet known. We identifiedSatb1variant 2 as the predominant transcript in trophoblasts. Histone marks, and RNA polymerase II occupancy in TS cells indicated active state of the promoter. A novel cis-regulatory region with active histone marks was identified ∼21kbp upstream of variant 2 promoter. CRISPR/Cas9 mediated disruption of this sequence decreasedSatb1expression in TS cells and chromatin conformation capture confirmed looping of this regulatory region into the promoter. Scanning position weight matrices across the enhancer predicted two ELF5 binding sites in close vicinity of SATB1 sites, which were confirmed by chromatin immunoprecipitation. Knockdown of ELF5 downregulatedSatb1expression in TS cells and overexpression of ELF5 increased the enhancer-reporter activity. Interestingly, ELF5 interacts with SATB1 in TS cells, and the enhancer activity was upregulated following SATB overexpression. Our findings indicate that trophoblast-specificSatb1expression is regulated by long-range chromatin looping of an enhancer that interacts with ELF5 and SATB proteins.
Optimizing mitochondrial maintenance in extended neuronal projections
Authors: Agrawal Anamika , Koslover Elena F. 
Published: September 2020

AbstractNeurons rely on localized mitochondria to fulfill spatially heterogeneous metabolic demands. Mitochondrial aging occurs on timescales shorter than the neuronal lifespan, necessitating transport of fresh material from the soma. Maintaining an optimal distribution of healthy mitochondria requires an interplay between a stationary pool localized to sites of high metabolic demand and a motile pool capable of delivering new material. Interchange between these pools can occur via transient fusion / fission events or by halting and restarting entire mitochondria. Our quantitative model of neuronal mitostasis identifies key parameters that govern steady-state mitochondrial health at discrete locations. Very infrequent exchange between stationary and motile pools optimizes this system. Exchange via transient fusion allows for robust maintenance, which can be further improved by selective recycling through mitophagy. These results provide a framework for quantifying how perturbations in organelle transport and interactions affect mitochondrial homeostasis in neurons, a key aspect underlying many neurodegenerative disorders.Author summaryNeurons contain long projections termed axons and dendrites and a small central body that is responsible for much of cellular biosynthesis. Mitochondria, the energy hubs of a cell, are synthesized in the soma and actively transported to distant sites of high energy demand. Given the extreme distances between these sites and the soma, maintaining distal mitochondrial health poses a substantial challenge. Defects in mitochondrial transport and maintenance are associated with several neurological disorders.Fortunately, mitochondria stationed at distant sites can be ‘serviced’ by passing mitochondria that emerge from the soma and move around the neuron, as well as through low levels of local protein synthesis. We develop mathematical models for two strategies of mitochondrial maintenance: one with direct protein exchange between moving and stationary mitochondria (‘Space Station’) and the other with moving mitchondria occasionally replacing stationary ones at the demand sites (‘Changing of the Guard’). We find that only a few servicing events and a small motile pool form optimal conditions for maintaining mitochondrial health. The system can be improved further by selectively removing and recycling some unhealthy mitochondria. Our results are consistent with observations of mitochondrial behavior in neurons and form a basis for future quantitative study of mitochondrial maintenance.
Modulation of cAMP metabolism for CFTR potentiation in human airway epithelial cells
Authors: Nguyen Jenny P. , Bianca Matthew , Huff Ryan D. , Tiessen Nicholas , Inman Mark D. , Hirota Jeremy A. 
Published: September 2020

ABSTRACTCystic fibrosis (CF) is a genetic disease characterized by CF transmembrane regulator (CFTR) dysfunction. With over 2000 CFTR variants identified, in addition to known patient to patient variability, there is a need for personalized treatment. The discovery of CFTR modulators has shown efficacy in certain CF populations, however there are still CF populations without valid therapeutic options. With evidence suggesting that single drug therapeutics are insufficient for optimal management of CF disease, there has been an increased pursuit of combinatorial therapies. Our aim was to test cyclic AMP (cAMP) modulation, through ATP Binding Cassette Transporter C4 (ABCC4) and phosphodiesterase-4 (PDE-4) inhibition, as a potential add-on therapeutic to a clinically approved CFTR modulator, VX-770, as a method for increasing CFTR activity. Human airway epithelial cells (Calu-3) were used to test the efficacy of cAMP modulation by ABCC4 and PDE-4 inhibition through a series of concentration-response studies. Our results showed that cAMP modulation, in combination with VX-770, led to an increase in CFTR activity via an increase in sensitivity when compared to treatment of VX-770 alone. Our study suggests that cAMP modulation has potential to be pursued as an add-on therapy for the optimal management of CF disease.
Expression of varicella-zoster virus VLT-ORF63 fusion transcript induces broad viral gene expression during reactivation from neuronal latency
Authors: Ouwendijk Werner J. D. , Depledge Daniel P. , Rajbhandari Labchan , Rovis Tihana Lenac , Jonjic Stipan , Breuer Judith , Venkatesan Arun , Verjans Georges M. G. M. , Sadaoka Tomohiko 
Published: September 2020

SummaryVaricella-zoster virus (VZV) establishes lifelong neuronal latency in most humans world-wide, reactivating in one-third to cause herpes zoster and occasionally chronic pain. How VZV establishes, maintains and reactivates from latency is largely unknown. Latent VZV gene expression is restricted to VZV latency-associated transcript (VLT) and open reading frame 63 (ORF63) in naturally VZV-infected human trigeminal ganglia (TG). Notably, these transcript levels positively correlated suggesting co-regulated transcription during latency. Here, we used direct RNA-sequencing to identify fusion transcripts that combine VLT and ORF63 loci (VLT-ORF63) and are expressed during both lytic and latent VZV infections. Furthermore, real-time PCR, RNAin situhybridization and 5’ rapid amplification of cDNA ends (RACE) all confirmed VLT-ORF63, but not canonical ORF63, expression in human TG. During lytic infection, one of the two major VLT-ORF63 isoforms encodes a novel fusion protein combining VLT and ORF63 proteins (pVLT-ORF63).In vitro, VLT is transcribed in latently VZV-infected human sensory neurons, whereas VLT-ORF63 expression is induced by reactivation stimuli. Moreover, the pVLT-ORF63-encoding VLT-ORF63 isoform induced transcription of lytic VZV genes. Collectively, our findings show that VZV expresses a unique set of VLT-ORF63 transcripts, potentially involved in the transition from latency to lytic VZV infection.
Regulation of Hippocampal Excitatory Synapses by the Zdhhc5 Palmitoyl Acyl Transferase
Authors: Shimell Jordan J. , Globa Andrea , Sepers Marja D. , Wild Angela R. , Matin Nusrat , Raymond Lynn A. , Bamji Shernaz X. 
Published: September 2020

ABSTRACTPalmitoylation is the most common post-translational lipid modification in the brain; however, the role of palmitoylation and palmitoylating enzymes in the nervous system remains elusive. One of these enzymes, Zdhhc5, has previously been shown to regulate synapse plasticity. Here, we report that Zdhhc5 is also essential for the formation of excitatory, but not inhibitory synapses bothin vitroandin vivo. We demonstratein vitrothat this is dependent on Zdhhc5’s enzymatic activity, its localization at the plasma membrane, and its C-terminal domain which has been shown to be truncated in a patient with schizophrenia. Loss of Zdhhc5 in mice results in a decrease in the density of excitatory hippocampal synapses accompanied by alterations in membrane capacitance and synaptic currents, consistent with an overall decrease in spine number and silent synapses. These findings reveal an important role for Zdhhc5 in the formation and/or maintenance of excitatory synapses.
GW182 Proteins Restrict Extracellular Vesicle Mediated Selective Export of Used miRNAs In Mammalian Cancer Cells
Authors: Ghosh Souvik , Chakrabarty Yogaditya , Mukherjee Kamalika , Ghoshal Bartika , Bhattacharyya Suvendra N. 
Published: September 2020

AbstractMicroRNAs are small regulatory RNAs of relatively long half-life in non-proliferative human cells. However, in cancer cells the half-lives of miRNAs are comparatively short. To understand the mechanism of rapid miRNA turn over in cancer cells, we explored the effect of “usage” of specific miRNAs for translation repression of their targets on the abundance of that miRNA. We have noted an accelerated extracellular vesicle mediated export of “used” miRNAs in mammalian cells and the miRNA-export process get retarded by Ago2 interacting protein GW182B. The GW182 group of proteins are localized to GW182 Bodies or RNA Processing Bodies in mammalian cells and GW182B dependent retardation of miRNA export depends on GW-body integrity and is independent of HuR mediated auxiliary pathway of miRNA export. Our data thus support existence of a HuR independent pathway of miRNA export in human cells that can be targeted to increase cellular miRNA levels in cancer cells to induce senescence.Graphical AbstractKey PointsUsage of miRNA is proportional with its export and turnoverGW182 proteins cause phase separation of Ago2 to P-bodies and restrict miRNA export via extracellular vesicles (EVs)HuR driven auxiliary path of miRNA export is independent of GW182 controlled main path of miRNA exclusion
MTFR2 regulates mitochondrial fission and impacts spindle integrity during mitosis
Authors: Luo Yibo , Liu Song-Tao 
Published: September 2020

AbstractPreviously we reported that mitochondrial fission regulator 2 (MTFR2, also termed DUFD1 or FAM54A) is co-transcribed with core centromere/kinetochore components, indicating a possible role in mitosis regulation. Here we show that human MTFR2 is a mitochondrial outer membrane protein and participates in DRP1 dependent mitochondrial fission. MultipleMTFR2variants identified in cancer samples are defective in triggering mitochondrial fission. InducibleMTFR2depletion caused prolonged mitotic duration and increased chromosome mis-segregation, resulting in multi-nucleated daughter cells.MTFR2knockout cells accumulated spindle defects, producing either multipolar spindles or short oscillating spindles due to loss of astral microtubules. MTFR2 is phosphorylated during mitosis. The phosphorylation mutant, as well as the cancer variants, failed to correct the prolonged mitotic duration.MTFR2knockout also rendered cells more resistant to apoptosis caused by taxol treatment. As overexpressing MFN1 or DRP1-K38A also caused spindle defects, we conclude that mitochondrial fragmentation during mitosis ensures spindle integrity and chromosomal stability, and MTFR2 plays a critical role in bridging proper mitochondrial fission and chromosome segregation.
A Fully Functional ROP Fluorescent Fusion Protein Reveals Roles for This GTPase in Subcellular and Tissue-Level Patterning
Authors: Cheng Xiaohang , Mwaura Bethany W. , Chang Stauffer Sophia R. , Bezanilla Magdalena 
Published: September 2020

Abstract
Rho of Plants (ROPs) are GTPases that regulate polarity and patterned wall deposition in plants. As these small, globular proteins have many interactors, it has been difficult to ensure that methods to visualize ROP in live cells do not affect ROP function. Here, motivated by work in fission yeast (Schizosaccharomyces pombe), we generated a fluorescent moss (Physcomitrium [Physcomitrella] patens) ROP4 fusion protein by inserting mNeonGreen after Gly-134. Plants harboring tagged ROP4 and no other ROP genes were phenotypically normal. Plants lacking all four ROP genes comprised an unpatterned clump of spherical cells that were unable to form gametophores, demonstrating that ROP is essentially for spatial patterning at the cellular and tissue levels. The functional ROP fusion protein formed a steep gradient at the apical plasma membranes of growing tip cells. ROP also predicted the site of branch formation in the apical cell at the onset of mitosis, which occurs one to two cell cycles before a branch cell emerges. While fluorescence recovery after photobleaching studies demonstrated that ROP dynamics do not depend on the cytoskeleton, acute depolymerization of the cytoskeleton removed ROP from the membrane only in recently divided cells, pointing to a feedback mechanism between the cell cycle, cytoskeleton, and ROP.
Practitioner experience of the impact of humanistic methods on autism practice: a preliminary study
Authors: Robinson Anna , Galbraith Ian , Carrick Lorna 
Published: September 2020

Purpose
Autistic people are subject to having their behaviour shaped from a variety of practitioners predominantly using behaviourist methodologies. Little is known about how learning alternative humanistic methodologies impacts practitioner experiences of relational encounters with autistic people. This paper aims to develop an understanding of practitioner experiences of using person-centred counselling (PCC) skills and contact reflections (CR) when engaging with autistic people.

Design/methodology/approach
This qualitative study used an interpretive approach to help elucidate perceptions of changing practice. It involved a framework analysis of 20 practitioner’s experiential case study accounts.

Findings
An overarching theme emerged: subtle transformations resulted from shifting practice paradigms. Four broad themes were identified: “A different way of being”; “Opening heightened channels of receptivity”; “Trust in self-actualising growth” and “Expanding relational ripples”. The findings suggest that PCC and CRs skills training shows promise in providing practitioners with a different way of being with autistic people that enhances their capacity towards neurotypical-neurodivergent intersubjectivity.

Social implications
The authors speculate on the power dynamics of care relationships and those who may identify as possessing autism expertise. The authors are curious as to whether this humanistic skills training can truly penetrate practitioner core values and see this as a fundamental issue which requires further investigation.

Originality/value
To the best of the authors’ knowledge, this is the first study to provide a qualitative account of autism practitioner reflections following training in humanistic methodologies. It challenges the concept of autism expertise, guided by a pathologiSing model, focused on fixing a problem located in the person, which conceals the removal of personhood.
Assessing the effect of playing games on the behavior of ASD and TD children
Authors: Alkhayat Laila Saud , Ibrahim Mohamed 
Published: September 2020

PurposePrevious researches point that children with Autism Spectrum Disorder (ASD) show particular interests in computers and other multimedia electronics (Mazurek et al., 2012). Experts in pediatric care contemplate the possibility of exploiting this relationship to inform the interventions among children with Autism. This paper aims to explore how video games can be used to aid the cognitive and social development among children with ASD and typically developing children (TDC).Design/methodology/approachThe study design used was experimental, with 112 children as the main participants. The researchers watched the behaviors of the children through controlled observation as they compared the behaviors with their established models. In this case, the structured models worked as the control group in the experiment. To understand the relationship between the variables: exposure to video games and children's social interactions, the researchers used multiple linear regression analysis, ANOVA and correlation coefficientsFindingsThe predictor model was effective because it accounted for at least 26% of the variation in the dependent variables at a statistical significance level ofp< 0.000. Other than the structured models, there were also individual predictors, which also established that when families played games with children, the children tended to calm down their negative behaviors. Hence, family playing games with children can help ease the symptoms of children with ASD and TDC at (t = 2.631, 4.180 and 0.024,p= 0.05). However, the duration of watching or playing the games did not contribute to children negative behavior such as poor school performance, failing to complete homework, playing games past bedtime and feeling agitated or isolated.Originality/valueTo the best of the authors’ knowledge, this paper is original, and it is first to report the findings of this type of study. This research used unique sample sizes and variables, though within the existing theoretical framework of social science experiments. All borrowed ideas have properly been cited to original owners’ efforts.