bluuebunny/crossref_metadata_2025_split huggingface dataset:
Is there a role of phase partitioning in coordinating DNA damage response?
Authors: Tosolini D. , Antoniali G. , Dalla E. , Tell G. 
Published: August 2020

AbstractDNA repair pathways are critical processes that need both spatial and temporal fine regulation. Liquid-liquid phase separation (LLPS) is a way to concentrate biochemical reactions, while excluding non-interacting components. Protein’s disordered domains, as well as RNA, favor condensation to modulate this process. Recent insights about phase-separation mechanisms pointed to new fascinating models that could explain how cells could cope with DNA damage responses. In this context, it is emerging that RNA-processing pathways and PARylation events, through the addition of an ADP-ribose moiety to both proteins and DNA, participate in different aspects of the DNA Damage Response (DDR). Remarkably, defects in these regulatory connections are associated with genomic instability and human pathologies. In addition, it has been recently noticed that several DNA repair enzymes, such as 53BP1 and APE1, are endowed with RNA binding abilities. APE1 is a multifunctional protein belonging to the Base Excision Repair (BER) pathway of non-distorting DNA lesions, bearing additional ‘non-canonical’ DNA-repair functions associated with processes coping with RNA metabolism. In this work, after reviewing the recent literature supporting a role of LLPS in DDR, we analyze, as a proof of principle, the interactome of APE1 using a bioinformatics approach to look for clues of LLPS in BER. Some of the APE1 interactors are associated with cellular processes in which LLPS has been either proved or proposed and are involved in several tumorigenic and amyloidogenic events. This work represents a paradigmatical pipeline for evaluating the relevance of LLPS in DDR.Statement of significanceIn this work, we aimed to test the hypothesis of an involvement of phase-separation in regulating the molecular mechanisms of the multifunctional enzyme APE1 starting from the analysis of its recently-characterized protein-protein interactome (PPI). We compared APE1-PPI to phase-separation databases and we performed functional enrichment analysis, uncovering links between APE1 and already known demixing factors, establishing an association with liquidliquid phase separation. This analysis could represent a starting point for implementing downstream experimental validations, using in vitro and in vivo approaches, to assess actual demixing.
DNA methylation inVerticillium dahliaerequires only one of three putative DNA methyltransferases, yet is dispensable for growth, development and virulence
Authors: Kramer H. Martin , Cook David E. , van den Berg Grardy C.M. , Seidl Michael F. , Thomma Bart P.H.J. 
Published: August 2020

ABSTRACTDNA methylation is an important epigenetic control mechanism that in many fungi is restricted to genomic regions containing transposons. Two DNA methyltransferases, Dim2 and Dnmt5, are known to perform methylation at cytosines in fungi. While most ascomycete fungi encode both Dim2 and Dnmt5, only few functional studies have been performed in species containing both. In this study, we report functional analysis of bothDim2andDnmt5in the plant pathogenic fungusVerticillium dahliae. Our results show that Dim2, but not Dnmt5 or the putative sexual-cycle related DNA methyltransferase Rid, is responsible for nearly all DNA methylation. Single or double DNA methyltransferase mutants did not show altered development, virulence, or transcription of genes or transposons. In contrast,Hp1andDim5mutants that are impacted in chromatin-associated processes upstream of DNA methylation are severely affected in development and virulence and display extensive transcriptional reprogramming in specific hypervariable genomic regions (so-called lineage-specific (LS) regions) that contain genes associated with host colonization. As these LS regions are largely devoid of DNA methylation and of Hp1- and Dim5-associated heterochromatin, the differential transcription is likely caused by pleiotropic effects rather than by differential DNA methylation. Overall, our study suggests that Dim2 is the main DNA methyltransferase inV. dahliaeand, in conjunction with work on other fungi, is likely the main active DNMT in ascomycetes, irrespective ofDnmt5presence. We speculate that Dnmt5 acts under specific, presently enigmatic, conditions or, alternatively, acts in DNA-associated processes other than DNA methylation.
CREB-binding protein gene,HAC701, negatively regulates WRKY45-dependent immunity in rice
Authors: Espinas Nino A. , Le Tu Ngoc , Saori Miura , Shimajiri Yasuka , Shirasu Ken , Saze Hidetoshi 
Published: August 2020

ABSTRACTCREB-binding protein (CBP) is a known transcriptional coactivator and an acetyltransferase that functions in several cellular processes by regulating gene expression. However, how it functions in plant immunity remains unexplored. By characterizinghac701, we demonstrate thatHAC701negatively regulates the immune responses in rice.hac701shows enhanced disease resistance against a bacterial pathogen,Pseudomonas syringaepv.oryzae(Pso), which causes bacterial halo blight of rice. Our transcriptomic analysis revealed that riceWRKY45, one of the main regulators of rice immunity, is upregulated inhac701and possibly conferring the resistance phenotype againstPso. The morphological phenotypes ofhac701single mutants were highly similar toWRKY45overexpression transgenic lines reported in previous studies. In addition, we also compared the list of genes in these studies whenWRKY45is overexpressed and chemically induced transiently with the differentially expressed genes (DEGs) inhac701, and found that they largely overlap. When we investigated forcis-elements found 1kb upstream ofWRKY45gene and WRKY45-dependent DEGs, we found thatWRKY45promoter contains the CRE motif, a possible target of HAC701-mediated regulation. Genome-wide H3K9 acetylation profiling showed depletion of acetylation at large set of genes inhac701. However, consistent with the upregulation ofWRKY45gene expression, our ChIP-sequencing analysis demonstrated that regions ofWRKY45promoter are enriched in H3K9 acetylation inhac701compared to the segregated wild type control in the mock condition.WRKY45promoter might be on the receiving end for possible genome-wide compensatory effects when a global regulator likeHAC701is mutated. Finally, we show thatHAC701may have roles in systemic immune signaling. We therefore propose that wild typeHAC701negatively regulatesWRKY45gene expression, thereby suppressing immune responses.SIGNIFICANCEHAC701 is a member of CREB-binding protein (CBP) family that acts as transcriptional coactivator and acetyltransferase. However, little is known how it regulates innate immunity in plants. Herein we reported that riceHAC701suppresses WRKY45-dependent defense pathway. Our study showed thatHAC701seemingly interacts genetically withWRKY45in rice to modulate immune responses against pathogens.
Heterochromatin-dependent transcription of satellite DNAs in theDrosophila melanogasterfemale germline
Authors: Wei Xiaolu , Eickbush Danna G. , Speece Iain , Larracuente Amanda M. 
Published: August 2020

ABSTRACTLarge blocks of tandemly repeated DNAs—satellite DNAs (satDNAs)—play important roles in heterochromatin formation and chromosome segregation. We know little about how satDNAs are regulated, however their misregulation is associated with genomic instability and human diseases. We use theDrosophila melanogastergermline as a model to study the regulation of satDNA transcription and chromatin. Here we show that complex satDNAs (>100-bp repeat units) are transcribed into long noncoding RNAs and processed into piRNAs (PIWI interacting RNAs). This satDNA piRNA production depends on the Rhino-Deadlock-Cutoff complex and the transcription factor Moonshiner—a previously-described non-canonical pathway that licenses heterochromatin-dependent transcription of dual-strand piRNA clusters. We show that this pathway is important for establishing heterochromatin at satDNAs. Therefore, satDNAs are regulated by piRNAs originating from their own genomic loci. This novel mechanism of satDNA regulation provides insight into the role of piRNA pathways in heterochromatin formation and genome stability.
A molecular taxonomy of tumors independent of tissue-of-origin
Authors: Nguyen Peter T. , Coetzee Simon G. , Lakeland Daniel L. , Hazelett Dennis J. 
Published: August 2020

AbstractCancer is a complex disease involving disrupted cellular metabolism, basic biochemical processes, and the microenvironment. However, despite some generally agreed upon unifying principles (Hanahan and Weinberg 2000, 2011), molecular signatures remain largely indistinguishable from tissue-of-origin, presenting a major barrier for precision health and individualized medicine. To address this challenge, we reduce mutation data to disruptions in a select set of pathways relevant to basic cell biology, from DNA replication to cellular communication. Using dimensionality reduction techniques, we assign tumor samples into ten clusters distinct from tissue-of-origin and largely free of bias from mutational burden or clinical stage. We show that the clusters vary in prognosis by modeling relative risk of death by cancer type and cluster. We identify cluster-specific mutations in different tissues, demonstrating that tissue-specific signatures contribute to common cellular phenotypes. Moreover, germline risk genes involved in replication fidelity and genome stability are equally distributed among clusters, contrary to the expectation that such genes are avatars of molecular subtype. We investigate metastatic and non-metastatic pathways, and show that most differences are cluster-specific. Some metastatic pathways from one cluster are cluster-specific pathways from non-metastatic tumors of another cluster, suggesting phenotypic convergence. Taken as a whole, our observations suggest that common driver genes combine with tissue-specific disruptions in tumor-promoting pathways to produce a limited number of distinct molecular phenotypes. Thus, we present a coherent view of global tumor biology, and explain how common cellular dysfunction might arise from tissue-specific mutations.
Effects of hyperbaric environment on endurance and metabolism are exposure time-dependent in well-trained mice
Authors: Suzuki Junichi 
Published: August 2020

AbstractHyperbaric exposure (1.3 atmospheres absolute with 20.9% O2) for 1 h a day was shown to improve exercise capacity. The present study was designed to reveal whether the daily exposure time affects exercise performance and metabolism in skeletal and cardiac muscles. Male mice in the training group were housed in a cage with a wheel activity device for 7 weeks from 5 weeks old. Trained mice were then subjected to hybrid training (HT, endurance exercise for 30 min followed by sprint interval exercise for 30 min). Hyperbaric exposure was applied following daily HT for 15 min (15HT), 30 min (30HT), or 60 min (60HT) for 4 weeks (each group, n = 10). In the endurance capacity test, maximal work values were significantly increased by 30HT and 60HT. In the left ventricle (LV), activity levels of 3-hydroxyacyl-CoA-dehydrogenase, citrate synthase, and carnitine palmitoyl transferase (CPT) 2 were significantly increased by 60HT. CPT2 activity levels were markedly increased by 60HT in the plantaris muscle (PL). Pyruvate dehydrogenase complex (PDHc) activity values in PL were enhanced more by 30HT and 60HT than by HT. In both 30HT and 60HT groups, lactate dehydrogenase activity levels were significantly increased and decreased, respectively, in the gastrocnemius muscle and LV. These results indicate that hyperbaric exposure for 30 min or longer has beneficial effects on endurance, and 60-min exposure has the potential to further increase performance by facilitating fatty acid metabolism in skeletal and cardiac muscles in highly-trained mice.
Genome-wide strand asymmetry in massively parallel reporter activity favors genic strands
Authors: Roberts Brian S. , Partridge E. Christopher , Moyers Bryan A. , Agarwal Vikram , Newberry Kimberly M. , Martin Beth K. , Shendure Jay , Myers Richard M. , Cooper Gregory M. 
Published: August 2020

AbstractMassively parallel reporter assays (MPRAs) are useful tools to discover and characterize regulatory elements in human genomes. Partly because enhancer function is assumed to be orientation independent with respect to each strand of the DNA helix, most reported MPRA results ignore stranded information. However, we find pervasive strand asymmetry of MPRA signals in datasets from multiple reporter configurations and in both published and newly reported data. These effects are reproducible across different cell types and in different treatments within a cell type, and are observed both within and outside of annotated regulatory elements. From elements in gene bodies, MPRA strand asymmetry favors the sense strand, suggesting that biological function related to endogenous transcription is driving the phenomenon. Similarly, within Alu mobile element insertions, we find that strand asymmetry favors the transcribed strand of the ancestral retrotransposon. The effect is consistent across the multiplicity of Alu elements in human genomes, and is more pronounced in younger, less diverged Alu elements. We find sequence features driving MPRA strand asymmetry and demonstrate its prediction from sequence alone. We see some evidence for both RNA stabilization and transcriptional activation mechanisms, and hypothesize that the effect is driven by natural selection favoring efficient transcription. Our results indicate that strand asymmetry, as a pervasive and reproducible feature, should be accounted for in analysis of MRPA data. More importantly, the fact that MPRA asymmetry favors naturally transcribed strands suggests that it stems from preserved biological functions that have a substantial, global impact on gene and genome evolution.
SARS-CoV-2 Nucleocapsid protein is decorated with multiple N- and O-glycans
Authors: Supekar Nitin T. , Shajahan Asif , Gleinich Anne S. , Rouhani Daniel , Heiss Christian , Azadi Parastoo 
Published: August 2020

AbstractSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which causes coronavirus disease (COVID-19) started at the end of 2019 in Wuhan, China has spread rapidly and became a pandemic. Since there is no therapy available that is proven as fully protective against COVID-19, a vaccine to protect against deadly COVID-19 is urgently needed. Nucleocapsid protein (N protein), is one of the most abundant proteins in coronaviruses and is a potential target for both vaccine development and point of care diagnostics. The variable mass of N protein (45 to 60 kDa), suggests the presence of post-translational modifications (PTMs), and it is critical to clearly define these PTMs to gain the structural understanding necessary for further vaccine research. There have been several reports suggesting that the N protein is phosphorylated but lacks glycosylation. Our comprehensive glycomics and glycoproteomics experiments confirm that the N protein is highly O-glycosylated and also contains significant levels of N-glycosylation. We were able to confirm the presence of O-glycans on seven sites with substantial glycan occupancy, in addition to less abundant O-glycans on four sites. We also detected N-glycans on two out of five potential N-glycosylation sites. Moreover, we were able to confirm one phosphorylation site. Recent studies have indicated that the N protein can serve as an important diagnostic marker for coronavirus disease and a major immunogen by priming protective immune responses. Thus, detailed structural characterization of the N protein may provide useful insights for understanding the roles of glycosylation on viral pathogenesis and also in vaccine design and development.
Deep learning to decipher the progression and morphology of axonal degeneration
Authors: Palumbo Alex , Grüning Philipp , Landt Svenja Kim , Heckmann Lara Eleen , Bartram Luisa , Pabst Alessa , Flory Charlotte , Ikhsan Maulana , Pietsch Sören , Schulz Reinhard , Kren Christopher , Koop Norbert , Boltze Johannes , Mamlouk Amir Madany , Zille Marietta 
Published: August 2020

AbstractBackgroundAxonal degeneration (AxD) is a pathological hallmark of many neurodegenerative diseases. Deciphering the morphological patterns of AxD will help to understand the underlying mechanisms and to develop effective therapeutic interventions. Here, we evaluated the progression of AxD in cortical neurons using a novel microfluidic device in combination with a deep learning tool, the EntireAxon, that we developed for the enhanced-throughput analysis of AxD on microscopic images.ResultsThe EntireAxon convolutional neural network sensitively and specifically segmented the features of AxD, including axons, axonal swellings, and axonal fragments, and its performance exceeded that of human expert raters. In anin vitromodel of AxD in hemorrhagic stroke induced by the hemolysis product hemin, we detected the concentration- and time-dependent degeneration of axons leading to a decrease in axon area, while the axonal swelling and axonal fragment area increased. Time course analysis revealed that axonal swellings preceded axon fragmentation, suggesting that swellings may be reliable predictors of AxD. Using a recurrent neural network, we further identified four morphological patterns of AxD (granular, retraction, swelling, and transport degeneration) in cortical axons subjected to hemin.ConclusionsThese findings indicate a morphological heterogeneity of AxD under pathophysiologic conditions. The combination of the microfluidic device with the EntireAxon deep learning tool enable the systematic analysis of AxD but also unravel a so far unknown intricacy in which AxD can occur in a disease context.
Boosting L-type Ca2+channel activity in tuberous sclerosis mitigates excess glutamate receptors
Authors: Niere Farr , Cacheaux Luisa P. , Egido-Betancourt Hailey X. , Taylor William C. , Raab-Graham Kimberly F. 
Published: August 2020

AbstractTuberous sclerosis complex (TS) is a dominant, multisystem disorder with devastating neurological symptoms. Approximately 85% of TS patients suffer from epilepsy over their lifespan and roughly 25-50% of those patients develop Autism Spectrum Disorder (1, 2). Current seizure therapies are effective in some, but not all, and often have significant risk factors associated with their use (1, 3). Thus, there is a critical need for new medication development or drug repositioning. Herein, we leveraged proteomic signatures of epilepsy and ASD, often comorbid in TS, to utilize anin silcoapproach to identify new drug therapies for TS-related seizures. We have discovered that activation of L-type voltage dependent calcium channels (L-VDCC) by Bay-K8644 (BayK) in a preclinical mouse model of TS rescues the excess expression of ionotropic, AMPA-subtype glutamate (GluA) receptors. As added proof of BayK working through L-VDCC to regulate GluA levels, we found that increasing expression of alpha2delta2 (α2δ2), an auxiliary calcium channel subunit that boosts L-VDCC surface expression, similarly lowers the surface expression of dendritic GluA in TS. These BayK-induced molecular alterations may potentially improve the quality of life of humans suffering from TS.Significance StatementCausal mechanisms of Tuberous Sclerosis (TS)-associated neurological disorders are under-characterized and treatment options are lacking. Using a computational approach of mTOR/DJ-1 target mRNAs to predict new medications, we report that boosting L-type voltage-dependent Ca2+channel (L-VDCC) activity in a preclinical TS mouse model that exhibits a deficit in dendritic L-VDCC activity ameliorates key molecular pathologies that are predicted to underlie seizures. Restoring the mTOR/DJ-1 pathway upstream of L-VDCC, therefore, may serve as a new therapeutic avenue to mitigate seizures and mortality in TS.
Modern, archaeological, and paleontological DNA analysis of a human-harvested marine gastropod (Strombus pugilis) from Caribbean Panama
Authors: Sullivan Alexis P. , Marciniak Stephanie , O’Dea Aaron , Wake Thomas A. , Perry George H. 
Published: August 2020

ABSTRACTAlthough protocols exist for the recovery of ancient DNA from land snail and marine bivalve shells, marine conch shells have yet to be studied from a paleogenomic perspective. We first present reference assemblies for both a 623.7 Mbp nuclear genome and a 15.4 kbp mitochondrial genome forStrombus pugilis, the West Indian fighting conch. We next detail a method to extract and sequence DNA from conch shells and apply it to conch from Bocas del Toro, Panama across three time periods: recently-eaten and discarded (n=3), Late Holocene (984-1258 BP) archaeological midden (n=5), and a mid-Holocene (5711-7187 BP) paleontological fossil coral reef (n=5). These results are compared to control DNA extracted from live-caught tissue and fresh shells (n=5). Using high-throughput sequencing, we were able to obtainS. pugilisnuclear sequence reads from shells across all age periods: up to 92.5 thousand filtered reads per sample in live-caught shell material, 4.57 thousand for modern discarded shells, 12.1 thousand reads for archaeological shells, and 114 reads in paleontological shells. We confirmed authenticity of the ancient DNA recovered from the archaeological and paleontological shells based on 5.7x higher average frequency of deamination-driven misincorporations and 15% shorter average read lengths compared to the modern shells. Reads also mapped to theS. pugilismitochondrial genome for all but the paleontological shells, with consistent ratios of mitochondrial to nuclear mapped reads across sample types. Our methods can be applied to diverse archaeological sites to facilitate reconstructions of the long-term impacts of human behavior on mollusc evolutionary biology.