bluuebunny/crossref_metadata_2025_split huggingface dataset:
High throughput screening identifies SOX2 as a Super Pioneer Factor that inhibits DNA methylation maintenance at its binding sites
Authors: Vanzan Ludovica , Soldati Hadrien , Ythier Victor , Anand Santosh , Francis Nicole , Murr Rabih 
Published: February 2020

AbstractAccess of mammalian transcription factors (TFs) to regulatory regions, an essential event for transcription regulation, is hindered by chromatin compaction involving nucleosome wrapping, repressive histone modifications and DNA methylation. Moreover, methylation of TF binding sites (TBSs) affects TF binding affinity to these sites. Remarkably, a special class of TFs called pioneer transcription factors (PFs) can access nucleosomal DNA, leading to nucleosome remodelling and chromatin opening. However, whether PFs can bind to methylated sites and induce DNA demethylation is largely unknown.Here, we set up a highly parallelized approach to investigate PF ability to bind methylated DNA and induce demethylation. Our results indicate that the interdependence between DNA methylation and TF binding is more complex than previously thought, even within a select group of TFs that have a strong pioneering activity; while most PFs do not induce changes in DNA methylation at their binding sites, we identified PFs that can protect DNA from methylation and PFs that can induce DNA demethylation at methylated binding sites. We called the latter “super pioneer transcription factors” (SPFs), as they are seemingly able to overcome several types of repressive epigenetic marks. Importantly, while most SPFs induce TET-dependent active DNA demethylation, SOX2 binding leads to passive demethylation by inhibition of the maintenance methyltransferase DNMT1 during replication. This important finding suggests a novel mechanism allowing TFs to interfere with the epigenetic memory during DNA replication.
Genomic evidence reveals SPA-regulated developmental and metabolic pathways in dark-grownArabidopsisseedlings
Authors: Pham Vinh Ngoc , Paik Inyup , Hoecker Ute , Huq Enamul 
Published: February 2020

AbstractPhotomorphogenesis is repressed in the dark mainly by an E3 ubiquitin ligase complex comprising CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1) and four homologous proteins called SUPPRESSOR OF PHYA-105 (SPA1-SPA4) in Arabidopsis. This complex induces the ubiquitination and subsequent degradation of positively acting transcription factors (e.g., HY5, HFR1, PAP1 and others) in the dark to repress photomorphogenesis. Genomic evidence showed a large number of genes regulated by COP1 in the dark, of which many are direct targets of HY5. However, the genomic basis for the constitute photomorphogenic phenotype ofspaQremains unknown. Here, we show that >7200 genes are differentially expressed in thespaQbackground compared to wild-type in the dark. Comparison of the RNA Sequencing (RNA-Seq) data betweencop1andspaQrevealed a large overlapping set of genes regulated by the COP1-SPA complex. In addition, many of the genes coordinately regulated by the COP1-SPA complex are also regulated by HY5 directly and indirectly. Taken together, our data reveal that SPA proteins repress photomorphogenesis by controlling gene expression in concert with COP1, likely through regulating the abundance of downstream transcription factors in light signaling pathways. Moreover, SPA proteins may function both in a COP1-dependent and –independent manner in regulating many biological processes and developmental pathways in Arabidopsis.Summary statementComparison of transcriptome analyses betweencop1andspaQmutants reveal overlapping pathways regulated by COP1 and SPAs.
The sperm epigenome does not display recurrent epimutations in patients with severely impaired spermatogenesis
Authors: Leitão Elsa , Persio Sara Di , Laurentino Sandra , Wöste Marius , Dugas Martin , Kliesch Sabine , Neuhaus Nina , Horsthemke Bernhard 
Published: February 2020

AbstractBackgroundIn the past 15 years, numerous studies have described aberrant DNA methylation of imprinted genes (e.g.MESTandH19) in sperm of infertile patients, but the prevalence and genomic extent of abnormal methylation patterns have remained unknown.ResultsUsing deep bisulfite sequencing (DBS), we screened swim-up sperm samples from 40 normozoospermic and 93 oligoasthenoteratozoospermic (OAT) patients forH19andMESTmethylation. Based on this screening, we defined three patient groups: normal controls (NC), abnormally methylated infertile (AMI; n=7) and normally methylated infertile (NMI; n=86). Whole genome bisulfite sequencing (WGBS) of five NC and five AMI samples revealed abnormal methylation levels of all 50 imprinting control regions in each AMI sample. To investigate whether this finding reflected epigenetic germ line mosaicism or the presence of residual somatic DNA, we made a genome-wide inventory of soma-germ cell specific DNA methylation. We found that >2,000 germ cell-specific genes are promoter-methylated in blood and that AMI samples had abnormal methylation levels at these genes, consistent with the presence of somatic cell DNA. The comparison between the five NC and six NMI samples revealed 19 differentially methylated regions (DMRs), none of which could be validated in an independent cohort of 40 men. Previous studies reported a higher incidence of epimutations at single CpG sites in the CTCF-binding region 6 ofH19in infertile patients. DBS analysis of this locus, however, revealed an association between DNA methylation levels and genotype (rs2071094), but not fertility phenotype.ConclusionsOur results suggest that somatic DNA contamination and genetic variation confound methylation studies in sperm of infertile men. While we cannot exclude the existence of rare patients with slightly abnormal sperm methylation at non-recurrent CpG sites, the prevalence of aberrant methylation in swim-up purified sperm of infertile men has likely been overestimated, which is reassuring for patients undergoing assisted reproduction.
Voltage-gated calcium channel subunit α2δ-3 shapes light responses of mouse retinal ganglion cells mainly in low and moderate light levels
Authors: Seitter Hartwig , Sothilingam Vithiyanjali , Benkner Boris , Garrido Marina Garcia , Kling Alexandra , Pirone Antonella , Seeliger Mathias , Münch Thomas A. 
Published: February 2020

AbstractLittle is known about the function of the auxiliary α2δ subunits of voltage-gated calcium channels in the retina. We investigated the role of α2δ-3 (Cacna2d3) using a mouse in which α2δ-3 was knocked out by LacZ insertion. Behavior experiments indicated a normal optokinetic reflex in α2δ-3 knockout animals. Strong expression of α2δ-3 could be localized to horizontal cells using the LacZ-reporter, but horizontal cell mosaic and currents carried by horizontal cell voltage-gated calcium channels were unchanged by the α2δ-3 knockout.In vivoelectroretinography revealed unaffected photoreceptor activity and signal transmission to depolarizing bipolar cells. We recorded visual responses of retinal ganglion cells with multi-electrode arrays in scotopic to photopic luminance levels and found subtle changes in α2δ-3 knockout retinas. Spontaneous activity in OFF ganglion cells was elevated in all luminance levels. Differential response strength to high- and low-contrast Gaussian white noise was compressed in ON ganglion cells during mesopic ambient luminance and in OFF ganglion cells during scotopic and mesopic ambient luminances. In a subset of ON ganglion cells, we found a sharp increase in baseline spiking after the presentation of drifting gratings in scotopic luminance. This increase happened after gratings of different spatial properties in knockout compared to wild type retinas. In a subset of ON ganglion cells of the α2δ-3 knockout, we found altered delays in rebound-like spiking to full-field contrast steps in scotopic luminance. In conclusion, α2δ-3 seems to participate in shaping visual responses mostly within brightness regimes when rods or both rods and cones are active.
Amyloid aggregates accumulate in melanoma metastasis driving YAP mediated tumor progression
Authors: Matafora Vittoria , Farris Francesco , Restuccia Umberto , Tamburri Simone , Martano Giuseppe , Bernardelli Clara , Pisati Federica , Casagrande Francesca , Lazzari Luca , Marsoni Silvia , Bonoldi Emanuela , Bachi Angela 
Published: February 2020

AbstractMelanoma progression is generally associated to increased Yes-associated protein (YAP) mediated transcription. Actually, mechanical signals from the extracellular matrix are sensed by YAP, which activates proliferative genes expression, promoting melanoma progression and drug resistance. Which and how extracellular signals induce mechanotransduction is not completely understood.Herein, by secretome studies, we revealed an extracellular accumulation of amyloidogenic proteins, i.e. premelanosome protein (PMEL), together with proteins that assist amyloids maturation into fibrils. Indeed, we confirmed the presence of amyloid-like aggregates similar to those detected in Alzheimer disease. These aggregates were enriched in metastatic cell lines as well as in human melanoma biopsies, compared to their primitive counterpart. Mechanistically, we proved that beta-secretase (BACE) regulates the maturation of these aggregates and that its inhibition hampers YAP activity. Moreover, recombinant PMEL fibrils induce per se mechanotransduction promoting YAP activation. Finally, BACE inhibition affects cell proliferation and increases drug sensitivity. These results highlight the importance of amyloids for melanoma survival and the potential of beta-secretase inhibitors as new therapeutic approach to metastatic melanoma.
A multimodal computational pipeline for 3D histology of the human brain
Authors: Mancini Matteo , Casamitjana Adrià , Peter Loic , Robinson Eleanor , Crampsie Shauna , Thomas David L. , Holton Janice L. , Jaunmuktane Zane , Iglesias Juan Eugenio 
Published: February 2020

AbstractEx vivoimaging enables analysis of the human brain at a level of detail that is not possiblein vivowith MRI. In particular, histology can be used to study brain tissue at the microscopic level, using a wide array of different stains that highlight different microanatomical features. Complementing MRI with histology has important applications inex vivoatlas building and in modeling the link between microstructure and macroscopic MR signal. However, histology requires sectioning tissue, hence distorting its 3D structure, particularly in larger human samples. Here, we present an open-source computational pipeline to produce 3D consistent histology reconstructions of the human brain. The pipeline relies on a volumetric MRI scan that serves as undistorted reference, and on an intermediate imaging modality (blockface photography) that bridges the gap between MRI and histology. We present results on 3D histology reconstruction of a whole human hemisphere.
Shedding light on the control of CatSper Ca2+channels by cAMP and chemicals used to probe cAMP signaling
Authors: Wang Tao , Young Samuel , Tüttelmann Frank , Röpke Albrecht , Krallmann Claudia , Kliesch Sabine , Zeng Xu-Hui , Brenker Christoph , Strünker Timo 
Published: February 2020

AbstractThe sperm-specific CatSper channel controls the influx of Ca2+into the flagellum and, thereby, the swimming behavior of sperm. A hallmark of human CatSper is its polymodal activation by membrane voltage, intracellular pH, and oviductal hormones. Whether CatSper is also activated by signaling pathways involving an increase of cAMP and ensuing activation of protein kinase A (PKA) is, however, a matter of controversy. Here, using kinetic ion-sensitive fluorimetry and patch-clamp recordings, we study transmembrane Ca2+flux and membrane currents in human sperm from healthy donors and from patients that lack functional CatSper channels. We show that human CatSper is neither activated by intracellular cAMP directly nor indirectly by the cAMP/PKA-signaling pathway. Moreover, we demonstrate that non-physiological concentrations of cAMP and membrane-permeable cAMP analogs used to mimic the action of intracellular cAMP activate human CatSper from the outside via a previously unknown extracellular cyclic nucleotide-binding site. Finally, we demonstrate that the effects of common PKA inhibitors on human CatSper rest on off-target drug actions on CatSper itself rather than on inhibition of PKA. We conclude that the concept of an intracellular cAMP/PKA-activation of CatSper is primarily based on unspecific effects of chemical probes used to interfere with cAMP signaling. Altogether, our findings solve several controversial issues, which has important bearings on future studies of cAMP and Ca2+signaling and the ligand-control of CatSper in sperm.
Accurate, scalable cohort variant calls using DeepVariant and GLnexus
Authors: Yun Taedong , Li Helen , Chang Pi-Chuan , Lin Michael F. , Carroll Andrew , McLean Cory Y. 
Published: February 2020

AbstractPopulation-scale sequenced cohorts are foundational resources for genetic analyses, but processing raw reads into analysis-ready variants remains challenging. Here we introduce an open-source cohort variant-calling method using the highly-accurate caller DeepVariant and scalable merging tool GLnexus. We optimized callset quality based on benchmark samples and Mendelian consistency across many sample sizes and sequencing specifications, resulting in substantial quality improvements and cost savings over existing best practices. We further evaluated our pipeline in the 1000 Genomes Project (1KGP) samples, showing superior quality metrics and imputation performance. We publicly release the 1KGP callset to foster development of broad studies of genetic variation.
Long-read Individual-molecule Sequencing Reveals CRISPR-induced Genetic Heterogeneity in Human ESCs
Authors: Bi Chongwei , Wang Lin , Yuan Baolei , Zhou Xuan , Pang Yu , Li  , Wang Sheng , Gao Yuhong Xin , Huang Yanyi , Li Mo 
Published: February 2020

AbstractAccurately quantifying the genetic heterogeneity of a cell population is essential to understanding of biological systems. We develop a universal method to label individual DNA molecules for analyzing diverse types of rare genetic variants, with frequency as low as 4×10−5, using short- or long-read sequencing. It enables base-resolution haplotype-resolved quantitative characterization of rare variants. It provides the first quantitative evidence of persistent nonrandom large deletions and insertions following DNA repair of double-strand breaks induced by CRISPR-Cas9 in human pluripotent stem cells.
Cell cycle-associated expression patterns predict gene function in mycobacteria
Authors: Bandekar Aditya C. , Subedi Sishir , Ioerger Thomas R. , Sassetti Christopher M. 
Published: February 2020

SummaryWhile the major events in prokaryotic cell cycle progression are likely to be coordinated with transcriptional and metabolic changes, these processes remain poorly characterized. Unlike many rapidly-growing bacteria, DNA replication and cell division are temporally-resolved in mycobacteria, making these slow-growing organisms a potentially useful system to investigate the prokaryotic cell cycle. To determine if cell-cycle dependent gene regulation occurs in mycobacteria, we characterized the temporal changes in the transcriptome of synchronously replicating populations ofMycobacterium tuberculosis(Mtb). By enriching for genes that display a sinusoidal expression pattern, we discover 485 genes that oscillate with a period consistent with the cell cycle. During cytokinesis, the timing of gene induction could be used to predict the timing of gene function, as mRNA abundance was found to correlate with the order in which proteins were recruited to the developing septum. Similarly, the expression pattern of primary metabolic genes could be used to predict the relative importance of these pathways for different cell cycle processes. Pyrimidine synthetic genes peaked during DNA replication and their depletion caused a filamentation phenotype that phenocopied defects in this process. In contrast, the IMP dehydrogenaseguaB2dedicated to guanosine synthesis displayed the opposite expression pattern and its depletion perturbed septation. Together, these data imply obligate coordination between primary metabolism and cell division, and identify periodically regulated genes that can be related to specific cell biological functions.
Diverse homeostatic and immunomodulatory roles of immune cells in the developing mouse lung revealed at single cell resolution
Authors: Domingo-Gonzalez Racquel , Zanini Fabio , Che Xibing , Liu Min , Jones Robert C. , Swift Michael A. , Quake Stephen R. , Cornfield David N. , Alvira Cristina M. 
Published: February 2020

AbstractAt birth, the lungs experience a sudden transition from a pathogen-free, hypoxic, fluid-filled environment to a pathogen-rich, rhythmically distended air-liquid interface. While many studies focus on adult tissue, the heterogeneity of immune cells in the perinatal lung remains unexplored. Here, we combine single cell transcriptomics within situhybridization to present an atlas of the murine lung immune compartment during a critical period of lung development. We show that the late embryonic lung is dominated by specialized proliferative macrophages with a surprising physical interaction with the developing vasculature. These macrophages disappear after birth and are replaced by a complex and dynamic mixture of macrophage subtypes, dendritic cells, granulocytes, and lymphocytes. Detailed characterization of macrophage diversity revealed a precise orchestration of five distinct subpopulations across postnatal development to fill context-specific functions in tissue remodeling, angiogenesis, and immunity. These data both broaden the putative roles for immune cells in the developing lung and provide a framework for understanding how external insults alter immune cell phenotype during a period of rapid lung growth and heightened vulnerability.
FOXO Transcription Factors Activate Alternative Major Immediate Early Promoters to Induce Human Cytomegalovirus Reactivation
Authors: Hale Andrew E , Collins-McMillen Donna , Lenarcic Erik M , Kamil Jeremy P , Goodrum Felicia , Moorman Nathaniel J 
Published: February 2020

AbstractA key step during viral reactivation from latency is the re-expression of viral genes. Hematopoietic progenitor cells (HPCs) support human cytomegalovirus (HCMV) latency, and their differentiation triggers cellular cues that drive reactivation. A key step during HCMV reactivation in latently infected HPCs is re-expression of viral genes. We recently determined that the major immediate early promoter (MIEP), which is primarily responsible for MIE gene expression during lytic replication, remains silent during reactivation. Instead, alternative promoters in the MIE locus are induced by reactivation stimuli. Here, we find that forkhead family (FOXO) transcription factors are critical for activation of alternative MIE promoters during HCMV reactivation, as mutating FOXO binding sites in alternative MIE promoters decreased HCMV IE gene expression upon reactivation and significantly decreased the production of infectious virus from latently infected primary CD34+HPCs. These findings establish a mechanistic link by which infected cells sense environmental cues to regulate latency and reactivation, and emphasize the role of contextual activation of alternative MIE promoters as the primary drivers of reactivation.SignificanceHuman cytomegalovirus infection is lifelong and persistent. Periodic reactivation of cytomegalovirus poses serious disease risk for immune-compromised patients. A critical driver of reactivation is expression of viral genes from the major immediate early locus. Recent paradigm-shifting evidence shows that reactivation is driven from promoters distinct from those that drive replication in permissive cells. Understanding the contextual control of these promoters and how they specifically respond to cellular cues that drive reactivation is critical for establishing future therapies that prevent reactivation. Our findings mechanistically define a previously enigmatic relationship between differentiation and reactivation, and provide potential targets for therapeutic intervention to prevent HCMV reactivation and disease.
Ecological success of sexual and asexual reproductive strategies invading an environmentally unstable habitat
Authors: Silva Willian T.A.F. , Nyqvist Anna , Jonsson Per R. , Harding Karin C. 
Published: February 2020

AbstractMany aspects of sexual and asexual reproduction have been studied empirically and theoretically. The differences between sexual and asexual reproduction within a species often lead to a biased geographical distribution of individuals with different reproductive strategies. While sexuals are more abundant in the core habitat, asexuals are often found in marginal habitats along the edge of the species distribution. This pattern, called geographic parthenogenesis, has been observed in many species but the mechanisms reponsible for generating it are poorly known. We used a quantitative approach using a metapopulation model to explore the ecological processes that can lead to geographic parthenogenesis and the invasion of new habitats by different reproductive strategies. We analyzed the Allee effect on sexual populations and the population sensitivity to environmental stress during the invasion of a marginal, unstable habitat to demonstrate that a complex interaction between the Allee effect, sensitivity to environmental stress and the environmental conditions can determine the relative success of competing reproductive strategies during the initial invasion and longterm establishment in the marginal habitat. We discuss our results in the light of previous empirical and theoretical studies.Author SummaryIndividuals can reproduce with or without sex. Very often, closely related species are distributed in a such a way that the sexually reproducing species is most frequently found in the core habitat while the asexually reproducing species is found on the edge of the habitat range. This biased distribution of reproductive strategies across a habitat range is called geographic parthenogenesis and has been observed in several species. While many processes have been proposed to explain such a pattern, a quantitative approach of the ecological processes was absent. We investigated important differences between sexual and asexual reproduction and how these differences affect the success of sexuals and asexuals invading a marginal, unstable environment. We showed that the relative frequency of each reproductive strategy in the marginal habitat depends on how much sexuals rely on population density to reproduce and how much asexuals are affected by environmental stress relative to sexuals. Our study presents a quantitative ecological explanation for geographic parthenogenesis and provides the conditions under which different distribution patterns can emerge.
Cell phone digital microscopy using an oil droplet
Authors: Szydlowski Nicole Anna , Jing Haoran , Alqashmi Mohamed , Hu Ying Samuel 
Published: February 2020

AbstractWe introduce an accessible imaging method using droplets of microscope immersion and consumer-grade oils and a cell phone camera. We found that oil droplets were more resistant to evaporation than water droplets. We characterized the transverse magnification of oil and water droplets using cell phone screens and a resolution target. We further harnessed the close refractive index of cooking oils to that of the immersion oil and demonstrated their use as lenses for cell phone microscopy. Our method enables stable droplet-based optical imaging without specialized setups or manufacturing processes.