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https://www.readbyqxmd.com/read/29220657/hnrnpk-recruits-pcgf3-5-prc1-to-the-xist-rna-b-repeat-to-establish-polycomb-mediated-chromosomal-silencing
#1
Greta Pintacuda, Guifeng Wei, Chloë Roustan, Burcu Anil Kirmizitas, Nicolae Solcan, Andrea Cerase, Alfredo Castello, Shabaz Mohammed, Benoît Moindrot, Tatyana B Nesterova, Neil Brockdorff
The Polycomb-repressive complexes PRC1 and PRC2 play a key role in chromosome silencing induced by the non-coding RNA Xist. Polycomb recruitment is initiated by the PCGF3/5-PRC1 complex, which catalyzes chromosome-wide H2A lysine 119 ubiquitylation, signaling recruitment of other PRC1 complexes, and PRC2. However, the molecular mechanism for PCGF3/5-PRC1 recruitment by Xist RNA is not understood. Here we define the Xist RNA Polycomb Interaction Domain (XR-PID), a 600 nt sequence encompassing the Xist B-repeat element...
December 7, 2017: Molecular Cell
https://www.readbyqxmd.com/read/29220646/dissecting-cell-type-composition-and-activity-dependent-transcriptional-state-in-mammalian-brains-by-massively-parallel-single-nucleus-rna-seq
#2
Peng Hu, Emily Fabyanic, Deborah Y Kwon, Sheng Tang, Zhaolan Zhou, Hao Wu
Massively parallel single-cell RNA sequencing can precisely resolve cellular diversity in a high-throughput manner at low cost, but unbiased isolation of intact single cells from complex tissues such as adult mammalian brains is challenging. Here, we integrate sucrose-gradient-assisted purification of nuclei with droplet microfluidics to develop a highly scalable single-nucleus RNA-seq approach (sNucDrop-seq), which is free of enzymatic dissociation and nucleus sorting. By profiling ∼18,000 nuclei isolated from cortical tissues of adult mice, we demonstrate that sNucDrop-seq not only accurately reveals neuronal and non-neuronal subtype composition with high sensitivity but also enables in-depth analysis of transient transcriptional states driven by neuronal activity, at single-cell resolution, in vivo...
December 7, 2017: Molecular Cell
https://www.readbyqxmd.com/read/29220569/crocadepsins-depsipeptides-from-the-myxobacterium-chondromyces-crocatus-found-by-a-genome-mining-approach
#3
Frank Surup, Konrad Viehrig, Shwan Rachid, Alberto Plaza, Christine K Maurer, Rolf W Hartmann, Rolf Müller
Analysis of the genome sequence of the myxobacterium Chondromyces crocatus Cm c5 revealed the presence of numerous cryptic megasynthetase gene clusters, one of which we here assign to two previously unknown chlorinated metabolites by a comparative gene inactivation and secondary metabolomics approach. Structure elucidation of these compounds revealed a unique cyclic depsipeptide skeleton featuring β- and δ-amide bonds of aspartic acid and 3-methyl ornithine moieties, respectively. Insights into their biosynthesis were obtained by targeted gene inactivation and feeding experiments employing isotope-labeled precursors...
December 8, 2017: ACS Chemical Biology
https://www.readbyqxmd.com/read/29220521/trypanosomatid-mitochondrial-rna-editing-dramatically-complex-transcript-repertoires-revealed-with-a-dedicated-mapping-tool
#4
Evgeny S Gerasimov, Anna A Gasparyan, Iosif Kaurov, Boris Tichý, Maria D Logacheva, Alexander A Kolesnikov, Julius Lukeš, Vyacheslav Yurchenko, Sara L Zimmer, Pavel Flegontov
RNA editing by targeted insertion and deletion of uridine is crucial to generate translatable mRNAs from the cryptogenes of the mitochondrial genome of kinetoplastids. This type of editing consists of a stepwise cascade of reactions generally proceeding from 3' to 5' on a transcript, resulting in a population of partially edited as well as pre-edited and completely edited molecules for each mitochondrial cryptogene of these protozoans. Often, the number of uridines inserted and deleted exceed the number of nucleotides that are genome-encoded...
December 6, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29220513/integrating-5hmc-and-gene-expression-data-to-infer-regulatory-mechanisms
#5
Cristina Mitrea, Priyanga Wijesinghe, Greg Dyson, Adéle Kruger, Douglas M Ruden, Sorin Draghici, Aliccia Bollig-Fischer
Motivation: Epigenetic mechanisms are known to play a major role in breast cancer. However, the role of 5-hydroxymethylcytosine (5hmC) remains understudied. We hypothesize that 5hmC mediates redox regulation of gene expression in an aggressive subtype known as triple negative breast cancer (TNBC). To address this, our objective was to highlight genes that may be the target of this process by identifying redox-regulated, antioxidant-sensitive, gene-localized 5hmC changes associated with mRNA changes in TNBC cells...
December 6, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29220494/soapnuke-a-mapreduce-acceleration-supported-software-for-integrated-quality-control-and-preprocessing-of-high-throughput-sequencing-data
#6
Yuxin Chen, Yongsheng Chen, Chunmei Shi, Zhibo Huang, Yong Zhang, Shengkang Li, Yan Li, Jia Ye, Chang Yu, Zhuo Li, Xiuqing Zhang, Jian Wang, Huanming Yang, Lin Fang, Qiang Chen
Quality Control (QC) and preprocessing are essential steps for sequencing data analysis to ensure the accuracy of results. However, existing tools cannot provide a satisfying solution with integrated comprehensive functions, proper architectures and highly-scalable acceleration. In this article, we demonstrate SOAPnuke as a tool with abundant functions for a "QC-Preprocess-QC" workflow and MapReduce acceleration framework. Four modules with different preprocessing functions are designed for processing datasets from genomic, small RNA (sRNA), Digital Gene Expression (DGE) and metagenomic experiments respectively...
December 4, 2017: GigaScience
https://www.readbyqxmd.com/read/29220483/prenatal-exposure-to-bisphenol-a-disrupts-naturally-occurring-bimodal-dna-methylation-at-proximal-promoter-of-fggy-an-obesity-relevant-gene-encoding-a-carbohydrate-kinase-in-gonadal-white-adipose-tissues-of-cd-1-mice
#7
Julia A Taylor, Keiko Shioda, Shino Mitsunaga, Shiomi Yawata, Brittany M Angle, Susan C Nagel, Frederick S Vom Saal, Toshi Shioda
Exposure of mammalian fetuses to endocrine disruptors can increase the risk of adult-onset diseases. For example, we previously showed that exposure of mouse fetuses to bisphenol A (BPA) caused adult-onset obesity. To obtain insights into roles of epigenetic changes in the delayed toxic effects of endocrine disruption, we determined effects of fetal mouse exposure to BPA on genome-wide DNA methylation and mRNA expression in gonadal white adipose tissues by deep sequencing (MBD-seq and RNA-seq), bisulfite pyrosequencing, and real-time qPCR...
December 6, 2017: Endocrinology
https://www.readbyqxmd.com/read/29220409/acquisition-of-functions-on-the-outer-capsid-surface-during-evolution-of-double-stranded-rna-fungal-viruses
#8
Carlos P Mata, Daniel Luque, Josué Gómez-Blanco, Javier M Rodríguez, José M González, Nobuhiro Suzuki, Said A Ghabrial, José L Carrascosa, Benes L Trus, José R Castón
Unlike their counterparts in bacterial and higher eukaryotic hosts, most fungal viruses are transmitted intracellularly and lack an extracellular phase. Here we determined the cryo-EM structure at 3.7 Å resolution of Rosellinia necatrix quadrivirus 1 (RnQV1), a fungal double-stranded (ds)RNA virus. RnQV1, the type species of the family Quadriviridae, has a multipartite genome consisting of four monocistronic segments. Whereas most dsRNA virus capsids are based on dimers of a single protein, the ~450-Å-diameter, T = 1 RnQV1 capsid is built of P2 and P4 protein heterodimers, each with more than 1000 residues...
December 8, 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/29218572/complete-genome-sequence-of-a-new-strain-of-lagenaria-siceraria-endornavirus-from-china
#9
Xiaoqin Peng, Hui Pan, Arif Muhammad, Hongliu An, Shouguo Fang, Weimin Li, Songbai Zhang
An RNA virus tentatively named Lagenaria siceraria endornavirus-Hubei (LsEV-HuB) was isolated from Lagenaria siceraria var. hispida in Hubei, China. The LsEV-HuB genome consists of 15,098 bp and contains a single open reading frame (ORF) encoding a large protein with several conserved domains, including one helicase domain, one glycosyltransferase domain, two capsular polysaccharide synthesis protein (CPS) domains, and one RNA-dependent RNA polymerase (RdRp) domain. LsEV-HuB has nucleotide and amino acid sequence identities of 72...
December 7, 2017: Archives of Virology
https://www.readbyqxmd.com/read/29218505/antibacterial-and-antibiofilm-activity-of-lactic-acid-bacteria-isolated-from-traditional-artisanal-milk-cheese-from-northeast-china-against-enteropathogenic-bacteria
#10
Xingyang Cui, Yunjia Shi, Shanshan Gu, Xin Yan, Hongyan Chen, Junwei Ge
The present study aims to investigate the probiotic properties of novel strains of lactic acid bacteria isolated from traditional artisanal milk cheese from Northeast China and to explore their antibacterial activity against enteropathogenic bacteria. Of the 321 isolates, 86 exhibited survival in low pH, resistance to pancreatin, and tolerance to bile salts; of these, 12 inhibited the growth of more than seven enteropathogenic bacteria and exhibited antibiofilm activities against Staphylococcus aureus CMCC26003 and/or Escherichia coli CVCC230...
December 7, 2017: Probiotics and Antimicrobial Proteins
https://www.readbyqxmd.com/read/29218439/characterization-and-expression-of-lin-28a-involved-in-lin28-let-7signal-pathway-during-early-development-of-p-olivaceus
#11
Yuanshuai Fu, Lina Gao, Zhiyi Shi, Feng You, Junling Zhang, Wenjuan Li
Heterochronic lin-28 is a conserved RNA-binding protein that plays a key role in the timing of developmental events in organisms. As a crucial heterochronic gene, the protein controls developmental events of the second of four larval stages in Caenorhabditi elegans. Heterochronic let-7 miRNAs are often present in various species and highly conserved in sequence and biological function and are required for various biological processes. Previous studies showed that ten let-7 miRNAs were identified in the Japanese flounder (Paralichthys olivaceus) and that they were primarily expressed during metamorphosis...
December 7, 2017: Fish Physiology and Biochemistry
https://www.readbyqxmd.com/read/29218397/can-we-better-predict-the-biologic-behavior-of-incidental-ipmn-a-comprehensive-analysis-of-molecular-diagnostics-and-biomarkers-in-intraductal-papillary-mucinous-neoplasms-of-the-pancreas
#12
Kiara A Tulla, Ajay V Maker
PURPOSE: Predicting the biologic behavior of intraductal papillary mucinous neoplasm (IPMN) remains challenging. Current guidelines utilize patient symptoms and imaging characteristics to determine appropriate surgical candidates. However, the majority of resected cysts remain low-risk lesions, many of which may be feasible to have under surveillance. We herein characterize the most promising and up-to-date molecular diagnostics in order to identify optimal components of a molecular signature to distinguish levels of IPMN dysplasia...
December 7, 2017: Langenbeck's Archives of Surgery
https://www.readbyqxmd.com/read/29218114/comparative-transcriptome-analysis-of-the-global-circular-rnas-expression-profiles-between-shee-and-sheec-cell-lines
#13
Jiachun Sun, Xiaozhi Yuan, Xiangming Li, Dengkui Wang, Tanyou Shan, Wei Wang, Qiuyan Wan, Xinshuai Wang, Junqiang Yan, Shegan Gao
Esophageal squamous cell carcinoma (ESCC) is widely regarded as one of the most lethal types of cancer around the world. The fact that early detection of ESCC could dramatically improve the treatment outcome of the patients has sparked considerable interest in searching for reliable and accurate diagnostic biomarkers. Recently, circular RNAs (circRNA) have emerged as a new type of non-coding RNAs with significant RNase resistance, wide abundance and remarkable internal diversity. There is also increasing evidence suggesting that circRNAs could be implicated in the pathogenesis of cancer and other diseases...
2017: American Journal of Translational Research
https://www.readbyqxmd.com/read/29217759/opposing-roles-of-dendritic-cell-subsets-in-experimental-gn
#14
Sebastian Brähler, Bernd H Zinselmeyer, Saravanan Raju, Maximilian Nitschke, Hani Suleiman, Brian T Saunders, Michael W Johnson, Alexander M C Böhner, Susanne F Viehmann, Derek J Theisen, Nicole M Kretzer, Carlos G Briseño, Konstantin Zaitsev, Olga Ornatsky, Qing Chang, Javier A Carrero, Jeffrey B Kopp, Maxim N Artyomov, Christian Kurts, Kenneth M Murphy, Jeffrey H Miner, Andrey S Shaw
Dendritic cells (DCs) are thought to form a dendritic network across barrier surfaces and throughout organs, including the kidney, to perform an important sentinel function. However, previous studies of DC function used markers, such as CD11c or CX3CR1, that are not unique to DCs. Here, we evaluated the role of DCs in renal inflammation using a CD11c reporter mouse line and two mouse lines with DC-specific reporters, Zbtb46-GFP and Snx22-GFP. Multiphoton microscopy of kidney sections confirmed that most of the dendritically shaped CD11c+ cells forming a network throughout the renal interstitium expressed macrophage-specific markers...
December 7, 2017: Journal of the American Society of Nephrology: JASN
https://www.readbyqxmd.com/read/29217679/miz1-controls-schwann-cell-proliferation-via-h3k36me2-demethylase-kdm8-to-prevent-peripheral-nerve-demyelination
#15
David Fuhrmann, Marco Mernberger, Andrea Nist, Thorsten Stiewe, Hans-Peter Elsässer
Schwann cell differentiation and myelination depends on chromatin remodeling, histone acetylation and methylation, which all have impact on Schwann cell proliferation. We previously reported that the deletion of the POZ domain of the transcription factor Miz1 (encoded by Zbtb17) in mouse Schwann cells (Miz1ΔPOZ) causes a neuropathy at 90 days after birth (P90), with a subsequent spontaneous regeneration. Here we show that RNA sequencing from Miz1ΔPOZ and control animals at P30 revealed a set of upregulated genes with a strong correlation to cell cycle regulation...
December 7, 2017: Journal of Neuroscience: the Official Journal of the Society for Neuroscience
https://www.readbyqxmd.com/read/29217403/transcriptome-analysis-reveals-a-positive-role-for-nerve-growth-factor-in-retinol-metabolism-in-primary-rat-hepatocytes
#16
Ying-Hsien Kao, Po-Huang Lee, Ting-Chia Chiu, Yu-Chun Lin, Cheuk-Kwan Sun, Po-Han Chen, Ming-Shian Tsai
Up-regulation of nerve growth factor (NGF) in parenchymal hepatocytes with cholestatic injury has been previously demonstrated to exert hepatoprotective effects in an autocrine manner; however, the overall impact of NGF up-regulation remains elusive. This study aimed to profile the effects of exogenous NGF on cultured primary rat hepatocytes using transcriptome analysis. Total RNA was isolated from hepatocytes with and without 24 h of NGF exposure, and subjected to RNA enrichment by PCR and RNA sequencing procedures...
December 4, 2017: Cytokine
https://www.readbyqxmd.com/read/29216888/telomere-heterogeneity-linked-to-metabolism-and-pluripotency-state-revealed-by-simultaneous-analysis-of-telomere-length-and-rna-seq-in-the-same-human-embryonic-stem-cell
#17
Hua Wang, Kunshan Zhang, Yifei Liu, Yudong Fu, Shan Gao, Peng Gong, Haiying Wang, Zhongcheng Zhou, Ming Zeng, Zhenfeng Wu, Yu Sun, Tong Chen, Siguang Li, Lin Liu
BACKGROUND: Telomere length heterogeneity has been detected in various cell types, including stem cells and cancer cells. Cell heterogeneity in pluripotent stem cells, such as embryonic stem cells (ESCs), is of particular interest; however, the implication and mechanisms underlying the heterogeneity remain to be understood. Single-cell analysis technology has recently been developed and effectively employed to investigate cell heterogeneity. Yet, methods that can simultaneously measure telomere length and analyze the global transcriptome in the same cell have not been available until now...
December 8, 2017: BMC Biology
https://www.readbyqxmd.com/read/29216844/comparative-analyses-of-plastid-genomes-from-fourteen-cornales-species-inferences-for-phylogenetic-relationships-and-genome-evolution
#18
Chao-Nan Fu, Hong-Tao Li, Richard Milne, Ting Zhang, Peng-Fei Ma, Jing Yang, De-Zhu Li, Lian-Ming Gao
BACKGROUND: The Cornales is the basal lineage of the asterids, the largest angiosperm clade. Phylogenetic relationships within the order were previously not fully resolved. Fifteen plastid genomes representing 14 species, ten genera and seven families of Cornales were newly sequenced for comparative analyses of genome features, evolution, and phylogenomics based on different partitioning schemes and filtering strategies. RESULTS: All plastomes of the 14 Cornales species had the typical quadripartite structure with a genome size ranging from 156,567 bp to 158,715 bp, which included two inverted repeats (25,859-26,451 bp) separated by a large single-copy region (86,089-87,835 bp) and a small single-copy region (18,250-18,856 bp) region...
December 8, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29216791/the-associations-of-two-snps-in-mirna-146a-and-one-snp-in-zbtb38-rasa2-with-the-disease-susceptibility-and-the-clinical-features-of-the-chinese-patients-of-scjd-and-ffi
#19
Chen Gao, Qiang Shi, Jing Wei, Wei Zhou, Kang Xiao, Jing Wang, Qi Shi, Xiao-Ping Dong
Prion diseases are a group of fatal neurodegenerative disorders that affect humans and animals. Besides of the pathological agent, prion, there are some elements that can influence or determine susceptibility to prion infection and the clinical phenotype of the diseases, e.g., the polymorphism in PRNP gene. Another polymorphism in ZBTB38-RASA2 has been observed to be associated with the susceptibility of sporadic Creutzfeldt-Jacob disease (sCJD) in UK. MicroRNAs are endogenous small noncoding RNAs that control gene expression by targeting mRNAs and triggering either translation repression or RNA degradation...
December 8, 2017: Prion
https://www.readbyqxmd.com/read/29216634/lysine-restriction-affects-feed-intake-and-amino-acid-metabolism-via-gut-microbiome-in-piglets
#20
Jie Yin, Hui Han, Yuying Li, Zhaojin Liu, Yurong Zhao, Rejun Fang, Xingguo Huang, Jie Zheng, Wenkai Ren, Fei Wu, Gang Liu, Xin Wu, Kai Wang, Liping Sun, Chunyong Li, Tiejun Li, Yulong Yin
BACKGROUND/AIMS: Our previous reports suggested that dietary supplementation with lysine influenced intestinal absorption and metabolism of amino acids. In this study, we further investigated the effect of lysine restriction (30%) on feed intake and we also tested the hypothesis that gut microbiome contributed to the potential mechanism of lysine restriction-mediated feeding behavior. Here, we profiled gut microbial communities by sequencing 16S ribosomal ribonucleic acid (rRNA) genes from gut samples as well as growth performance, serum hormones, and intestinal lysine transport in a piglet model...
December 6, 2017: Cellular Physiology and Biochemistry
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