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https://www.readbyqxmd.com/read/29679569/ddx1-regulates-alternative-splicing-and-insulin-secretion-in-pancreatic-%C3%AE-cells
#1
Wen Zhong, Zonghong Li, Maoge Zhou, Tao Xu, You Wang
DEAD-box helicase 1 (DDX1) is a multifunction protein involved in diverse cellular processes including transcription, viral replication, mRNA/miRNA processing, and tRNA splicing. Here, we report a novel function of DDX1 in mRNA alternative splicing in pancreatic β cells. By performing integrated data analysis of high-throughput RNA sequencing (RNA-Seq), and cross-linking and immunoprecipitation coupled with deep sequencing (CLIP-Seq), we identify hundreds of alternative splicing genes that are targeted by DDX1...
April 18, 2018: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/29679239/comparative-analysis-of-the-root-transcriptomes-of-cultivated-and-wild-rice-varieties-in-response-to-magnaporthe-oryzae-infection-revealed-both-common-and-species-specific-pathogen-responses
#2
Lei Tian, Shaohua Shi, Fahad Nasir, Chunling Chang, Weiqiang Li, Lam-Son Phan Tran, Chunjie Tian
BACKGROUND: Magnaporthe oryzae, the causal fungus of rice blast disease, negatively impacts global rice production. Wild rice (Oryza rufipogon), a relative of cultivated rice (O. sativa), possesses unique attributes that enable it to resist pathogen invasion. Although wild rice represents a major resource for disease resistance, relative to current cultivated rice varieties, no prior studies have compared the immune and transcriptional responses in the roots of wild and cultivated rice to M...
April 20, 2018: Rice
https://www.readbyqxmd.com/read/29679052/differential-contribution-of-cis-and-trans-gene-transcription-regulatory-mechanisms-in-amygdala-and-prefrontal-cortex-and-modulation-by-social-stress
#3
Eli Reuveni, Dmitry Getselter, Oded Oron, Evan Elliott
While both individual transcription factors and cis-acting sites have been studied in relation to psychiatric disorders, there is little knowledge of the relative contribution of trans-acting and cis-acting factors to gene transcription in the brain. Using an RNA-seq approach in mice bred from two evolutionary-distinct mice strains, we determined the contribution of cis and trans factors to gene expression in the prefrontal cortex and amygdala, two regions of the brain relevant to the stress response, and the contribution of cis and trans factors in the prefrontal cortex after Chronic Social Defeat (CSD) in mice...
April 20, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29679021/systematic-evaluation-of-rna-quality-microarray-data-reliability-and-pathway-analysis-in-fresh-fresh-frozen-and-formalin-fixed-paraffin-embedded-tissue-samples
#4
Isabella Wimmer, Anna R Tröscher, Florian Brunner, Stephen J Rubino, Christian G Bien, Howard L Weiner, Hans Lassmann, Jan Bauer
Formalin-fixed paraffin-embedded (FFPE) tissues are valuable resources commonly used in pathology. However, formalin fixation modifies nucleic acids challenging the isolation of high-quality RNA for genetic profiling. Here, we assessed feasibility and reliability of microarray studies analysing transcriptome data from fresh, fresh-frozen (FF) and FFPE tissues. We show that reproducible microarray data can be generated from only 2 ng FFPE-derived RNA. For RNA quality assessment, fragment size distribution (DV200) and qPCR proved most suitable...
April 20, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29678883/ribosome-maturation-by-the-endoribonuclease-ybey-stabilises-a-type-iii-secretion-system-transcript-required-for-virulence-of-enterohemorrhagic-escherichia-coli
#5
Sean P McAteer, Brandon M Sy, Julia L Wong, David Tollervey, David L Gally, Jai J Tree
Enterohemorrhagic Escherichia coli (EHEC) is a significant human pathogen that colonizes humans and its reservoir host, cattle. Colonization requires the expression of a type III secretion (T3S) system that injects a cocktail of effector proteins into host cells, to promote bacterial attachment and disease progression. The T3S system is tightly regulated by a complex network of transcriptional and post-transcriptional regulators. Using transposon mutagenesis, here we identified the ybeZYX-int operon as being required for normal T3S levels...
April 20, 2018: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29678171/analysis-of-hepatic-transcriptome-demonstrates-altered-lipid-metabolism-following-lactobacillus-johnsonii-bs15-prevention-in-chickens-with-subclinical-necrotic-enteritis
#6
Xiaodan Qing, Dong Zeng, Hesong Wang, Xueqin Ni, Jing Lai, Lei Liu, Abdul Khalique, Kangcheng Pan, Bo Jing
BACKGROUND: Subclinical necrotic enteritis (SNE) widely outbreaks in chickens which inflicted growth-slowing, causing enormous social and economic burdens. To better understand the molecular underpinnings of SNE on lipid metabolism and explore novel preventative strategies against SNE, we studied the regulatory mechanism of a potential probiotic, Lactobacillus johnsonii BS15 on the lipid metabolism pathways involved in chickens with SNE. METHODS: One hundred eighty one-day-old chickens were randomly divided into three groups and arranged with basal diet (control and SNE group)...
April 20, 2018: Lipids in Health and Disease
https://www.readbyqxmd.com/read/29677519/suspended-graphene-oxide-nanosheets-maintain-the-self-renewal-of-mouse-embryonic-stem-cells-via-down-regulating-the-expression-of-vinculin
#7
Guoxin Jing, Zhaojie Wang, Xizhen Zhuang, Xiaolie He, Huijun Wu, Qingxiu Wang, Liming Cheng, Zhongmin Liu, Shilong Wang, Rongrong Zhu
Graphene oxide (GO), with good hydrophilicity and biocompatibility, is widely explored as a carrier for various factors in the field of stem cell differentiation. However, its function of sustaining the stemness of mouse embryonic stem cells (mESCs) and the underlying mechanisms of this process remains undiscovered. Herein, we explored the biofunction of GO on mESCs and revealed the involved signaling pathways and key gene. The alkaline phosphatase activity detection, pluripotency genes quantification and the teratomas formation in vivo confirmed that GO nanosheets could sustain the self-renewal ability of mESCs instead of influencing its pluripotency...
April 11, 2018: Biomaterials
https://www.readbyqxmd.com/read/29676999/sex-differences-in-transcriptomic-profiles-in-aged-kidney-cells-of-renin-lineage
#8
Yuliang Wang, Diana G Eng, Jeffrey W Pippin, Sina A Gharib, Aaron McClelland, Kenneth W Gross, Stuart J Shankland
Renin expressing cells in the kidney's juxta-glomeruluar compartment likely also serve as progenitors for adult glomerular cells in disease. Although these cells of renin lineage (CoRL) decrease in number with advancing kidney age, accompanied by less responsiveness to typical stimuli such as ACE-inhibition, mechanisms and the impact of sex as a biological variable with age are not known. Accordingly, labeled CoRL were sorted from individual young (2m) and aged (27m) male and female Ren1cCre|ZsGreen reporter mice, and their transcriptomic profiles analyzed by RNA seq...
April 18, 2018: Aging
https://www.readbyqxmd.com/read/29676772/functional-roles-of-eriocalyxin-b-in-zebrafish-revealed-by-transcriptome-analysis
#9
Xunian Zhou, Cyanne Ye Cao, Angel Tsz-Yau Wan, Grace Gar-Lee Yue, Frankie Hin-Fai Kwok, Kwok-Pui Fung, Handong Sun, Clara Bik-San Lau, Pema-Tenzin Puno, Stephen Kwok-Wing Tsui
BACKGROUND: Eriocalyxin B (EriB) is a natural ent-kaurane diterpenoid obtained from Isodon eriocalyx var. laxiflora (family Lamiaceae), which has multiple biological activities (e.g. anti-tumor and anti-inflammatory) via the alteration of gene expression and signaling transduction. Recently, RNA sequencing (RNA-seq) has been developed as a dynamic transcriptome approach to analyze the transcriptional profile and in addition use such gene expression profiles to identify novel candidate genes in a zebrafish model...
April 20, 2018: Molecular omics
https://www.readbyqxmd.com/read/29675428/ptx3-a-potential-biomarker-in-thyroid-associated-ophthalmopathy
#10
Pei Mou, Ziyu Chen, Lihong Jiang, Jinwei Cheng, Ruili Wei
Background: Thyroid associated ophthalmopathy (TAO) is an autoimmune disease, which involves inflammation and tissue remodeling. Pentraxin-3 (PTX3) is a component of innate immune system and recently implicated in autoimmunity. This observation may indicate that PTX3 participates in the inflammatory process of TAO. Methods: All studies were performed on TAO patients and healthy controls (45: 28 in total). RNA-seq was used to detect differential gene expression of orbital adipose-connective tissue...
2018: BioMed Research International
https://www.readbyqxmd.com/read/29674954/bioinformatic-integration-of-molecular-networks-and-major-pathways-involved-in-mice-cochlear-and-vestibular-supporting-cells
#11
Teresa Requena, Alvaro Gallego-Martinez, Jose A Lopez-Escamez
Background : Cochlear and vestibular epithelial non-hair cells (ENHCs) are the supporting elements of the cellular architecture in the organ of Corti and the vestibular neuroepithelium in the inner ear. Intercellular and cell-extracellular matrix interactions are essential to prevent an abnormal ion redistribution leading to hearing and vestibular loss. The aim of this study is to define the main pathways and molecular networks in the mouse ENHCs. Methods : We retrieved microarray and RNA-seq datasets from mouse epithelial sensory and non-sensory cells from gEAR portal (http://umgear...
2018: Frontiers in Molecular Neuroscience
https://www.readbyqxmd.com/read/29674595/developmental-and-oncogenic-programs-in-h3k27m-gliomas-dissected-by-single-cell-rna-seq
#12
Mariella G Filbin, Itay Tirosh, Volker Hovestadt, McKenzie L Shaw, Leah E Escalante, Nathan D Mathewson, Cyril Neftel, Nelli Frank, Kristine Pelton, Christine M Hebert, Christine Haberler, Keren Yizhak, Johannes Gojo, Kristof Egervari, Christopher Mount, Peter van Galen, Dennis M Bonal, Quang-De Nguyen, Alexander Beck, Claire Sinai, Thomas Czech, Christian Dorfer, Liliana Goumnerova, Cinzia Lavarino, Angel M Carcaboso, Jaume Mora, Ravindra Mylvaganam, Christina C Luo, Andreas Peyrl, Mara Popović, Amedeo Azizi, Tracy T Batchelor, Matthew P Frosch, Maria Martinez-Lage, Mark W Kieran, Pratiti Bandopadhayay, Rameen Beroukhim, Gerhard Fritsch, Gad Getz, Orit Rozenblatt-Rosen, Kai W Wucherpfennig, David N Louis, Michelle Monje, Irene Slavc, Keith L Ligon, Todd R Golub, Aviv Regev, Bradley E Bernstein, Mario L Suvà
Gliomas with histone H3 lysine27-to-methionine mutations (H3K27M-glioma) arise primarily in the midline of the central nervous system of young children, suggesting a cooperation between genetics and cellular context in tumorigenesis. Although the genetics of H3K27M-glioma are well characterized, their cellular architecture remains uncharted. We performed single-cell RNA sequencing in 3321 cells from six primary H3K27M-glioma and matched models. We found that H3K27M-glioma primarily contain cells that resemble oligodendrocyte precursor cells (OPC-like), whereas more differentiated malignant cells are a minority...
April 20, 2018: Science
https://www.readbyqxmd.com/read/29674374/changes-in-free-amino-acid-concentrations-and-associated-gene-expression-profiles-in-the-abdominal-muscle-of-kuruma-shrimp-marsupenaeus-japonicus-acclimated-at-different-salinities
#13
Hiroki Koyama, Nanami Mizusawa, Masataka Hoashi, Engkong Tan, Ko Yasumoto, Mitsuru Jimbo, Daisuke Ikeda, Takehiko Yokoyama, Shuichi Asakawa, Sanit Piyapattanakorn, Shugo Watabe
Shrimps inhabiting the coastal water can survive in a wide range of salinity. However, the molecular mechanisms involved in their acclimation to different environmental salinities have remained largely unknown. In the present study, we acclimated kuruma shrimp Marsupenaeus japonicus at 1.7 %, 3.4 % and 4.0 % salinities. After acclimating for 6, 12, 24 and 72 h, we determined free amino acid concentrations in their abdominal muscle, and performed RNA-seq analysis on this muscle. The concentrations of free amino acids were clearly altered depending on salinity after acclimating for 24 h...
April 19, 2018: Journal of Experimental Biology
https://www.readbyqxmd.com/read/29673856/2-3-7-8-tetrachlorodibenzo-p-dioxin-dose-dependently-increases-bone-mass-and-decreases-marrow-adiposity-in-juvenile-mice
#14
Kelly A Fader, Rance Nault, Sandi Raehtz, Laura R McCabe, Timothy R Zacharewski
2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) and other aryl hydrocarbon receptor (AhR) agonists have been shown to regulate bone development and remodeling in a species-, ligand-, and age-specific manner, however the underlying mechanisms remain poorly understood. In this study, we characterized the effect of 0.01-30 μg/kg TCDD on the femoral morphology of male and female juvenile mice orally gavaged every 4 days for 28 days and used RNA-Seq to investigate gene expression changes associated with the resultant phenotype...
April 16, 2018: Toxicology and Applied Pharmacology
https://www.readbyqxmd.com/read/29673323/indel-detection-from-dna-and-rna-sequencing-data-with-transindel
#15
Rendong Yang, Jamie L Van Etten, Scott M Dehm
BACKGROUND: Insertions and deletions (indels) are a major class of genomic variation associated with human disease. Indels are primarily detected from DNA sequencing (DNA-seq) data but their transcriptional consequences remain unexplored due to challenges in discriminating medium-sized and large indels from splicing events in RNA-seq data. RESULTS: Here, we developed transIndel, a splice-aware algorithm that parses the chimeric alignments predicted by a short read aligner and reconstructs the mid-sized insertions and large deletions based on the linear alignments of split reads from DNA-seq or RNA-seq data...
April 19, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29673127/cstf2t-regulates-expression-of-histones-and-histone-like-proteins-in-male-germ-cells
#16
P N Grozdanov, J Li, P Yu, W Yan, C C MacDonald
Formation of the 3' ends of mature mRNAs requires recognition of the correct site within the last exon, cleavage of the nascent pre-mRNA, and, for most mRNAs, addition of a poly(A) tail. Several factors are involved in recognition of the correct 3'-end site. The cleavage stimulation factor (CstF) has three subunits, CstF-50 (gene symbol Cstf1), CstF-64 (Cstf2), and CstF-77 (Cstf3). Of these, CstF-64 is the RNA-binding subunit that interacts with the pre-mRNA downstream of the cleavage site. In male germ cells where CstF-64 is not expressed, a paralog, τCstF-64 (gene symbol Cstf2t) assumes its functions...
April 19, 2018: Andrology
https://www.readbyqxmd.com/read/29672674/trumicount-correctly-counting-absolute-numbers-of-molecules-using-unique-molecular-identifiers
#17
Florian G Pflug, Arndt von Haeseler
Motivation: Counting molecules using next-generation sequencing (NGS) suffers from PCR amplification bias, which reduces the accuracy of many quantitative NGS-based experimental methods such as RNASeq. This is true even if molecules are made distinguishable using unique molecular identifiers (UMIs) before PCR amplification, and distinct UMIs are counted instead of reads: Molecules that are lost entirely during the sequencing process will still cause underestimation of the molecule count, and amplification artifacts like PCR chimeras create phantom UMIs and thus cause over-estimation...
April 16, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29672568/rna-seq-transcriptome-analysis-of-amaranthus-palmeri-with-differential-tolerance-to-glufosinate-herbicide
#18
Reiofeli A Salas-Perez, Christopher A Saski, Rooksana E Noorai, Subodh K Srivastava, Amy L Lawton-Rauh, Robert L Nichols, Nilda Roma-Burgos
Amaranthus palmeri (Amaranthaceae) is a noxious weed in several agroecosystems and in some cases seriously threatens the sustainability of crop production in North America. Glyphosate-resistant Amaranthus species are widespread, prompting the use of alternatives to glyphosate such as glufosinate, in conjunction with glufosinate-resistant crop cultivars, to help control glyphosate-resistant weeds. An experiment was conducted to analyze the transcriptome of A. palmeri plants that survived exposure to 0.55 kg ha-1 glufosinate...
2018: PloS One
https://www.readbyqxmd.com/read/29672513/rna-seq-reveals-differentially-expressed-genes-affecting-polyunsaturated-fatty-acids-percentage-in-the-huangshan-black-chicken-population
#19
Shaohua Yang, Ying Wang, Lulu Wang, Zhaoyuan Shi, Xiaoqian Ou, Dan Wu, Xinmiao Zhang, Hao Hu, Jia Yuan, Wei Wang, Fuhu Cao, Guoqing Liu
Fatty acids metabolic products determine meat quality in chickens. Identifying genes associated with fatty acids composition could provide valuable information for the complex genetic networks of genes with underlying variations in fatty acids synthesis. RNA sequencing (RNA-Seq) was conducted to explore the chicken transcriptome from the thigh muscle tissue of 6 Huangshan Black Chickens with 3 extremely high and low phenotypic values for percentage of polyunsaturated fatty acids (PUFAs). In total, we obtained 41,139,108-44,901,729 uniquely mapped reads, which covered 74...
2018: PloS One
https://www.readbyqxmd.com/read/29671889/two-long-non-coding-rnas-prcat17-3-and-prcat38-could-efficiently-discriminate-benign-prostate-hyperplasia-from-prostate-cancer
#20
Hamid Bayat, Behzad Narouie, Seyed-Amir Mohsen Ziaee, Seyed Javad Mowla
BACKGROUND: Long non-coding RNAs (lncRNAs) have recently appeared as new players in cancer biology. Recently, a number of new prostate cancer-associated lncRNAs has been listed via RNA-seq approach by Mitranscriptome project. By analyzing this data we chose four lncRNAs (Prcat17.3, Prcat38, Prcat47, and Cat2184.4) and evaluated their expressions and their abilities to discriminate prostate tumors from benign prostate hyperplasia (BPH). METHODS: Fresh Prostate tissue samples (30 BPH, and 30 tumor samples) and urine samples (19 BPH, and 19 tumor samples) were collected and their total RNA extracted for cDNA syntheses...
April 19, 2018: Prostate
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