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https://www.readbyqxmd.com/read/28214646/new-rna-seq-approaches-for-the-study-of-bacterial-pathogens
#1
REVIEW
Antoine-Emmanuel Saliba, Sara C Santos, Jörg Vogel
Understanding how bacteria cause disease requires knowledge of which genes are expressed and how they are regulated during infection. While RNA-seq is now a routine method for gene expression analysis in bacterial pathogens, the past years have also witnessed a surge of novel RNA-seq based approaches going beyond standard mRNA profiling. These include variations of the technique to capture post-transcriptional networks controlled by small RNAs and to discover associated RNA-binding proteins in the pathogen itself...
February 16, 2017: Current Opinion in Microbiology
https://www.readbyqxmd.com/read/28214471/che-1-sustains-hypoxic-response-of-colorectal-cancer-cells-by-affecting-hif-1%C3%AE-stabilization
#2
Tiziana Bruno, Mariacristina Valerio, Luca Casadei, Francesca De Nicola, Frauke Goeman, Matteo Pallocca, Valeria Catena, Simona Iezzi, Cristina Sorino, Agata Desantis, Cesare Manetti, Giovanni Blandino, Aristide Floridi, Maurizio Fanciulli
BACKGROUND: Solid tumours are less oxygenated than normal tissues. Consequently, cancer cells acquire to be adapted to a hypoxic environment. The poor oxygenation of solid tumours is also a major indicator of an adverse cancer prognosis and leads to resistance to conventional anticancer treatments. We previously showed the involvement of Che-1/AATF (Che-1) in cancer cell survival under stress conditions. Herein we hypothesized that Che-1 plays a role in the response of cancer cells to hypoxia...
February 18, 2017: Journal of Experimental & Clinical Cancer Research: CR
https://www.readbyqxmd.com/read/28213567/vitamin-d-receptor-as-a-target-for-breast-cancer-therapy
#3
Alyson Murray, Stephen Madden, Naoise C Synnott, Rut Klinger, Darran O'Connor, Norma O'Donovan, William Gallagher, John Crown, Michael Duffy
Considerable epidemiological evidence suggests that high levels of circulating vitamin D (VD) are associated with a decreased incidence and increased survival from cancer, i.e., VD may possess anti-cancer properties. The aim of this investigation was therefore to investigate the anti-cancer potential of a low calcemic vitamin D analogue, i.e., inecalcitol and compare it with the active form of vitamin D, i.e., calcitriol, in a panel of breast cancer cell lines (n = 15). Using the MTT assay, IC50 concentrations for response to calcitriol varied from 0...
February 17, 2017: Endocrine-related Cancer
https://www.readbyqxmd.com/read/28213474/a-bayesian-approach-for-analysis-of-whole-genome-bisulphite-sequencing-data-identifies-disease-associated-changes-in-dna-methylation
#4
Owen J L Rackham, Sarah R Langley, Thomas Oates, Eleni Vradi, Nathan Harmston, Prashant K Srivastava, Jacques Behmoaras, Petros Dellaportas, Leonardo Bottolo, Enrico Petretto
DNA methylation is a key epigenetic modification involved in gene regulation whose contribution to disease susceptibility remains to be fully understood. Here, we present a novel Bayesian smoothing approach (called ABBA) to detect differentially methylated regions (DMRs) from whole-genome bisulphite sequencing (WGBS). We also show how this approach can be leveraged to identify disease-associated changes in DNA methylation, suggesting mechanisms through which these alterations might affect disease. From a data modeling perspective, ABBA has the distinctive feature of automatically adapting to different correlation structures in CpG methylation levels across the genome whilst taking into account the distance between CpG sites as a covariate...
February 17, 2017: Genetics
https://www.readbyqxmd.com/read/28213379/slowed-decay-of-mrnas-enhances-platelet-specific-translation
#5
Eric W Mills, Rachel Green, Nicholas T Ingolia
Platelets are anucleate cytoplasmic fragments that lack genomic DNA, but continue to synthesize protein using a pool of mRNAs, ribosomes, and regulatory small RNAs inherited from the precursor megakaryocyte (MK). The regulatory processes that shape the platelet transcriptome and the full scope of platelet translation have remained elusive. Using RNA-Seq and ribosome profiling of primary human platelets, we show the platelet transcriptome encompasses a subset of transcripts detected by RNA-Seq analysis of in vitro derived MK cells and these platelet-enriched transcripts are broadly occupied by ribosomes...
February 17, 2017: Blood
https://www.readbyqxmd.com/read/28213091/convergence-of-hepcidin-deficiency-systemic-iron-overloading-heme-accumulation-and-rev-erb%C3%AE-%C3%AE-activation-in-aryl-hydrocarbon-receptor-elicited-hepatotoxicity
#6
Kelly A Fader, Rance Nault, Mathew P Kirby, Gena Markous, Jason Matthews, Timothy R Zacharewski
Persistent aryl hydrocarbon receptor (AhR) agonists elicit dose-dependent hepatic lipid accumulation, oxidative stress, inflammation, and fibrosis in mice. Iron (Fe) promotes AhR-mediated oxidative stress by catalyzing reactive oxygen species (ROS) production. To further characterize the role of Fe in AhR-mediated hepatotoxicity, male C57BL/6 mice were orally gavaged with sesame oil vehicle or 0.01-30μg/kg 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) every 4days for 28days. Duodenal epithelial and hepatic RNA-Seq data were integrated with hepatic AhR ChIP-Seq, capillary electrophoresis protein measurements, and clinical chemistry analyses...
February 14, 2017: Toxicology and Applied Pharmacology
https://www.readbyqxmd.com/read/28212749/comparative-analysis-of-single-cell-rna-sequencing-methods
#7
Christoph Ziegenhain, Beate Vieth, Swati Parekh, Björn Reinius, Amy Guillaumet-Adkins, Martha Smets, Heinrich Leonhardt, Holger Heyn, Ines Hellmann, Wolfgang Enard
Single-cell RNA sequencing (scRNA-seq) offers new possibilities to address biological and medical questions. However, systematic comparisons of the performance of diverse scRNA-seq protocols are lacking. We generated data from 583 mouse embryonic stem cells to evaluate six prominent scRNA-seq methods: CEL-seq2, Drop-seq, MARS-seq, SCRB-seq, Smart-seq, and Smart-seq2. While Smart-seq2 detected the most genes per cell and across cells, CEL-seq2, Drop-seq, MARS-seq, and SCRB-seq quantified mRNA levels with less amplification noise due to the use of unique molecular identifiers (UMIs)...
February 16, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28212626/a-global-characterization-of-the-translational-and-transcriptional-programs-induced-by-methionine-restriction-through-ribosome-profiling-and-rna-seq
#8
Ke Zou, Qi Ouyang, Hao Li, Jiashun Zheng
BACKGROUND: Among twenty amino acids, methionine has a special role as it is coded by the translation initiation codon and methionyl-tRNAi (Met-tRNAi) is required for the assembly of the translation initiation complex. Thus methionine may play a special role in global gene regulation. Methionine has also been known to play important roles in cell growth, development, cancer, and aging. In this work, we characterize the translational and transcriptional programs induced by methionine restriction (MetR) and investigate the potential mechanisms through which methionine regulates gene expression, using the budding yeast S...
February 17, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28212614/transcriptomic-profiling-provides-molecular-insights-into-hydrogen-peroxide-induced-adventitious-rooting-in-mung-bean-seedlings
#9
Shi-Weng Li, Yan Leng, Rui-Fang Shi
BACKGROUND: Hydrogen peroxide (H2O2) has been known to function as a signalling molecule involved in the modulation of various physiological processes in plants. H2O2 has been shown to act as a promoter during adventitious root formation in hypocotyl cuttings. In this study, RNA-Seq was performed to reveal the molecular mechanisms underlying H2O2-induced adventitious rooting. RESULTS: RNA-Seq data revealed that H2O2 treatment greatly increased the numbers of clean reads and expressed genes and abundance of gene expression relative to the water treatment...
February 17, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28212444/sumo-modification-of-a-heterochromatin-histone-demethylase-jmjd2a-enables-viral-gene-transactivation-and-viral-replication
#10
Wan-Shan Yang, Mel Campbell, Pei-Ching Chang
Small ubiquitin-like modifier (SUMO) modification of chromatin has profound effects on transcription regulation. By using Kaposi's sarcoma associated herpesvirus (KSHV) as a model, we recently demonstrated that epigenetic modification of viral chromatin by SUMO-2/3 is involved in regulating gene expression and viral reactivation. However, how this modification orchestrates transcription reprogramming through targeting histone modifying enzymes remains largely unknown. Here we show that JMJD2A, the first identified Jumonji C domain-containing histone demethylase, is the histone demethylase responsible for SUMO-2/3 enrichment on the KSHV genome during viral reactivation...
February 17, 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28212420/transcriptome-using-illumina-sequencing-reveals-the-traits-of-spermatogenesis-and-developing-testes-in-eriocheir-sinensis
#11
Gen-Liang Li, Hui Qian
Chinese mitten crab (Eriocheir sinensis) has the spermatozoa with typical aflagellate, decondensed chromatin, cup-shaped nuclei, and radial arms. However, the mechanism of spermatogenesis during which the specific spermatozoa are generated in this species is yet unclear. Here, the transcriptome of developing testis in E. sinensis was analyzed using the ways of RNA-seq and bioinformatics analysis to identify candidate genes potentially involved in development of testis and spermatogenesis. The Illumina HiSeq2500 sequencing of three replicons of samples produced a total of 145...
2017: PloS One
https://www.readbyqxmd.com/read/28212394/de-novo-transcriptome-analysis-and-microsatellite-marker-development-for-population-genetic-study-of-a-serious-insect-pest-rhopalosiphum-padi-l-hemiptera-aphididae
#12
Xinle Duan, Kang Wang, Sha Su, Ruizheng Tian, Yuting Li, Maohua Chen
The bird cherry-oat aphid, Rhopalosiphum padi (L.), is one of the most abundant aphid pests of cereals and has a global distribution. Next-generation sequencing (NGS) is a rapid and efficient method for developing molecular markers. However, transcriptomic and genomic resources of R. padi have not been investigated. In this study, we used transcriptome information obtained by RNA-Seq to develop polymorphic microsatellites for investigating population genetics in this species. The transcriptome of R. padi was sequenced on an Illumina HiSeq 2000 platform...
2017: PloS One
https://www.readbyqxmd.com/read/28212285/transcriptomic-analysis-reveals-selective-metabolic-adaptation-of-streptococcus-suis-to-porcine-blood-and-cerebrospinal-fluid
#13
Anna Koczula, Michael Jarek, Christian Visscher, Peter Valentin-Weigand, Ralph Goethe, Jörg Willenborg
Streptococcus suis is a zoonotic pathogen that can cause severe pathologies such as septicemia and meningitis in its natural porcine host as well as in humans. Establishment of disease requires not only virulence of the infecting strain but also an appropriate metabolic activity of the pathogen in its host environment. However, it is yet largely unknown how the streptococcal metabolism adapts to the different host niches encountered during infection. Our previous isotopologue profiling studies on S. suis grown in porcine blood and cerebrospinal fluid (CSF) revealed conserved activities of central carbon metabolism in both body fluids...
February 15, 2017: Pathogens
https://www.readbyqxmd.com/read/28211524/epigenetic-and-genetic-dissections-of-uv-induced-global-gene-dysregulation-in-skin-cells-through-multi-omics-analyses
#14
Yao Shen, Milda Stanislauskas, Gen Li, Deyou Zheng, Liang Liu
To elucidate the complex molecular mechanisms underlying the adverse effects UV radiation (UVR) on skin homeostasis, we performed multi-omics studies to characterize UV-induced genetic and epigenetic changes. Human keratinocytes from a single donor treated with or without UVR were analyzed by RNA-seq, exome-seq, and H3K27ac ChIP-seq at 4 h and 72 h following UVR. Compared to the relatively moderate mutagenic effects of UVR, acute UV exposure induced substantial epigenomic and transcriptomic alterations, illuminating a previously underappreciated role of epigenomic and transcriptomic instability in skin pathogenesis...
February 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28211215/zkscan1-gene-and-its-related-circular-rna-circzkscan1-both-inhibit-hepatocellular-carcinoma-cell-growth-migration-and-invasion-but-through-different-signaling-pathways
#15
Zhicheng Yao, Jingyan Luo, Kunpeng Hu, Jizong Lin, He Huang, Qiangliang Wang, Peng Zhang, Zhiyong Xiong, Zejian Huang, Chonghua He, Bo Liu, Yang Yang
There is increasing evidence that circular RNAs (circRNAs) are involved in cancer development, but the regulation and function of human circRNAs remain largely unknown. In this study, we demonstrated that ZKSCAN1, a zinc finger family gene, is expressed in both linear and circular (circZKSCAN1) forms of RNA in human hepatocellular carcinoma (HCC) tissues and cell lines. Here, we analyzed a cohort of 102 patients and found that expression of both ZKSCAN1 mRNA and circZKSCAN1 was significantly lower (P<0.05) in the HCC samples compared with that in matched adjacent non-tumorous tissues by reverse transcription PCR (RT-PCR)...
February 16, 2017: Molecular Oncology
https://www.readbyqxmd.com/read/28210265/rna-seq-of-guar-cyamopsis-tetragonoloba-l-taub-leaves-de-novo-transcriptome-assembly-functional-annotation-and-development-of-genomic-resources
#16
Umesh K Tanwar, Vikas Pruthi, Gursharn S Randhawa
Genetic improvement in industrially important guar (Cyamopsis tetragonoloba, L. Taub.) crop has been hindered due to the lack of sufficient genomic or transcriptomic resources. In this study, RNA-Seq technology was employed to characterize the transcriptome of leaf tissues from two guar varieties, namely, M-83 and RGC-1066. Approximately 30 million high-quality pair-end reads of each variety generated by Illumina HiSeq platform were used for de novo assembly by Trinity program. A total of 62,146 non-redundant unigenes with an average length of 679 bp were obtained...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28209995/rna-seq-based-transcriptomic-and-metabolomic-analysis-reveal-stress-responses-and-programmed-cell-death-induced-by-acetic-acid-in-saccharomyces-cerevisiae
#17
Yachen Dong, Jingjin Hu, Linlin Fan, Qihe Chen
As a typical harmful inhibitor in cellulosic hydrolyzates, acetic acid not only hinders bioethanol production, but also induces cell death in Saccharomyces cerevisiae. Herein, we conducted both transcriptomic and metabolomic analyses to investigate the global responses under acetic acid stress at different stages. There were 295 up-regulated and 427 down-regulated genes identified at more than two time points during acetic acid treatment (150 mM, pH 3.0). These differentially expressed genes (DEGs) were mainly involved in intracellular homeostasis, central metabolic pathway, transcription regulation, protein folding and stabilization, ubiquitin-dependent protein catabolic process, vesicle-mediated transport, protein synthesis, MAPK signaling pathways, cell cycle, programmed cell death, etc...
February 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28209810/genome-sequence-of-southern-tomato-virus-in-asymptomatic-tomato-sweet-hearts
#18
Ricardo I Alcalá-Briseño, Sevgi Coşkan, Maria A Londoño, Jane E Polston
The genome sequence of Southern tomato virus in asymptomatic Solanum lycopersicum 'Sweet Hearts' (STV-Florida) in Florida was assembled from small RNAs sequenced by Illumina RNA-seq. The STV-Florida genome shared 99.0 to 99.9% similarity with full genome sequences from Bangladesh, China, Mexico, and the United States (Mississippi and North Carolina).
February 16, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28209632/high-resolution-profiling-of-nmd-targets-in-yeast-reveals-translational-fidelity-as-a-basis-for-substrate-selection
#19
Alper Celik, Richard Baker, Feng He, Allan Jacobson
Nonsense-mediated mRNA decay (NMD) plays an important role in eukaryotic gene expression yet the scope and the defining features of NMD-targeted transcripts remain elusive. To address these issues, we re-evaluated the genome-wide expression of annotated transcripts in yeast cells harboring deletions of the UPF1, UPF2, or UPF3 genes. Our new RNA-Seq analyses confirm previous results of microarray studies, but also uncover hundreds of new NMD-regulated transcripts that had escaped previous detection, including many intron-containing pre-mRNAs and several non-coding RNAs...
February 16, 2017: RNA
https://www.readbyqxmd.com/read/28209615/targeted-degradation-of-bet-proteins-in-triple-negative-breast-cancer
#20
Longchuan Bai, Bing Zhou, Chao-Yie Yang, Jiao Ji, Donna McEachern, Sally Przybranowski, Hui Jiang, Jiantao Hu, Fuming Xu, Yujun Zhao, Liu Liu, Ester Fernandez-Salas, Jing Xu, Yali Dou, Bo Wen, Duxin Sun, Jennifer L Meagher, Jeanne Stuckey, Daniel F Hayes, Shunqiang Li, Matthew J Ellis, Shaomeng Wang
Triple-negative breast cancers (TNBC) remain clinically challenging with a lack of options for targeted therapy. In this study, we report the development of a second-generation BET bromodomain (BRD) inhibitor, BETd-246, which exhibits superior selectivity, potency and antitumor activity. In human TNBC cells, BETd-246 induced degradation of BET transcription factors at low nanomolar concentrations within 1 hr of exposure, resulting in robust growth inhibition and apoptosis. BETd-246 was more potent and effective in TNBC cells than its parental BET inhibitor compound BETi-211...
February 16, 2017: Cancer Research
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