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https://www.readbyqxmd.com/read/28651382/assignment-of-sigma-factors-of-rna-polymerase-to-promoters-in-corynebacterium-glutamicum
#1
Hana Dostálová, Jiří Holátko, Tobias Busche, Lenka Rucká, Andrey Rapoport, Petr Halada, Jan Nešvera, Jörn Kalinowski, Miroslav Pátek
Corynebacterium glutamicum is an important industrial producer of various amino acids and other metabolites. The C. glutamicum genome encodes seven sigma subunits (factors) of RNA polymerase: the primary sigma factor SigA (σ(A)), the primary-like σ(B) and five alternative sigma factors (σ(C), σ(D), σ(E), σ(H) and σ(M)). We have developed in vitro and in vivo methods to assign particular sigma factors to individual promoters of different classes. In vitro transcription assays and measurements of promoter activity using the overexpression of a single sigma factor gene and the transcriptional fusion of the promoter to the gfpuv reporter gene enabled us to reliably define the sigma factor dependency of promoters...
December 2017: AMB Express
https://www.readbyqxmd.com/read/28651089/validation-of-commercial-real-time-pcr-arrays-for-environmental-risk-assessment-application-to-the-study-of-p-p%C3%A2-dde-toxicity-in-mus-spretus-mice-liver
#2
Noelia Morales-Prieto, Carmen Pueyo, Nieves Abril
Data on gene transcription profiles provide a comprehensive assessment of the toxic and defensive mechanisms that are triggered by pollutants. PCR-arrays have emerged as a reliable tool for analyzing the expression of a panel of relevant, pathway- or disease-focused genes under uniform cycling conditions. By using SYBR Green-optimized primer assays, it is possible to simultaneously amplify a sample with high specificity and amplification efficiencies. However, commercial PCR-arrays target a limited group of organisms, excluding most of those with environmental relevance, as is the case with Mus spretus mice...
June 23, 2017: Environmental Pollution
https://www.readbyqxmd.com/read/28650973/interferon-signaling-in-peromyscus-leucopus-confers-a-potent-and-specific-restriction-to-vector-borne-flaviviruses
#3
Adaeze O Izuogu, Kristin L McNally, Stephen E Harris, Brian H Youseff, John B Presloid, Christopher Burlak, Jason Munshi-South, Sonja M Best, R Travis Taylor
Tick-borne flaviviruses (TBFVs), including Powassan virus and tick-borne encephalitis virus cause encephalitis or hemorrhagic fevers in humans with case-fatality rates ranging from 1-30%. Despite severe disease in humans, TBFV infection of natural rodent hosts has little noticeable effect. Currently, the basis for resistance to disease is not known. We hypothesize that the coevolution of flaviviruses with their respective hosts has shaped the evolution of potent antiviral factors that suppress virus replication and protect the host from lethal infection...
2017: PloS One
https://www.readbyqxmd.com/read/28650965/epigenetic-adaptation-of-the-placental-serotonin-transporter-gene-slc6a4-to-gestational-diabetes-mellitus
#4
Sofia Blazevic, Marina Horvaticek, Maja Kesic, Peter Zill, Dubravka Hranilovic, Marina Ivanisevic, Gernot Desoye, Jasminka Stefulj
We tested the hypothesis that gestational diabetes mellitus (GDM) alters the DNA methylation pattern of the fetal serotonin transporter gene (SLC6A4), and examined the functional relevance of DNA methylation for regulation of the SLC6A4 expression in the human placenta. The study included 50 mother-infant pairs. Eighteen mothers were diagnosed with GDM and 32 had normal glucose tolerance (NGT). All neonates were of normal birth weight and born at term by planned Cesarean section. DNA and RNA were isolated from samples of tissue collected from the fetal side of the placenta immediately after delivery...
2017: PloS One
https://www.readbyqxmd.com/read/28650433/the-evening-complex-coordinates-environmental-and-endogenous-signals-in-arabidopsis
#5
Daphne Ezer, Jae-Hoon Jung, Hui Lan, Surojit Biswas, Laura Gregoire, Mathew S Box, Varodom Charoensawan, Sandra Cortijo, Xuelei Lai, Dorothee Stöckle, Chloe Zubieta, Katja E Jaeger, Philip A Wigge
Plants maximize their fitness by adjusting their growth and development in response to signals such as light and temperature. The circadian clock provides a mechanism for plants to anticipate events such as sunrise and adjust their transcriptional programmes. However, the underlying mechanisms by which plants coordinate environmental signals with endogenous pathways are not fully understood. Using RNA-sequencing and chromatin immunoprecipitation sequencing experiments, we show that the evening complex (EC) of the circadian clock plays a major role in directly coordinating the expression of hundreds of key regulators of photosynthesis, the circadian clock, phytohormone signalling, growth and response to the environment...
June 26, 2017: Nature Plants
https://www.readbyqxmd.com/read/28650214/distinct-dna-methylation-profiles-in-bone-and-blood-of-osteoporotic-and-healthy-postmenopausal-women
#6
Sjur Reppe, Tonje G Lien, Yi-Hsiang Hsu, Vigdis T Gautvik, Ole K Olstad, Rona Yu, Hege G Bakke, Robert Lyle, Marianne K Kringen, Ingrid K Glad, Kaare M Gautvik
DNA methylation affects expression of associated genes and may contribute to the missing genetic effects from genome-wide association studies of osteoporosis. To improve insight into the mechanisms of postmenopausal osteoporosis, we combined transcript profiling with DNA methylation analyses in bone. RNA and DNA were isolated from 84 bone biopsies of postmenopausal donors varying markedly in bone mineral density (BMD). In all, 2529 CpGs in the top 100 genes most significantly associated with BMD were analyzed...
June 26, 2017: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/28649985/attenuation-of-rna-polymerase-ii-pausing-mitigates-brca1-associated-r-loop-accumulation-and-tumorigenesis
#7
Xiaowen Zhang, Huai-Chin Chiang, Yao Wang, Chi Zhang, Sabrina Smith, Xiayan Zhao, Sreejith J Nair, Joel Michalek, Ismail Jatoi, Meeghan Lautner, Boyce Oliver, Howard Wang, Anna Petit, Teresa Soler, Joan Brunet, Francesca Mateo, Miguel Angel Pujana, Elizabeth Poggi, Krysta Chaldekas, Claudine Isaacs, Beth N Peshkin, Oscar Ochoa, Frederic Chedin, Constantine Theoharis, Lu-Zhe Sun, Tyler J Curiel, Richard Elledge, Victor X Jin, Yanfen Hu, Rong Li
Most BRCA1-associated breast tumours are basal-like yet originate from luminal progenitors. BRCA1 is best known for its functions in double-strand break repair and resolution of DNA replication stress. However, it is unclear whether loss of these ubiquitously important functions fully explains the cell lineage-specific tumorigenesis. In vitro studies implicate BRCA1 in elimination of R-loops, DNA-RNA hybrid structures involved in transcription and genetic instability. Here we show that R-loops accumulate preferentially in breast luminal epithelial cells, not in basal epithelial or stromal cells, of BRCA1 mutation carriers...
June 26, 2017: Nature Communications
https://www.readbyqxmd.com/read/28649496/de-novo-transcriptome-assembly-of-loggerhead-sea-turtle-nesting-of-the-colombian-caribbean
#8
Javier Hernández-Fernández, Andrés Pinzón, Leonardo Mariño-Ramírez
Loggerhead sea turtle Caretta caretta is widely distributed in the oceans of tropical and subtropical latitude. This turtle is an endangered species due to anthropic and natural factors that have decreased their population levels. In this study, RNA sequencing and de-novo assembly of genes expressed in blood were performed. The raw FASTQ files have been deposited on NCBI's SRA database with accession number SRX2629512. A total of 5.4 Gb raw sequence data were obtained, corresponding to 48,257,019 raw reads...
September 2017: Genomics Data
https://www.readbyqxmd.com/read/28649424/an-alanine-expanded-pabpn1-causes-increased-utilization-of-intronic-polyadenylation-sites
#9
Tooba Abbassi-Daloii, Soheil Yousefi, Eleonora de Klerk, Laurens Grossouw, Muhammad Riaz, Peter A C 't Hoen, Vered Raz
In eukaryote genomes, the polyadenylation site marks termination of mature RNA transcripts by a poly-adenine tail. The polyadenylation site is recognized by a dynamic protein complex, among which the poly-adenine-binding protein nuclear1 plays a key role. Reduced poly-adenine-binding protein nuclear1 levels are found in aged muscles and are even lower in oculopharyngeal muscular dystrophy patients. Oculopharyngeal muscular dystrophy is a rare, late onset autosomal dominant myopathy, and is caused by an alanine expansion mutation in poly-adenine-binding protein nuclear1...
2017: NPJ Aging and Mechanisms of Disease
https://www.readbyqxmd.com/read/28649404/comparative-transcriptomic-analysis-of-gardnerella-vaginalis-biofilms-vs-planktonic-cultures-using-rna-seq
#10
Joana Castro, Angela França, Katie R Bradwell, Myrna G Serrano, Kimberly K Jefferson, Nuno Cerca
Bacterial vaginosis is the most common gynecological disorder affecting women of reproductive age. Bacterial vaginosis is frequently associated with the development of a Gardnerella vaginalis biofilm. Recent data indicates that G. vaginalis biofilms are more tolerant to antibiotics and are able to incorporate other bacterial vaginosis -associated species, yielding a multi-species biofilm. However, despite its apparent role in bacterial vaginosis, little is known regarding the molecular determinants involved in biofilm formation by G...
2017: NPJ Biofilms and Microbiomes
https://www.readbyqxmd.com/read/28649315/effects-of-a-social-stimulus-on-gene-expression-in-a-mouse-model-of-fragile-x-syndrome
#11
Tiffany D Rogers, Allison M J Anacker, Travis M Kerr, C Gunnar Forsberg, Jing Wang, Bing Zhang, Jeremy Veenstra-VanderWeele
BACKGROUND: People with fragile X syndrome (FXS) often have deficits in social behavior, and a substantial portion meet criteria for autism spectrum disorder. Though the genetic cause of FXS is known to be due to the silencing of FMR1, and the Fmr1 null mouse model representing this lesion has been extensively studied, the contributions of this gene and its protein product, FMRP, to social behavior are not well understood. METHODS: Fmr1 null mice and wildtype littermates were exposed to a social or non-social stimulus...
2017: Molecular Autism
https://www.readbyqxmd.com/read/28649263/survey-of-high-throughput-rna-seq-data-reveals-potential-roles-for-lncrnas-during-development-and-stress-response-in-bread-wheat
#12
Shumayla, Shailesh Sharma, Mehak Taneja, Shivi Tyagi, Kashmir Singh, Santosh K Upadhyay
Long non-coding RNAs (lncRNAs) are a family of regulatory RNAs that play essential role in the various developmental processes and stress responses. Recent advances in sequencing technology and computational methods enabled identification and characterization of lncRNAs in certain plant species, but they are less known in Triticum aestivum (bread wheat). Herein, we analyzed 52 RNA seq data (>30 billion reads) and identified 44,698 lncRNAs in T. aestivum genome, which were characterized in comparison to the coding sequences (mRNAs)...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28649178/hotair-a-key-regulator-in-gynecologic-cancers
#13
REVIEW
Jing Li, Jing Wang, Yan Zhong, Ruixia Guo, Danxia Chu, Haifeng Qiu, Zhongfu Yuan
Long non-coding RNAs (lncRNAs) play critical roles in the initiation and progression of human cancers. HOX transcript antisense RNA (HOTAIR) is an lncRNA localized to the mammalian HOXC gene cluster; it can interact with polycomb repressive complex 2 and the lysine-specific histone demethylase/CoREST/REST complex, and it manipulates the expression of various genes. HOTAIR promotes tumor invasion and metastasis by silencing tumor suppressors, and activating oncogenes and signaling pathways. HOTAIR is deregulated in many human cancers; despite its critical roles in health and disease, the underlying mechanisms governing HOTAIR function are unknown...
2017: Cancer Cell International
https://www.readbyqxmd.com/read/28649092/aryl-hydrocarbon-receptor-ahr-is-a-potential-tumour-suppressor-in-pituitary-adenomas
#14
Robert Formosa, Joseph Borg, Josanne Vassallo
Pituitary adenomas (PA) represent the largest group of intracranial neoplasms, yet the molecular mechanisms driving this disease remain largely unknown. The aim of this study was to use high-throughput screening to identify molecular pathways that may be playing a significant and consistent role in PA. RNA profiling using microarrays on eight local PAs identified the aryl hydrocarbon receptor (AHR) signalling pathway as a key canonical pathway down-regulated in all PA types. This was confirmed by qPCR in 31 tumours...
June 25, 2017: Endocrine-related Cancer
https://www.readbyqxmd.com/read/28649000/suppression-of-the-mads-box-gene-slmbp8-accelerates-fruit-ripening-of-tomato-solanum-lycopersicum
#15
Wencheng Yin, Zongli Hu, Baolu Cui, Xuhu Guo, Jingtao Hu, Zhiguo Zhu, Guoping Chen
MADS-box genes encode important transcription factors that are involved in many biological processes of plants, including fruit ripening. In our research, a MADS-box gene, SlMBP8, was identified, and its tissue-specific expression profiles were analysed. SlMBP8 was highly expressed in fruits of the B+4 stage, in senescent leaves and in sepals. To further characterize its function, an RNA interference (RNAi) expression vector of SlMBP8 was constructed and transferred into tomato. In the transgenic plants, the ripening of fruits was shortened by 2-4 days compared to that of wild type...
June 15, 2017: Plant Physiology and Biochemistry: PPB
https://www.readbyqxmd.com/read/28648996/rnai-knock-down-of-the-bemisia-tabaci-toll-gene-bttoll-increases-mortality-after-challenge-with-destruxin-a
#16
Can Zhang, Shao-Qiao Yan, Bin-Bin Shen, Shaukat Ali, Xing-Min Wang, Feng-Liang Jin, Andrew G S Cuthbertson, Bao-Li Qiu
Bemisia tabaci (Gennadius) Middle East-Asia Minor 1 (MEAM1) is a well known invasive insect species. Little information is available on immune system of B. tabaci to date. In this study, one of the Toll-like receptors (TLR; namely BtToll) was cloned in MEAM1 B. tabaci which contains an open reading frame of 3153bp, encoding putative 1050 amino acids. Phylogenetic analysis indicated that BtToll is highly identitical with other members of the TLR family. Transcripts of BtToll detected through qRT-PCR were expressed in all developmental stages of B...
June 22, 2017: Molecular Immunology
https://www.readbyqxmd.com/read/28648844/novel-functions-for-the-rna-binding-protein-etr-1-in-caenorhabditis-elegans-reproduction-and-engulfment-of-germline-apoptotic-cell-corpses
#17
Ruby Boateng, Ken C Q Nguyen, David H Hall, Andy Golden, Anna K Allen
RNA-binding proteins (RBPs) are essential regulators of gene expression that act through a variety of mechanisms to ensure the proper post-transcriptional regulation of their target RNAs. RBPs in multiple species have been identified as playing crucial roles during development and as having important functions in various adult organ systems, including the heart, nervous, muscle, and reproductive systems. ETR-1, a highly conserved ELAV-Type RNA-binding protein belonging to the CELF/Bruno protein family, has been previously reported to be involved in C...
June 22, 2017: Developmental Biology
https://www.readbyqxmd.com/read/28648780/the-histone-acetyltransferase-mst2-protects-active-chromatin-from-epigenetic-silencing-by-acetylating-the-ubiquitin-ligase-brl1
#18
Valentin Flury, Paula Raluca Georgescu, Vytautas Iesmantavicius, Yukiko Shimada, Tahsin Kuzdere, Sigurd Braun, Marc Bühler
Faithful propagation of functionally distinct chromatin states is crucial for maintaining cellular identity, and its breakdown can lead to diseases such as cancer. Whereas mechanisms that sustain repressed states have been intensely studied, regulatory circuits that protect active chromatin from inactivating signals are not well understood. Here we report a positive feedback loop that preserves the transcription-competent state of RNA polymerase II-transcribed genes. We found that Pdp3 recruits the histone acetyltransferase Mst2 to H3K36me3-marked chromatin...
June 14, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28648779/natural-rna-polymerase-aptamers-regulate-transcription-in-e-coli
#19
Nadezda Sedlyarova, Philipp Rescheneder, Andrés Magán, Niko Popitsch, Natascha Rziha, Ivana Bilusic, Vitaly Epshtein, Bob Zimmermann, Meghan Lybecker, Vitaly Sedlyarov, Renée Schroeder, Evgeny Nudler
In search for RNA signals that modulate transcription via direct interaction with RNA polymerase (RNAP), we deep sequenced an E. coli genomic library enriched for RNAP-binding RNAs. Many natural RNAP-binding aptamers, termed RAPs, were mapped to the genome. Over 60% of E. coli genes carry RAPs in their mRNA. Combining in vitro and in vivo approaches, we characterized a subset of inhibitory RAPs (iRAPs) that promote Rho-dependent transcription termination. A representative iRAP within the coding region of the essential gene, nadD, greatly reduces its transcriptional output in stationary phase and under oxidative stress, demonstrating that iRAPs control gene expression in response to changing environment...
June 19, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28648755/high-expression-of-long-noncoding-rna-malat1-indicates-a-poor-prognosis-and-promotes-clinical-progression-and-metastasis-in%C3%A2-bladder-cancer
#20
Chao Li, Yu Cui, Long-Fei Liu, Wen-Biao Ren, Qia-Qia Li, Xu Zhou, Yang-Le Li, Yang Li, Xiang-Yang Bai, Xiong-Bing Zu
BACKGROUND: Recent studies have demonstrated that the expression of long noncoding RNA metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) promotes cancer cell proliferation, invasion, and metastasis in many tumor types, but the association between bladder cancer and MALAT1 remains unknown. MATERIALS: The expression of MALAT1 was tested by in situ hybridization (ISH) in 120 bladder cancer specimens. The association between MALAT1 expression and clinicopathological features and prognosis of the patients with bladder cancer was analyzed...
May 10, 2017: Clinical Genitourinary Cancer
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