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https://www.readbyqxmd.com/read/28434904/deep-sequencing-approaches-for-the-analysis-of-prokaryotic-transcriptional-boundaries-and-dynamics
#1
REVIEW
Katherine James, Simon J Cockell, Nikolay Zenkin
The identification of the protein-coding regions of a genome is straightforward due to the universality of start and stop codons. However, the boundaries of the transcribed regions, conditional operon structures, non-coding RNAs and the dynamics of transcription, such as pausing of elongation, are non-trivial to identify, even in the comparatively simple genomes of prokaryotes. Traditional methods for the study of these areas, such as tiling arrays, are noisy, labour-intensive and lack the resolution required for densely-packed bacterial genomes...
April 20, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28431015/large-scale-collection-of-full-length-cdna-and-transcriptome-analysis-in-hevea-brasiliensis
#2
Yuko Makita, Kiaw Kiaw Ng, G Veera Singham, Mika Kawashima, Hideki Hirakawa, Shusei Sato, Ahmad Sofiman Othman, Minami Matsui
Natural rubber has unique physical properties that cannot be replaced by products from other latex-producing plants or petrochemically produced synthetic rubbers. Rubber from Hevea brasiliensis is the main commercial source for this natural rubber that has a cis-polyisoprene configuration. For sustainable production of enough rubber to meet demand elucidation of the molecular mechanisms involved in the production of latex is vital. To this end, we firstly constructed rubber full-length cDNA libraries of RRIM 600 cultivar and sequenced around 20,000 clones by the Sanger method and over 15,000 contigs by Illumina sequencer...
April 1, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/28429829/molecular-adaptation-in-the-world-s-deepest-living-animal-insights-from-transcriptome-sequencing-of-the-hadal-amphipod-hirondellea-gigas
#3
Yi Lan, Jin Sun, Renmao Tian, Douglas H Bartlett, Runsheng Li, Yue Him Wong, Weipeng Zhang, Jian-Wen Qiu, Ting Xu, Li-Sheng He, Harry G Tabata, Pei-Yuan Qian
The Challenger Deep in the Mariana Trench is the deepest point in the oceans of our planet. Understanding how animals adapt to this harsh environment characterized by high hydrostatic pressure, food-limited, dark, and cold is of great scientific interest. Of the animals dwelling in the Challenger Deep, amphipods have been captured using baited traps. In the present study, we sequenced the transcriptome of the amphipod Hirondellea gigas collected at a depth of 10,929 m from the East Pond of the Challenger Deep...
April 21, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28429322/photo-and-nutritional-regulation-of-euglena-organelle-development
#4
Steven D Schwartzbach
Euglena can use light and CO2, photosynthesis, as well as a large variety of organic molecules as the sole source of carbon and energy for growth. Light induces the enzymes, in this case an entire organelle, the chloroplast, that is required to use CO2 as the sole source of carbon and energy for growth. Ethanol, but not malate, inhibits the photoinduction of chloroplast enzymes and induces the synthesis of the glyoxylate cycle enzymes that comprise the unique metabolic pathway leading to two carbon, ethanol and acetate, assimilation...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/28428215/blocked-transcription-through-kvdmr1-results-in-absence-of-methylation-and-gene-silencing-resembling-beckwith-wiedemann-syndrome
#5
Vir B Singh, Sirinapa Sribenja, Kayla E Wilson, Kristopher M Attwood, Joanna C Hillman, Shilpa Pathak, Michael J Higgins
The maternally methylated KvDMR1 ICR regulates imprinted expression of a cluster of maternally-expressed genes on human chromosome 11p15.5. Disruption of imprinting leads to Beckwith-Wiedemann syndrome (BWS), an overgrowth and cancer predisposition condition. In the majority of BWS patients, maternal-specific methylation at KvDMR1 is absent and genes under its control are repressed. We analyzed a mouse model carrying a poly(A) truncation cassette inserted to prevent RNA transcripts from elongation through KvDMR1...
April 20, 2017: Development
https://www.readbyqxmd.com/read/28426789/gre-factors-mediated-control-of-hild-transcription-is-essential-for-the-invasion-of-epithelial-cells-by-salmonella-enterica-serovar-typhimurium
#6
Tania Gaviria-Cantin, Youssef El Mouali, Soazig Le Guyon, Ute Römling, Carlos Balsalobre
The invasion of epithelial cells by Salmonella enterica serovar Typhimurium is a very tightly regulated process. Signaling cascades triggered by different environmental and physiological signals converge to control HilD, an AraC regulator that coordinates the expression of several virulence factors. The expression of hilD is modulated at several steps of the expression process. Here, we report that the invasion of epithelial cells by S. Typhimurium strains lacking the Gre factors, GreA and GreB, is impaired...
April 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28426669/a-dynamic-genetic-hormonal-regulatory-network-model-explains-multiple-cellular-behaviors-of-the-root-apical-meristem-of-arabidopsis-thalian
#7
Mónica L García-Gómez, Eugenio Azpeitia, Elena R Álvarez-Buylla
The study of the concerted action of hormones and transcription factors is fundamental to understand cell differentiation and pattern formation during organ development. The root apical meristem of Arabidopsis thaliana is a useful model to address this. It has a stem cell niche near its tip conformed of a quiescent organizer and stem or initial cells around it, then a proliferation domain followed by a transition domain, where cells diminish division rate before transiting to the elongation zone; here, cells grow anisotropically prior to their final differentiation towards the plant base...
April 20, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28426094/sirt7-dependent-deacetylation-of-cdk9-activates-rna-polymerase-ii-transcription
#8
Maximilian F Blank, Sifan Chen, Fabian Poetz, Martina Schnölzer, Renate Voit, Ingrid Grummt
SIRT7 is an NAD+-dependent protein deacetylase that regulates cell growth and proliferation. Previous studies have shown that SIRT7 is required for RNA polymerase I (Pol I) transcription and pre-rRNA processing. Here, we took a proteomic approach to identify novel molecular targets and characterize the role of SIRT7 in non-nucleolar processes. We show that SIRT7 interacts with numerous proteins involved in transcriptional regulation and RNA metabolism, the majority of interactions requiring ongoing transcription...
March 17, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28424725/a-genome-scale-analysis-of-the-pin-gene-family-reveals-its-functions-in-cotton-fiber-development
#9
Yuzhou Zhang, Peng He, Zuoren Yang, Gai Huang, Limin Wang, Chaoyou Pang, Hui Xiao, Peng Zhao, Jianing Yu, Guanghui Xiao
The PIN-FORMED (PIN) protein, the most important polar auxin transporter, plays a critical role in the distribution of auxin and controls multiple biological processes. However, characterizations and functions of this gene family have not been identified in cotton. Here, we identified the PIN family in Gossypium hirsutum, Gossypium arboreum, and Gossypium raimondii. This gene family was divided into seven subgroups. A chromosomal distribution analysis showed that GhPIN genes were evenly distributed in eight chromosomes and that the whole genome and dispersed duplications were the main duplication events for GhPIN expansion...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28423510/genistein-inhibits-the-growth-and-regulates-the-migration-and-invasion-abilities-of-melanoma-cells-via-the-fak-paxillin-and-mapk-pathways
#10
Shuna Cui, Juan Wang, Qingqing Wu, Jing Qian, Changshui Yang, Ping Bo
Genistein is one of the main components of soy-based foods, which are widely known for their many benefits, including anti-cancer, anti-inflammatory, and antioxidant effects. In this study, we investigated the anti-metastasis effects of genistein on B16F10 melanoma cells. Our results showed that genistein strongly inhibited B16F10 cell proliferation and induced apoptosis in time- and concentration-dependent manners. Genistein altered the morphology of B16F10 cells to an elongated shape with slim pseudopodia-like protrusions...
March 28, 2017: Oncotarget
https://www.readbyqxmd.com/read/28423325/rapid-genome-wide-recruitment-of-rna-polymerase-ii-drives-transcription-splicing-and-translation-events-during-t-cell-responses
#11
Kathrin Davari, Johannes Lichti, Christian Gallus, Franziska Greulich, N Henriette Uhlenhaut, Matthias Heinig, Caroline C Friedel, Elke Glasmacher
Activation of immune cells results in rapid functional changes, but how such fast changes are accomplished remains enigmatic. By combining time courses of 4sU-seq, RNA-seq, ribosome profiling (RP), and RNA polymerase II (RNA Pol II) ChIP-seq during T cell activation, we illustrate genome-wide temporal dynamics for ∼10,000 genes. This approach reveals not only immediate-early and posttranscriptionally regulated genes but also coupled changes in transcription and translation for >90% of genes. Recruitment, rather than release of paused RNA Pol II, primarily mediates transcriptional changes...
April 18, 2017: Cell Reports
https://www.readbyqxmd.com/read/28423001/pre-hatching-embryo-dependent-and-independent-programming-of-endometrial-function-in-cattle
#12
Mariana Sponchiado, Nathália Souza Gomes, Patrícia Kubo Fontes, Thiago Martins, Maite Del Collado, Athos de Assumpção Pastore, Guilherme Pugliesi, Marcelo Fábio Gouveia Nogueira, Mario Binelli
The bovine pre-implantation embryo secretes bioactive molecules from early development stages, but effects on endometrial function are reported to start only after elongation. Here, we interrogated spatially defined regions of the endometrium transcriptome for responses to a day 7 embryo in vivo. We hypothesize that exposure to an embryo changes the abundance of specific transcripts in the cranial region of the pregnant uterine horn. Endometrium was collected from the uterotubal junction (UTJ), anterior (IA), medial (IM) and posterior (IP) regions of the uterine horn ipsilateral to the CL 7 days after estrus from sham-inseminated (Con) or artificially inseminated, confirmed pregnant (Preg) cows...
2017: PloS One
https://www.readbyqxmd.com/read/28422315/regulation-of-the-alternative-splicing-and-function-of-cyclin-t1-by-the-serine-arginine-rich-protein-asf-sf2
#13
Jieqiong Zhou, Guozhen Gao, Panpan Hou, Chun-Mei Li, Deyin Guo
Positive transcription elongation factor-b (P-TEFb) is required for the release of RNA polymerase II (RNAPII) from its pause near the gene promoters and thus for efficient proceeding to the transcription elongation. It consists of two core subunits - CDK9 and one of T-typed or K-typed cyclin, of which, cyclin T1/CDK9 is the major and most studied combination. We have previously identified a novel splice variant of cyclin T1, cyclin T1b, which negatively regulates the transcription elongation of HIV-1 genes as well as several host genes...
April 19, 2017: Journal of Cellular Biochemistry
https://www.readbyqxmd.com/read/28419960/preferentially-enhancing-anti-cancer-isothiocyanates-over-glucosinolates-in-broccoli-sprouts-how-nacl-and-salicylic-acid-affect-their-formation
#14
Azadeh Esfandiari, Ali Saei, Marian J McKenzie, Adam J Matich, Mesbah Babalar, Donald A Hunter
Broccoli (Brassica oleracea L. var. italica) sprouts contain glucosinolates (GLs) that when hydrolysed yield health promoting isothiocyanates such as sulforaphane (SF). SF content can be increased by salt (NaCl) stress, although high salt concentrations negatively impact plant growth. Salicylic acid (SA) treatments can attenuate the negative effects of salt on growth. To test whether sprout isothiocyanate content could be elevated without sprout growth being compromised, broccoli seed were germinated and grown for seven days in salt (0, 80 and 160 mM) alone and in combination with 100 μM SA...
April 7, 2017: Plant Physiology and Biochemistry: PPB
https://www.readbyqxmd.com/read/28419137/transcriptional-changes-in-litchi-litchi-chinensis-sonn-inflorescences-treated-with-uniconazole
#15
Yongzan Wei, Chen Dong, Hongna Zhang, Xuewen Zheng, Bo Shu, Shengyou Shi, Weicai Li
In Arabidopsis, treating shoots with uniconazole can result in enhanced primary root elongation and bolting delay. Uniconazole spraying has become an important cultivation technique in controlling the flowering and improving the fruit-setting of litchi. However, the mechanism by which uniconazole regulates the complicated developmental processes in litchi remains unclear. This study aimed to determine which signal pathways and genes drive the responses of litchi inflorescences to uniconazole treatment. We monitored the transcriptional activity in inflorescences after uniconazole treatment by Illumina sequencing technology...
2017: PloS One
https://www.readbyqxmd.com/read/28418397/bap180-baf180-is-required-to-maintain-homeostasis-of-intestinal-innate-immune-response-in-drosophila-and-mice
#16
Xiaomeng He, Junjing Yu, Min Wang, Yang Cheng, Yanan Han, Shuo Yang, Guizhi Shi, Lei Sun, Ying Fang, Si-Tang Gong, Zhong Wang, Yang-Xin Fu, Lei Pan, Hong Tang
Immune homeostasis is a prerequisite to protective immunity against gastrointestinal infections. In Drosophila, immune deficiency (IMD) signalling (tumour necrosis factor receptor/interleukin-1 receptor, TNFR/IL-1R in mammals) is indispensable for intestinal immunity against invading bacteria. However, how this local antimicrobial immune response contributes to inflammatory regulation remains poorly defined. Here, we show that flies lacking intestinal Bap180 (a subunit of the chromatin-remodelling switch/sucrose non-fermentable (SWI/SNF) complex) are susceptible to infection as a result of hyper-inflammation rather than bacterial overload...
April 18, 2017: Nature Microbiology
https://www.readbyqxmd.com/read/28414811/tissue-expression-profiles-and-transcriptional-regulation-of-elongase-of-very-long-chain-fatty-acid-6-in-bovine-mammary-epithelial-cells
#17
Si Chen, Hua He, Xiaolin Liu
In mammals, very long chain fatty acids (VLCFAs) perform pleiotropic roles in a wide range of biological processes, such as cell membrane formation, cell signal transduction, and endocrine regulation. Beef and milk are abundant of palmitic acid which can be further elongated into stearic acid for synthesizing VLCFAs. Elongase of very long chain fatty acid 6 (ELOVL6) is a rate-limiting enzyme for converting palmitic acid to stearic acid. Consequently, investigating the tissue expression patterns and transcriptional regulation of bovine ELOVL6 can provide new insights into improving the composition of beneficial fats in cattle and expanding the knowledge of transcriptional regulation mechanism among domestic animals...
2017: PloS One
https://www.readbyqxmd.com/read/28409381/dash-type-cryptochromes-regulate-fruiting-body-development-and-secondary-metabolism-differently-than-cmwc-1-in-the-fungus-cordyceps-militaris
#18
Fen Wang, Xinhua Song, Xiaoming Dong, Jiaojiao Zhang, Caihong Dong
Cryptochromes (CRYs) belong to the photolyase/cryptochrome flavoprotein family, which is widely distributed in all kingdoms. A phylogenetic analysis indicated that three Cordyceps militaris proteins [i.e., cryptochrome DASH (CmCRY-DASH), (6-4) photolyase, and cyclobutane pyrimidine dimer (CPD) class I photolyase] belong to separate fungal photolyase/cryptochrome subfamilies. CmCRY-DASH consists of DNA photolyase and flavin adenine dinucleotide-binding domains, with RGG repeats in a C-terminal extension. Considerably, more carotenoids and cordycepin accumulated in the ΔCmcry-DASH strain than in the wild-type or ΔCmwc-1 strains, indicating an inhibitory role for CmCRY-DASH in these biosynthetic pathways...
April 13, 2017: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/28408604/architecture-of-a-transcribing-translating-expressome
#19
R Kohler, R A Mooney, D J Mills, R Landick, P Cramer
DNA transcription is functionally coupled to messenger RNA (mRNA) translation in bacteria, but how this is achieved remains unclear. Here we show that RNA polymerase (RNAP) and the ribosome of Escherichia coli can form a defined transcribing and translating "expressome" complex. The cryo-electron microscopic structure of the expressome reveals continuous protection of ~30 nucleotides of mRNA extending from the RNAP active center to the ribosome decoding center. The RNAP-ribosome interface includes the RNAP subunit α carboxyl-terminal domain, which is required for RNAP-ribosome interaction in vitro and for pronounced cell growth defects upon translation inhibition in vivo, consistent with its function in transcription-translation coupling...
April 14, 2017: Science
https://www.readbyqxmd.com/read/28408437/the-myc-mrna-3-utr-couples-rna-polymerase-ii-function-to-glutamine-and-ribonucleotide-levels
#20
Francesca R Dejure, Nadine Royla, Steffi Herold, Jacqueline Kalb, Susanne Walz, Carsten P Ade, Guido Mastrobuoni, Jens T Vanselow, Andreas Schlosser, Elmar Wolf, Stefan Kempa, Martin Eilers
Deregulated expression of MYC enhances glutamine utilization and renders cell survival dependent on glutamine, inducing "glutamine addiction". Surprisingly, colon cancer cells that express high levels of MYC due to WNT pathway mutations are not glutamine-addicted but undergo a reversible cell cycle arrest upon glutamine deprivation. We show here that glutamine deprivation suppresses translation of endogenous MYC via the 3'-UTR of the MYC mRNA, enabling escape from apoptosis. This regulation is mediated by glutamine-dependent changes in adenosine-nucleotide levels...
April 13, 2017: EMBO Journal
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