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https://www.readbyqxmd.com/read/28096443/stem-loop-rna-labeling-can-affect-nuclear-and-cytoplasmic-mrna-processing
#1
Stephanie Heinrich, Corinne L Sidler, Claus M Azzalin, Karsten Weis
The binding of sequence-specific RNA-interacting proteins, such as the bacteriophage MS2 or PP7 coat proteins, to their corresponding target sequences has been extremely useful and widely used to visualize single mRNAs in vivo. However, introduction of MS2 stem-loops into yeast mRNAs has recently been shown to lead to the accumulation of RNA fragments, suggesting that the loops impair mRNA decay. This result was questioned, because fragment occurrence was mainly assessed using ensemble methods, and their cellular localization and its implications had not been addressed on a single transcript level...
February 2017: RNA
https://www.readbyqxmd.com/read/28095188/mir-148a-and-mir-17-5p-synergistically-regulate-milk-tag-synthesis-via-ppargc1a-and-ppara-in-goat-mammary-epithelial-cells
#2
Zhi Chen, Jun Luo, Shuang Sun, Duoyao Cao, Huaiping Shi, Juan J Loor
MicroRNA (miRNA) are a class of '18-25' nt RNA molecules which regulate gene expression and play an important role in several biological processes including fatty acid metabolism. Here we utilized S-Poly (T) and high-throughput sequencing to evaluate the expression of miRNA and mRNA during early-lactation and in the non-lactating ("dry") period in goat mammary gland tissue. Results indicated that miR-148a, miR-17-5p, PPARGC1A and PPARA are highly expressed in the goat mammary gland in early-lactation and non-lactating periods...
January 17, 2017: RNA Biology
https://www.readbyqxmd.com/read/28093566/estrogen-dependent-association-of-hdac4-with-fear-in-female-mice-and-women-with-ptsd
#3
S A Maddox, V Kilaru, J Shin, T Jovanovic, L M Almli, B G Dias, S D Norrholm, N Fani, V Michopoulos, Z Ding, K N Conneely, E B Binder, K J Ressler, A K Smith
Women are at increased risk of developing post-traumatic stress disorder (PTSD) following a traumatic event. Recent studies suggest that this may be mediated, in part, by circulating estrogen levels. This study evaluated the hypothesis that individual variation in response to estrogen levels contributes to fear regulation and PTSD risk in women. We evaluated DNA methylation from blood of female participants in the Grady Trauma Project and found that serum estradiol levels associates with DNA methylation across the genome...
January 17, 2017: Molecular Psychiatry
https://www.readbyqxmd.com/read/28091410/molecular-mechanisms-of-increased-heart-rate-in-shenxianshengmai-treated-bradycardia-rabbits
#4
Zhou-Ying Liu, Jian Huang, Na-Na Liu, Min Zheng, Tao Zhao, Bu-Chang Zhao, Yi-Min Wang, Jie-Lin Pu
BACKGROUND: The molecular mechanisms of Shenxianshengmai (SXSM), a traditional Chinese medicine, on bradycardia have been incompletely understood. The study tried to investigate the gene expression profile and proteomics of bradycardia rabbits' hearts after SXSM treatment. METHODS: Twenty-four adult rabbits were randomly assigned in four groups: sham, model, model plus SXSM treatment, and sham plus SXSM treatment groups. Heart rate was recorded in all rabbits. Then, total RNA of atria and proteins of ventricle were isolated and quantified, respectively...
2017: Chinese Medical Journal
https://www.readbyqxmd.com/read/28077653/characterizing-hiv-1-splicing-using-next-generation-sequencing
#5
Ann Emery, Shuntai Zhou, Elizabeth Pollom, Ronald Swanstrom
: Full-length HIV-1 RNA serves as the genome or as an mRNA, or this RNA undergoes splicing using four donors and ten acceptors to create over 50 physiologically relevant transcripts in two size classes (1.8 kb and 4 kb). We developed an assay using Primer ID-tagged deep sequencing to quantify HIV-1 splicing. Using the NL4-3 lab strain we found that A5 (env/nef) is the most commonly used acceptor (about 50%) with A3 (tat) the least used (about 3%). Two small exons are made when a splice to acceptor A1 or A2 is followed by activation of donor D2 or D3, and the high-level use of D2 and D3 dramatically reduces the amount of vif and vpr transcripts...
January 11, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28065320/imaging-cytokinesis-of-drosophila-s2-cells
#6
A Kechad, G R X Hickson
Animal cell cytokinesis proceeds through three successive stages: a contractile ring stage, an intercellular bridge stage, and an abscission stage. Many studies have identified a complex network of key proteins required for successful cytokinesis. While each component interacts with, and depends on, several other components, our understanding of how these proteins cooperate in space and time to ensure faithful progression through the stages of cytokinesis remains incomplete. A full understanding of the complexity of the process and its underlying machinery necessitates experimental systems that allow both genetic manipulation and real-time visualization of the various components throughout the successive stages of cytokinesis...
2017: Methods in Cell Biology
https://www.readbyqxmd.com/read/28064188/upset-the-drosophila-homologue-of-set3-is-required-for-viability-and-the-proper-balance-of-active-and-repressive-chromatin-marks
#7
Kyle A McElroy, Youngsook Lucy Jung, Barry M Zee, Charlotte I Wang, Peter J Park, Mitzi I Kuroda
Chromatin plays a critical role in faithful implementation of gene expression programs. Different post-translational modifications of histone proteins reflect the underlying state of gene activity, and many chromatin proteins write, erase, bind, or are repelled by these histone marks. One such protein is UpSET, the Drosophila homolog of yeast Set3 and mammalian KMT2E (MLL5). Here we show that UpSET is necessary for the proper balance between active and repressed states. Using CRISPR/Cas-9 editing, we generated S2 cells which are mutant for upset We found that loss of UpSET is tolerated in S2 cells, but that heterochromatin is misregulated, as evidenced by a strong decrease in H3K9me2 levels assessed by bulk histone post-translational modification quantification...
January 6, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28062756/phylogenetic-origin-and-diversification-of-rnai-pathway-genes-in-insects
#8
Daniel Dowling, Thomas Pauli, Alexander Donath, Karen Meusemann, Lars Podsiadlowski, Malte Petersen, Ralph S Peters, Christoph Mayer, Shanlin Liu, Xin Zhou, Bernhard Misof, Oliver Niehuis
RNA interference (RNAi) refers to the set of molecular processes found in eukaryotic organisms in which small RNA molecules mediate the silencing or down-regulation of target genes. In insects, RNAi serves a number of functions, including regulation of endogenous genes, anti-viral defense, and defense against transposable elements. Despite being well studied in model organisms, such as Drosophila, the distribution of core RNAi pathway genes and their evolution in insects is not well understood. Here we present the most comprehensive overview of the distribution and diversity of core RNAi pathway genes across 100 insect species, encompassing all currently recognized insect orders...
January 6, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28042969/the-response-of-growth-and-patulin-production-of-postharvest-pathogen-penicillium-expansum-to-exogenous-potassium-phosphite-treatment
#9
Tongfei Lai, Ying Wang, Yaya Fan, Yingying Zhou, Ying Bao, Ting Zhou
In this study, the effects of exogenous potassium phosphite (Phi) on growth and patulin production of postharvest pathogen Penicillium expansum were assessed. The results indicated that P. expansum under 5mmol/L Phi stress presented obvious development retardation, yield reduction of patulin and lower infectivity to apple fruit. Meanwhile, expression analysis of 15 genes related to patulin biosynthesis suggested that Phi mainly affected the early steps of patulin synthetic route at transcriptional level. Furthermore, a global view of proteome and transcriptome alteration of P...
December 28, 2016: International Journal of Food Microbiology
https://www.readbyqxmd.com/read/28039930/interacting-protein-partners-of-arabidopsis-rna-binding-protein-atrbp45b
#10
Meenakumari Muthuramalingam, Yixing Wang, Yongfang Li, Ramamurthy Mahalingam
• RNA binding proteins (RBPs), important players in post-transcriptional gene regulation usually exist in ribonuclear complexes. However, even in model systems like Arabidopsis characterization of RBP associated proteins are limited. In this study, we investigated the interacting proteins of the Arabidopsis AtRBP45b, which is involved in stress signaling. • In vivo localization of AtRBP45b was conducted using 35S-GFP. FLAG-tagged AtRBP45b under the control of 35S promoter in the Atrbp45b-1 mutant background was used to pull down AtRBP45b interacting proteins...
December 31, 2016: Plant Biology
https://www.readbyqxmd.com/read/28024915/how-do-megakaryocytic-microparticles-target-and-deliver-cargo-to-alter-the-fate-of-hematopoietic-stem-cells
#11
Jinlin Jiang, Chen-Yuan Kao, Eleftherios T Papoutsakis
Megakaryocytic microparticles (MkMPs), the most abundant MPs in circulation, can induce the differentiation of hematopoietic stem and progenitor cells (HSPCs) into functional megakaryocytes. This MkMP capability could be explored for applications in transfusion medicine but also for delivery of nucleic acids and other molecules to HSPCs for targeted molecular therapy. Understanding how MkMPs target, deliver cargo and alter the fate of HSPCs is important for exploring such applications. We show that MkMPs, which are distinct from Mk exosomes (MkExos), target HSPCs with high specificity since they have no effect on other ontologically or physiologically related cells, namely mesenchymal stem cells, endothelial cells or granulocytes...
December 24, 2016: Journal of Controlled Release: Official Journal of the Controlled Release Society
https://www.readbyqxmd.com/read/28008926/long-term-propagation-of-tree-shrew-spermatogonial-stem-cells-in-culture-and-successful-generation-of-transgenic-offspring
#12
Chao-Hui Li, Lan-Zhen Yan, Wen-Zan Ban, Qiu Tu, Yong Wu, Lin Wang, Rui Bi, Shuang Ji, Yu-Hua Ma, Wen-Hui Nie, Long-Bao Lv, Yong-Gang Yao, Xu-Dong Zhao, Ping Zheng
Tree shrews have a close relationship to primates and have many advantages over rodents in biomedical research. However, the lack of gene manipulation methods has hindered the wider use of this animal. Spermatogonial stem cells (SSCs) have been successfully expanded in culture to permit sophisticated gene editing in the mouse and rat. Here, we describe a culture system for the long-term expansion of tree shrew SSCs without the loss of stem cell properties. In our study, thymus cell antigen 1 was used to enrich tree shrew SSCs...
December 23, 2016: Cell Research
https://www.readbyqxmd.com/read/28004741/deep-sequencing-of-wheat-srna-transcriptome-reveals-distinct-temporal-expression-pattern-of-mirnas-in-response-to-heat-light-and-uv
#13
Raja Ragupathy, Sridhar Ravichandran, Md Safiur Rahman Mahdi, Douglas Huang, Elsa Reimer, Michael Domaratzki, Sylvie Cloutier
Understanding of plant adaptation to abiotic stresses has implications in plant breeding, especially in the context of climate change. MicroRNAs (miRNAs) and short interfering RNAs play a crucial role in gene regulation. Here, wheat plants were exposed to one of the following stresses: continuous light, heat or ultraviolet radiations over five consecutive days and leaf tissues from three biological replicates were harvested at 0, 1, 2, 3, 7 and 10 days after treatment (DAT). A total of 72 small RNA libraries were sequenced on the Illumina platform generating ~524 million reads corresponding to ~129 million distinct tags from which 232 conserved miRNAs were identified...
December 22, 2016: Scientific Reports
https://www.readbyqxmd.com/read/28003131/crispr-cas9-mediated-integration-enables-tag-eclip-of-endogenously-tagged-rna-binding-proteins
#14
Eric L Van Nostrand, Chelsea Gelboin-Burkhart, Ruth Wang, Gabriel A Pratt, Steven M Blue, Gene W Yeo
Identification of in vivo direct RNA targets for RNA binding proteins (RBPs) provides critical insight into their regulatory activities and mechanisms. Recently, we described a methodology for enhanced crosslinking and immunoprecipitation followed by high-throughput sequencing (eCLIP) using antibodies against endogenous RNA binding proteins. However, in many cases it is desirable to profile targets of an RNA binding protein for which an immunoprecipitation-grade antibody is lacking. Here we describe a scalable method for using CRISPR/Cas9-mediated homologous recombination to insert a peptide tag into the endogenous RNA binding protein locus...
December 18, 2016: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28002932/expression-of-egr3-in-mouse-gonads-and-its-localization-and-function-in-oocytes
#15
Hyejin Shin, Dong-Won Seol, Minyeong Nam, Haengseok Song, Dong Ryul Lee, Hyunjung Jade Lim
Objective: The early growth response (Egr) family consists of four members (Egr1, Egr2, Egr3, and Egr4) that are zinc finger transcription factors. Among them, Egr3 is involved in transcriptional regulation of target genes during muscle spindle formation and neurite outgrowth. We previously showed that the immunoreactive Egr3 is localized on oocyte spindle and accumulate near the microtubule organizing center (MTOC) during meiosis I in mice. Egr3 was also shown to be localized on spermatocytes...
December 17, 2016: Asian-Australasian Journal of Animal Sciences
https://www.readbyqxmd.com/read/27999137/cystatin-c-is-a-crucial-endogenous-protective-determinant-against-stroke
#16
Zongping Fang, Jiao Deng, Zhixin Wu, Beibei Dong, Shiquan Wang, Xiaodan Chen, Huang Nie, Hailong Dong, Lize Xiong
BACKGROUND AND PURPOSERESULTS: Endogenous neuroprotection can be induced by ischemic and nonischemic preconditioning. However, not all subjects that undergo preconditioning exhibit similar favorable outcome. This study is to explore the molecules responsible for this phenomenon and find new therapeutic targets for stroke. METHODS: Adult male Sprague-Dawley rats were subjected to transient middle cerebral artery occlusion. High-throughput proteomic technique, isobaric tag for relative and absolute quantification, was used to screen differentially expressed proteins in the rats that developed ischemic tolerance from hyperbaric oxygen (HBO) preconditioning...
December 20, 2016: Stroke; a Journal of Cerebral Circulation
https://www.readbyqxmd.com/read/27998286/ultrasensitive-single-genome-sequencing-accurate-targeted-next-generation-sequencing-of-hiv-1-rna
#17
Valerie F Boltz, Jason Rausch, Wei Shao, Junko Hattori, Brian Luke, Frank Maldarelli, John W Mellors, Mary F Kearney, John M Coffin
BACKGROUND: Although next generation sequencing (NGS) offers the potential for studying virus populations in unprecedented depth, PCR error, amplification bias and recombination during library construction have limited its use to population sequencing and measurements of unlinked allele frequencies. Here we report a method, termed ultrasensitive Single-Genome Sequencing (uSGS), for NGS library construction and analysis that eliminates PCR errors and recombinants, and generates single-genome sequences of the same quality as the "gold-standard" of HIV-1 single-genome sequencing assay but with more than 100-fold greater depth...
December 20, 2016: Retrovirology
https://www.readbyqxmd.com/read/27997115/sirt7-is-an-rna-activated-protein-lysine-deacylase
#18
Zhen Tong, Miao Wang, Yi Wang, David D Kim, Jennifer K Grenier, Ji Cao, Sushabhan Sadhukhan, Quan Hao, Hening Lin
Mammalian SIRT7 is a member of the sirtuin family that regulates multiple biological processes including genome stability, metabolic pathways, stress responses, and tumorigenesis. SIRT7 has been shown to be important for ribosome biogenesis and transcriptional regulation. SIRT7 knockout mice exhibit complications associated with fatty liver and increased aging in hematopoietic stem cells. However, the molecular basis for its biological function remains unclear, in part due to the lack of efficient enzymatic activity in vitro...
December 20, 2016: ACS Chemical Biology
https://www.readbyqxmd.com/read/27995376/double-stranded-rna-binding-protein-drb3-negatively-regulates-anthocyanin-biosynthesis-by-modulating-pap1-expression-in-arabidopsis-thaliana
#19
Hikaru Sawano, Takuma Matsuzaki, Tomoyuki Usui, Midori Tabara, Akihito Fukudome, Akihiro Kanaya, Daichi Tanoue, Akihiro Hiraguri, Gorou Horiguchi, Misato Ohtani, Taku Demura, Toshinori Kozaki, Kazuo Ishii, Hiromitsu Moriyama, Toshiyuki Fukuhara
The model plant Arabidopsis thaliana has five double-stranded RNA-binding proteins (DRB1-DRB5), two of which, DRB1 and DRB4, are well characterized. In contrast, the functions of DRB2, DRB3 and DRB5 have yet to be elucidated. In this study, we tried to uncover their functions using drb mutants and DRB-over-expressed lines. In over-expressed lines of all five DRB genes, the over-expression of DRB2 or DRB3 (DRB2ox or DRB3ox) conferred a downward-curled leaf phenotype, but the expression profiles of ten small RNAs were similar to that of the wild-type (WT) plant...
January 2017: Journal of Plant Research
https://www.readbyqxmd.com/read/27995348/mitochondrial-genome-of-pteronotus-personatus-chiroptera-mormoopidae-comparison-with-selected-bats-and-phylogenetic-considerations
#20
Ricardo López-Wilchis, Miguel Ángel Del Río-Portilla, Luis Manuel Guevara-Chumacero
We described the complete mitochondrial genome (mitogenome) of the Wagner's mustached bat, Pteronotus personatus, a species belonging to the family Mormoopidae, and compared it with other published mitogenomes of bats (Chiroptera). The mitogenome of P. personatus was 16,570 bp long and contained a typically conserved structure including 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and one control region (D-loop). Most of the genes were encoded on the H-strand, except for eight tRNA and the ND6 genes...
December 19, 2016: Genetica
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