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https://www.readbyqxmd.com/read/28087610/long-non-coding-rna-exchange-during-the-oocyte-to-embryo-transition-in-mice
#1
Rosa Karlic, Sravya Ganesh, Vedran Franke, Eliska Svobodova, Jana Urbanova, Yutaka Suzuki, Fugaku Aoki, Kristian Vlahovicek, Petr Svoboda
The oocyte-to-embryo transition (OET) transforms a differentiated gamete into pluripotent blastomeres. The accompanying maternal-zygotic RNA exchange involves remodeling of the long non-coding RNA (lncRNA) pool. Here, we used next generation sequencing and de novo transcript assembly to define the core population of 1,600 lncRNAs expressed during the OET (lncRNAs). Relative to mRNAs, OET lncRNAs were less expressed and had shorter transcripts, mainly due to fewer exons and shorter 5' terminal exons. Approximately half of OET lncRNA promoters originated in retrotransposons suggesting their recent emergence...
January 13, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/28086865/rnai-reveals-proteins-for-metabolism-and-protein-processing-associated-with-langat-virus-infection-in-ixodes-scapularis-black-legged-tick-ise6-cells
#2
Jeffrey M Grabowski, Monika Gulia-Nuss, Richard J Kuhn, Catherine A Hill
BACKGROUND: Tick-borne flaviviruses (TBFs) cause thousands of human cases of encephalitis worldwide each year, with some TBF infections progressing to hemorrhagic fever. TBFs are of medical and veterinary importance and strategies to reduce flavivirus transmission by the tick vector may have significant application. Analyses of the proteome of ISE6 cells derived from the black legged tick, Ixodes scapularis infected with the TBF, Langat virus (LGTV), have provided insights into proteins and cellular processes involved with LGTV infection...
January 13, 2017: Parasites & Vectors
https://www.readbyqxmd.com/read/28086748/genetic-mechanisms-of-bone-digestion-and-nutrient-absorption-in-the-bone-eating-worm-osedax-japonicus-inferred-from-transcriptome-and-gene-expression-analyses
#3
Norio Miyamoto, Masa-Aki Yoshida, Hiroyuki Koga, Yoshihiro Fujiwara
BACKGROUND: Bone-eating worms of the genus Osedax (Annelida, Siboglinidae) have adapted to whale fall environments by acquiring a novel characteristic called the root, which branches and penetrates into sunken bones. The worms lack a digestive tract and mouth opening, and it has been suggested that Osedax degrade vertebrate bones and uptake nutrients through acidification and secretion of enzymes from the root. Symbiotic bacteria in the root tissue may have a crucial role in the metabolism of Osedax...
January 13, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28077560/mechanistic-insights-into-type-i-toxin-antitoxin-systems-in-helicobacter-pylori-the-importance-of-mrna-folding-in-controlling-toxin-expression
#4
Hélène Arnion, Dursun Nizam Korkut, Sara Masachis Gelo, Sandrine Chabas, Jérémy Reignier, Isabelle Iost, Fabien Darfeuille
Type I toxin-antitoxin (TA) systems have been identified in a wide range of bacterial genomes. Here, we report the characterization of a new type I TA system present on the chromosome of the major human gastric pathogen, Helicobacter pylori We show that the aapA1 gene encodes a 30 amino acid peptide whose artificial expression in H. pylori induces cell death. The synthesis of this toxin is prevented by the transcription of an antitoxin RNA, named IsoA1, expressed on the opposite strand of the toxin gene. We further reveal additional layers of post-transcriptional regulation that control toxin expression: (i) transcription of the aapA1 gene generates a full-length transcript whose folding impedes translation (ii) a 3' end processing of this message generates a shorter transcript that, after a structural rearrangement, becomes translatable (iii) but this rearrangement also leads to the formation of two stem-loop structures allowing formation of an extended duplex with IsoA1 via kissing-loop interactions...
January 10, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28075024/uncovering-iron-regulation-with-species-specific-transcriptome-patterns-in-atlantic-and-coho-salmon-during-a-caligus-rogercresseyi-infestation
#5
V Valenzuela-Muñoz, S Boltaña, C Gallardo-Escárate
Salmon species cultured in Chile evidence different levels of susceptibility to the sea louse Caligus rogercresseyi. These differences have mainly been associated with specific immune responses. Moreover, iron regulation seems to be an important mechanism to confer immunity during the host infestation. This response called nutritional immunity has been described in bacterial infections, despite that no comprehensive studies involving in marine ectoparasites infestation have been reported. With this aim, we analysed the transcriptome profiles of Atlantic and coho salmon infected with C...
January 11, 2017: Journal of Fish Diseases
https://www.readbyqxmd.com/read/28070636/extracellular-matrix-loss-in-chondrocytes-after-exposure-to-interleukin-1%C3%AE-in-nadph-oxidase-dependent-manner
#6
Sakie Funato, Rika Yasuhara, Kentaro Yoshimura, Yoichi Miyamoto, Kotaro Kaneko, Tetsuo Suzawa, Daichi Chikazu, Kenji Mishima, Kazuyoshi Baba, Ryutaro Kamijo
Osteoarthritis is a degenerative joint disease caused by excessive death of chondrocytes and loss of the extracellular matrix (ECM) in articular cartilage. We previously reported that reactive oxygen species (ROS) generated by the NADPH oxidase (NOX) isoform NOX-2 are involved in chondrocyte death induced by interleukin-1β (IL-1β). In this study, we investigate the role of NOX-2 in the production and degradation of ECM by chondrocytes. Although IL-1β lowered the mRNA expression of type II collagen (Col2a1) and aggrecan (Acan) in mouse chondrocyte-like ATDC5 cells, RNA silencing of Nox2 did not change the mRNA expression of these major components of the ECM of cartilage...
January 9, 2017: Cell and Tissue Research
https://www.readbyqxmd.com/read/28069372/rna-exosome-and-non-coding-rna-coupled-mechanisms-in-aid-mediated-genomic-alterations
#7
REVIEW
Brice Laffleur, Uttiya Basu, Junghyun Lim
The eukaryotic RNA exosome is a well-conserved protein complex with ribonuclease activity implicated in RNA metabolism. Various families of non-coding RNAs have been identified as substrates of the complex, underscoring its role as a non-coding RNA processing/degradation unit. However, the role of RNA exosome and its RNA processing activity on DNA mutagenesis/alteration events have not been investigated until recently. B lymphocytes use two DNA alteration mechanisms, class switch recombination (CSR) and somatic hypermutation (SHM), to re-engineer their antibody gene expressing loci until a tailored antibody gene for a specific antigen is satisfactorily generated...
January 6, 2017: Journal of Molecular Biology
https://www.readbyqxmd.com/read/28068668/the-hippo-kinases-lats1-and-2-control-human-breast-cell-fate-via-crosstalk-with-er%C3%AE
#8
Adrian Britschgi, Stephan Duss, Sungeun Kim, Joana Pinto Couto, Heike Brinkhaus, Shany Koren, Duvini De Silva, Kirsten D Mertz, Daniela Kaup, Zsuzsanna Varga, Hans Voshol, Alexandra Vissieres, Cedric Leroy, Tim Roloff, Michael B Stadler, Christina H Scheel, Loren J Miraglia, Anthony P Orth, Ghislain M C Bonamy, Venkateshwar A Reddy, Mohamed Bentires-Alj
Cell fate perturbations underlie many human diseases, including breast cancer. Unfortunately, the mechanisms by which breast cell fate are regulated are largely unknown. The mammary gland epithelium consists of differentiated luminal epithelial and basal myoepithelial cells, as well as undifferentiated stem cells and more restricted progenitors. Breast cancer originates from this epithelium, but the molecular mechanisms that underlie breast epithelial hierarchy remain ill-defined. Here, we use a high-content confocal image-based short hairpin RNA screen to identify tumour suppressors that regulate breast cell fate in primary human breast epithelial cells...
January 9, 2017: Nature
https://www.readbyqxmd.com/read/28068319/fbxo32-suppresses-breast-cancer-tumorigenesis-through-targeting-klf4-to-proteasomal-degradation
#9
H Zhou, Y Liu, R Zhu, F Ding, Y Wan, Y Li, Z Liu
Krüppel-like factor 4 (KLF4, GKLF) is a zinc-finger transcription factor involved in a large variety of cellular processes, including apoptosis, cell cycle progression, as well as stem cell renewal. KLF4 is critical for cell fate decision and has an ambivalent role in tumorigenesis. Emerging data keep reminding us that KLF4 dysregulation either facilitates or impedes tumor progression, making it important to clarify the regulating network of KLF4. Like most transcription factors, KLF4 has a rather short half-life within the cell and its turnover must be carefully orchestrated by ubiquitination and ubiquitin-proteasome system...
January 9, 2017: Oncogene
https://www.readbyqxmd.com/read/28067952/plastomes-on-the-edge-the-evolutionary-breakdown-of-mycoheterotroph-plastid-genomes
#10
REVIEW
Sean W Graham, Vivienne K Y Lam, Vincent S F T Merckx
I. II. III. References SUMMARY: We examine recent evidence for ratchet-like genome degradation in mycoheterotrophs, plants that obtain nutrition from fungi. Initial loss of the NADH dehydrogenase-like (NDH) complex may often set off an irreversible evolutionary cascade of photosynthetic gene losses. Genes for plastid-encoded subunits of RNA polymerase and photosynthetic enzymes with secondary functions (Rubisco and ATP synthase) can persist initially, with nonsynchronous and quite broad windows in the relative timing of their loss...
January 9, 2017: New Phytologist
https://www.readbyqxmd.com/read/28067898/clay-nanosheets-for-topical-delivery-of-rnai-for-sustained-protection-against-plant-viruses
#11
Neena Mitter, Elizabeth A Worrall, Karl E Robinson, Peng Li, Ritesh G Jain, Christelle Taochy, Stephen J Fletcher, Bernard J Carroll, G Q Max Lu, Zhi Ping Xu
Topical application of pathogen-specific double-stranded RNA (dsRNA) for virus resistance in plants represents an attractive alternative to transgenic RNA interference (RNAi). However, the instability of naked dsRNA sprayed on plants has been a major challenge towards its practical application. We demonstrate that dsRNA can be loaded on designer, non-toxic, degradable, layered double hydroxide (LDH) clay nanosheets. Once loaded on LDH, the dsRNA does not wash off, shows sustained release and can be detected on sprayed leaves even 30 days after application...
January 9, 2017: Nature Plants
https://www.readbyqxmd.com/read/28065570/conservative-tracer-bromide-inhibits-pesticide-mineralisation-in-soil
#12
Tina B Bech, Annette E Rosenbom, Sebastian R Sørensen, Carsten S Jacobsen
Bromide is a conservative tracer that is often applied with non-conservative solutes such as pesticides to estimate their retardation in the soil. It has been applied in concentrations of up to 250 g Br L(-1), levels at which the growth of single-celled organisms can be inhibited. Bromide applications may therefore affect the biodegradation of non-conservative solutes in soil. The present study investigated the effect of potassium bromide (KBr) on the mineralisation of three pesticides - glyphosate, MCPA and metribuzin - in four agricultural A-horizon soils...
January 5, 2017: Environmental Pollution
https://www.readbyqxmd.com/read/28064006/versatile-rna-tetra-u-helix-linking-motif-as-a-toolkit-for-nucleic-acid-nanotechnology
#13
My N Bui, M Brittany Johnson, Mathias Viard, Emily Satterwhite, Angelica N Martins, Zhihai Li, Ian Marriott, Kirill A Afonin, Emil F Khisamutdinov
RNA nanotechnology employs synthetically modified ribonucleic acid (RNA) to engineer highly stable nanostructures in one, two, and three dimensions for medical applications. Despite the tremendous advantages in RNA nanotechnology, unmodified RNA itself is fragile and prone to enzymatic degradation. In contrast to use traditionally modified RNA strands e.g. 2'-fluorine, 2'-amine, 2'-methyl, we studied the effect of RNA/DNA hybrid approach utilizing a computer-assisted de novo RNA tetra-uracil (tetra-U) motif as a toolkit to address questions related to assembly efficiency, versatility, stability, and the production costs of hybrid RNA/DNA nanoparticles...
January 4, 2017: Nanomedicine: Nanotechnology, Biology, and Medicine
https://www.readbyqxmd.com/read/28063307/sharpin-facilitates-p53-degradation-in-breast-cancer-cells
#14
Huijie Yang, Sifan Yu, Weilong Wang, Xin Li, Yingxiang Hou, Zhenhua Liu, Yuanyuan Shi, Kun Mu, Gang Niu, Juntao Xu, Hui Wang, Jian Zhu, Ting Zhuang
The ubiquitin binding protein SHAPRIN is highly expressed in human breast cancer, one of the most frequent female malignancies worldwide. Here, we perform SHARPIN depletion in breast cancer cells together with RNA sequencing. The global expression profiling showed p53 signaling as a potential SHARPIN target. SHARPIN depletion decreased cell proliferation, which effect could be rescue by p53 knocking down. Depletion SHARPIN significantly increases p53 protein level and its target genes in multiple breast cancer cell lines...
January 4, 2017: Neoplasia: An International Journal for Oncology Research
https://www.readbyqxmd.com/read/28063231/exosomes-nanoparticulate-tools-for-rna-interference-and-drug-delivery
#15
REVIEW
Fahimeh Shahabipour, Nastaran Barati, Thomas P Johnston, Giuseppe Derosa, Pamela Maffioli, Amirhossein Sahebkar
Exosomes are naturally occurring extracellular vesicles released by most mammalian cells in all body fluids. Exosomes are known as key mediators in cell-cell communication and facilitate the transfer of genetic and biochemical information between distant cells. Structurally, exosomes are composed of lipids, proteins, and also several types of RNAs which enable these vesicles to serve as important disease biomarkers. Moreover, exosomes have emerged as novel drug and gene delivery tools owing to their multiple advantages over conventional delivery systems...
January 7, 2017: Journal of Cellular Physiology
https://www.readbyqxmd.com/read/28062037/single-molecule-insight-into-target-recognition-by-crispr-cas-complexes
#16
M Rutkauskas, A Krivoy, M D Szczelkun, C Rouillon, R Seidel
Ribonucleoprotein (RNP) complexes from CRISPR-Cas systems have attracted enormous interest since they can be easily and flexibly reprogrammed to target any desired locus for genome engineering and gene regulation applications. Basis for the programmability is a short RNA (crRNA) inside these complexes that recognizes the target nucleic acid by base pairing. For CRISPR-Cas systems that target double-stranded DNA this results in local DNA unwinding and formation of a so-called R-loop structure. Here we provide an overview how this target recognition mechanism can be dissected in great detail at the level of a single molecule...
2017: Methods in Enzymology
https://www.readbyqxmd.com/read/28061811/the-nature-and-nurture-of-cell-heterogeneity-accounting-for-macrophage-gene-environment-interactions-with-single-cell-rna-seq
#17
Quin F Wills, Esther Mellado-Gomez, Rory Nolan, Damien Warner, Eshita Sharma, John Broxholme, Benjamin Wright, Helen Lockstone, William James, Mark Lynch, Michael Gonzales, Jay West, Anne Leyrat, Sergi Padilla-Parra, Sarah Filippi, Chris Holmes, Michael D Moore, Rory Bowden
BACKGROUND: Single-cell RNA-Seq can be a valuable and unbiased tool to dissect cellular heterogeneity, despite the transcriptome's limitations in describing higher functional phenotypes and protein events. Perhaps the most important shortfall with transcriptomic 'snapshots' of cell populations is that they risk being descriptive, only cataloging heterogeneity at one point in time, and without microenvironmental context. Studying the genetic ('nature') and environmental ('nurture') modifiers of heterogeneity, and how cell population dynamics unfold over time in response to these modifiers is key when studying highly plastic cells such as macrophages...
January 7, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28061773/differential-long-term-stability-of-micrornas-and-rnu6b-snrna-in-12-20-year-old-archived-formalin-fixed-paraffin-embedded-specimens
#18
Sarah B Peskoe, John R Barber, Qizhi Zheng, Alan K Meeker, Angelo M De Marzo, Elizabeth A Platz, Shawn E Lupold
BACKGROUND: The quantitative analysis of microRNA (miRNA) gene expression in archived formalin-fixed, paraffin embedded (FFPE) tissues has been instrumental to identifying their potential roles in cancer biology, diagnosis, and prognosis. However, it remains unclear whether miRNAs remain stable in FFPE tissues stored for long periods of time. METHODS: Here we report Taqman real-time RT-PCR quantification of miR-21, miR-141, miR-221, and RNU6B small nuclear RNA (snRNA) levels from 92 radical prostatectomy specimens stored for 12-20 years in FFPE blocks...
January 6, 2017: BMC Cancer
https://www.readbyqxmd.com/read/28061446/%C3%AE-40p53-is-involved-in-the-inactivation-of-autophagy-and-contributes-to-inhibition-of-cell-death-in-hct116-%C3%AE-40p53-cells
#19
Yunjin Zang, Ying Shi, Kai Liu, Luxin Qiao, Xianghua Guo, Dexi Chen
Δ40p53 is an isoform of wild-type p53 (wtp53). Here, we assessed whether Δ40p53 has the same functions as wild-type p53 in the regulation of cell death and autophagy. First, we used HCT116 (p53+/+) and H1299 (p53-free) cells to produce two cell lines (HCT116-Δ40p53 and H1299-Δ40p53) that express exogenous Δ40p53 but not wtp53. By using these cell lines, we determined that Δ40p53 inhibited starvation-induced autophagy, as does wtp53. This inhibition arises from both Δ40p53 and wtp53 having 3'-5' exonuclease activity, which reduces the levels of double-stranded RNA (dsRNA) and then inhibits PKR/eIF2α-induced autophagy in cells exposed to starvation...
January 3, 2017: Oncotarget
https://www.readbyqxmd.com/read/28061331/ribonuclease-e-chopping-knife-and-sculpting-tool
#20
Joel G Belasco
In this issue of Molecular Cell, Chao et al. (2017) investigate the important role of the low-specificity endonuclease RNase E in shaping the transcriptome of a bacterial pathogen by functioning as both a degradative enzyme and an RNA maturase.
January 5, 2017: Molecular Cell
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