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Rna Interactions

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https://read.qxmd.com/read/30763910/comprehensive-investigation-of-mirnome-identifies-novel-candidate-mirna-mrna-interactions-implicated-in-t-cell-acute-lymphoblastic-leukemia
#1
Małgorzata Dawidowska, Roman Jaksik, Monika Drobna, Bronisława Szarzyńska-Zawadzka, Maria Kosmalska, Łukasz Sędek, Ludomiła Machowska, Anna Lalik, Monika Lejman, Marek Ussowicz, Krzysztof Kałwak, Jerzy R Kowalczyk, Tomasz Szczepański, Michał Witt
T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive malignancy originating from T-cell precursors. The genetic landscape of T-ALL has been largely characterized by next-generation sequencing. Yet, the transcriptome of miRNAs (miRNome) of T-ALL has been less extensively studied. Using small RNA sequencing, we characterized the miRNome of 34 pediatric T-ALL samples, including the expression of isomiRs and the identification of candidate novel miRNAs (not previously annotated in miRBase). For the first time, we show that immunophenotypic subtypes of T-ALL present different miRNA expression profiles...
February 11, 2019: Neoplasia: An International Journal for Oncology Research
https://read.qxmd.com/read/30763816/intrahost-viral-evolution-during-chronic-sapovirus-infections
#2
Corinna Pietsch, Uwe G Liebert
BACKGROUND: Sapovirus is a common cause of self-limiting diarrhea. In immunocompromised individuals chronic infections occur, but are incompletely investigated. OBJECTIVES: To investigate viral evolution in immunocompromised hosts during chronic sapovirus infection. STUDY DESIGN: From January 2010 to September 2018 stool samples of 5333 in-patients were analyzed for the presence of sapovirus RNA by real-time RT-PCR. In follow-up samples of chronic diarrhea cases nucleic acid sequencing of sapovirus genomes was performed...
February 7, 2019: Journal of Clinical Virology: the Official Publication of the Pan American Society for Clinical Virology
https://read.qxmd.com/read/30763793/fmrp-interacts-with-c-d-box-snorna-in-the-nucleus-and-regulates-ribosomal-rna-methylation
#3
Michelle Ninochka D'Souza, Naveen Kumar Chandappa Gowda, Vishal Tiwari, Rosana Ottakandathil Babu, Praveen Anand, Sudhriti Ghosh Dastidar, Randhir Singh, Owen G James, Bhuvaneish Selvaraj, Rakhi Pal, Arati Ramesh, Sumantra Chattarji, Siddharthan Chandran, Akash Gulyani, Dasaradhi Palakodeti, Ravi S Muddashetty
No abstract text is available yet for this article.
February 11, 2019: iScience
https://read.qxmd.com/read/30763669/long-term-and-high-dose-dexamethasone-injection-decreases-the-expression-of-immunoglobulin-heavy-light-chain-variable-region-genes-igh-l-vs-in-the-mouse-spleen
#4
Yuanhui Qi, Qiying Yi, Yamin Liu, Yanxia Hu, Dongshen Ni, Jianing Liu, Qin Zhou, Yajun Xie
Glucocorticoid hormones have been widely used in clinical practice as potent anti-inflammatory and immunosuppressive agents. However, the underlying mechanisms of how they work remain unaddressed. Here, we used RNA-set to profile spleen gene expression in adult mice after consistent intraperitoneal injection of dexamethasone. We identified 13565 genes in control (injected with 0.9% NaCl) and 13702 genes in dexamethasone-injected group, 12920 genes were expressed in both, but 645 genes were identified only in control and 782 genes were identified only in the dexamethasone group...
February 11, 2019: Gene
https://read.qxmd.com/read/30763382/analysis-of-pseudomonas-aeruginosa-biofilm-membrane-vesicles-supports-multiple-mechanisms-of-biogenesis
#5
Adam C Cooke, Alexander V Nello, Robert K Ernst, Jeffrey W Schertzer
Outer Membrane Vesicles (OMVs) are ubiquitous in bacterial environments and enable interactions within and between species. OMVs are observed in lab-grown and environmental biofilms, but our understanding of their function comes primarily from planktonic studies. Planktonic OMVs assist in toxin delivery, cell-cell communication, horizontal gene transfer, small RNA trafficking, and immune system evasion. Previous studies reported differences in size and proteomic cargo between planktonic and agar plate biofilm OMVs, suggesting possible differences in function between OMV types...
2019: PloS One
https://read.qxmd.com/read/30763315/iris-eda-an-integrated-rna-seq-interpretation-system-for-gene-expression-data-analysis
#6
Brandon Monier, Adam McDermaid, Cankun Wang, Jing Zhao, Allison Miller, Anne Fennell, Qin Ma
Next-Generation Sequencing has made available substantial amounts of large-scale Omics data, providing unprecedented opportunities to understand complex biological systems. Specifically, the value of RNA-Sequencing (RNA-Seq) data has been confirmed in inferring how gene regulatory systems will respond under various conditions (bulk data) or cell types (single-cell data). RNA-Seq can generate genome-scale gene expression profiles that can be further analyzed using correlation analysis, co-expression analysis, clustering, differential gene expression (DGE), among many other studies...
February 14, 2019: PLoS Computational Biology
https://read.qxmd.com/read/30763090/design-of-n-benzoxaborole-benzofuran-gsk8175-optimization-of-human-pk-inspired-by-metabolites-of-a-failed-clinical-hcv-inhibitor
#7
Pek Yoke Chong, J Brad Shotwell, John F Miller, Daniel J Price, Andy Maynard, Christian Voitenleitner, Amanda Mathis, Shawn Williams, Jeffrey Pouliot, Katrina Creech, Feng Wang, Jing M Fang, Huichang Zhang, Vincent Tai, Elizabeth Turner, Kristen M Kahler, Renae Crosby, Andrew J Peat
We previously described the discovery of GSK5852 (1), a non-nucleoside polymerase (NS5B) inhibitor of hepatitis C virus (HCV), in which a N-benzyl boronic acid was essential for potent antiviral activity. Unfortunately, facile benzylic oxidation resulted in a short plasma half-life (5 h) in human volunteers, and a backup program was initiated to remove metabolic liabilities associated with 1. Herein we describe second generation NS5B inhibitors including GSK8175 (49), a sulfonamide-N-benzoxaborole analog with low in vivo clearance across preclinical species and broad-spectrum activity against HCV replicons...
February 14, 2019: Journal of Medicinal Chemistry
https://read.qxmd.com/read/30761752/mimicry-deception-and-competition-the-life-of-competing-endogenous-rnas
#8
REVIEW
Marc P Grüll, Eric Massé
Since their discovery, small regulatory RNAs (sRNAs) were thought to be regulated exclusively at the transcriptional level. However, accumulating data from recent reports indicate that posttranscriptional signals can also modulate the function and stability of sRNAs. One of these posttranscriptional signals are competing endogenous RNAs (ceRNAs). Commonly called RNA sponges, ceRNAs can effectively sequester sRNAs and prevent them from binding their cognate target messenger RNAs (mRNAs). Subsequently, they prevent sRNA-dependent regulation of translation and stability of mRNA targets...
February 13, 2019: Wiley Interdisciplinary Reviews. RNA
https://read.qxmd.com/read/30761743/mutant-hfgf23-a12d-stimulates-osteoblast-differentiation-through-fgfr3
#9
Yilin Tu, Taoran Qu, Fengshan Chen
Fibroblast growth factor (FGF) 23 is a member of the FGF family involved in bone development by interacting with FGFRs. In a previous study, we discovered a mutant human FGF (hFGF) 23 (A12D) in the mandibular prognathism (MP) pedigree. However, the exact role of hFGF23(A12D) during bone formation remains unclear. The aim of this study was to identify the function of hFGF23(A12D) in bone formation. We infected isolated rat calvaria (RC) cells with the recombinant lentivirus containing mutant hFGF23(A12D) and WT hFGF23 respectively...
February 13, 2019: Journal of Cellular and Molecular Medicine
https://read.qxmd.com/read/30761015/long-non-coding-rnas-at-the-heart-of-cardiac-dysfunction
#10
REVIEW
Lisa Hobuß, Christian Bär, Thomas Thum
During the past decade numerous studies highlighted the importance of long non-coding RNAs (lncRNAs) in orchestrating cardiovascular cell signaling. Classified only by a transcript size of more than 200 nucleotides and their inability to code for proteins, lncRNAs constitute a heterogeneous group of RNA molecules with versatile functions and interaction partners, thus interfering with numerous endogenous signaling pathways. Intrinsic transcriptional regulation of lncRNAs is not only specific for different cell types or developmental stages, but may also change in response to stress factors or under pathological conditions...
2019: Frontiers in Physiology
https://read.qxmd.com/read/30760872/l3mbtl2-regulates-chromatin-remodeling-during-spermatogenesis
#11
Chenling Meng, Jinyue Liao, Danfeng Zhao, Huihui Huang, Jinzhong Qin, Tin-Lap Lee, Degui Chen, Wai-Yee Chan, Yin Xia
Lethal (3) malignant brain tumor like 2 (L3MBTL2) is a member of the MBT-domain proteins, which are involved in transcriptional repression and implicated in chromatin compaction. Our previous study has shown that L3MBTL2 is highly expressed in the testis, but its role in spermatogenesis remains unclear. In the present study, we found that L3MBTL2 was most highly expressed in pachytene spermatocytes within the testis. Germ cell-specific ablation of L3mbtl2 in the testis led to increased abnormal spermatozoa, progressive decrease of sperm counts and premature testicular failure in mice...
February 13, 2019: Cell Death and Differentiation
https://read.qxmd.com/read/30760608/implementation-of-a-crispr-based-system-for-gene-regulation-in-candida-albicans
#12
Elvira Román, Ioana Coman, Daniel Prieto, Rebeca Alonso-Monge, Jesús Pla
Clustered regularly interspaced short palindromic repeat (CRISPR) methodology is not only an efficient tool in gene editing but also an attractive platform to facilitate DNA, RNA, and protein interactions. We describe here the implementation of a CRISPR-based system to regulate expression in the clinically important yeast Candida albicans By fusing an allele of Streptococcus pyogenes Cas9 devoid of nuclease activity to a transcriptional repressor (Nrg1) or activator (Gal4), we were able to show specific repression or activation of the tester gene CAT1 , encoding the cytosolic catalase...
February 13, 2019: MSphere
https://read.qxmd.com/read/30760574/genome-characterization-prevalence-and-transmission-mode-of-a-novel-picornavirus-associated-with-the-threespine-stickleback-fish-gasterosteus-aculeatus
#13
Megan A Hahn, Nolwenn M Dheilly
The complete genome sequence of an RNA virus was assembled from RNA sequencing of virus particles purified from threespine stickleback intestine tissue samples. This new virus is most closely related to the Eel Picornavirus and can be assigned to the genus Potamipivirus in the family Picornaviridae Its unique genetic properties are enough to establish a new species, dubbed the Threespine Stickleback Picornavirus (TSPV). Due to their broad geographic distribution throughout the northern hemisphere and parallel adaptation to freshwater, threespine sticklebacks have become a model in evolutionary ecology...
February 13, 2019: Journal of Virology
https://read.qxmd.com/read/30760572/manipulation-of-aphid-behavior-by-a-persistent-plant-virus
#14
Maliheh Safari, Matthew J Ferrari, Marilyn J Roossinck
Plants are frequently infected with cytoplasmic RNA viruses that persist for many generations through nearly 100% vertical transmission without producing any symptoms. Movement between plant cells and horizontal transmission has not been observed in these viruses; instead they are distributed to all host cells through host cell division. Jalapeño peppers ( Capsicum annuum ) are all infected with Pepper cryptic virus 1 (PCV 1, family Partitiviridae ). We compared the effect of odor cues from PCV 1 infected (J+) and virus free (J-) Jalapeño pepper on the aphid Myzus periscae , a common vector of acute plant viruses...
February 13, 2019: Journal of Virology
https://read.qxmd.com/read/30760564/rna-binding-motif-protein-48-is-required-for-u12-splicing-and-maize-endosperm-differentiation
#15
Fang Bai, Jacob Corll, Donya N Shodja, Ruth Davenport, Guanqiao Feng, Janaki S Mudunkothge, Christian J Brigolin, Federico Martin, Gertraud Spielbauer, Chi-Wah Tseung, Amy E Siebert, William Bradley Barbazuk, Shailesh K Lal, A Mark Settles
The last eukaryotic common ancestor had two classes of introns that are still found in most eukaryotic lineages. Common U2-type and rare U12-type introns are spliced by the major and minor spliceosomes, respectively. Relatively few splicing factors have been shown to be specific to the minor spliceosome. We found that the maize RNA Binding Motif Protein48 (RBM48) is a U12 splicing factor that functions to promote cell differentiation and repress cell proliferation. RBM48 is coselected with the U12 splicing factor, ZRSR2/RGH3...
February 13, 2019: Plant Cell
https://read.qxmd.com/read/30760522/nrf2-activation-in-cancer-from-dna-to-protein
#16
REVIEW
Erica W Cloer, Dennis Goldfarb, Travis P Schrank, Bernard E Weissman, Michael B Major
The Cancer Genome Atlas catalogued alterations in the Kelch-like ECH-associated protein 1 and nuclear factor erythroid 2-related factor 2 (NRF2) signaling pathway in 6.3% of patient samples across 226 studies, with significant enrichment in lung and upper airway cancers. These alterations constitutively activate NRF2-dependent gene transcription to promote many of the cancer hallmarks, including cellular resistance to oxidative stress, xenobiotic efflux, proliferation, and metabolic reprogramming. Almost universally, NRF2 activity strongly associates with poor patient prognosis and chemo- and radioresistance...
February 13, 2019: Cancer Research
https://read.qxmd.com/read/30760198/the-plastid-and-mitochondrial-genomes-of-eucalyptus-grandis
#17
Desre Pinard, Alexander A Myburg, Eshchar Mizrachi
BACKGROUND: Land plant organellar genomes have significant impact on metabolism and adaptation, and as such, accurate assembly and annotation of plant organellar genomes is an important tool in understanding the evolutionary history and interactions between these genomes. Intracellular DNA transfer is ongoing between the nuclear and organellar genomes, and can lead to significant genomic variation between, and within, species that impacts downstream analysis of genomes and transcriptomes...
February 13, 2019: BMC Genomics
https://read.qxmd.com/read/30760197/identification-and-characterization-of-genes-with-absolute-mrna-abundances-changes-in-tumor-cells-with-varied-transcriptome-sizes
#18
Hao Cai, Xiangyu Li, Jun He, Wenbin Zhou, Kai Song, You Guo, Huaping Liu, Qingzhou Guan, Haidan Yan, Xianlong Wang, Zheng Guo
BACKGROUND: The amount of RNA per cell, namely the transcriptome size, may vary under many biological conditions including tumor. If the transcriptome size of two cells is different, direct comparison of the expression measurements on the same amount of total RNA for two samples can only identify genes with changes in the relative mRNA abundances, i.e., cellular mRNA concentration, rather than genes with changes in the absolute mRNA abundances. RESULTS: Our recently proposed RankCompV2 algorithm identify differentially expressed genes (DEGs) through comparing the relative expression orderings (REOs) of disease samples with that of normal samples...
February 13, 2019: BMC Genomics
https://read.qxmd.com/read/30760025/mg53-a-novel-regulator-of-kchip2-and-i-to-f-plays-a-critical-role-in-electrophysiological-remodeling-in-cardiac-hypertrophy
#19
Wenjuan Liu, Gang Wang, Cuicui Zhang, Wenwen Ding, Wanwen Cheng, Yizhi Luo, Chaoliang Wei, Jie Liu
BACKGROUND: KChIP2 (K+ channel interacting protein) is the auxiliary subunit of the fast transient outward K+ current (Ito,f ) in heart, and insufficient KChIP2 expression induces Ito,f downregulation and arrhythmogenesis in cardiac hypertrophy. Studies have shown muscle-specific mitsugumin 53 (MG53) has promiscuity of function in the context of normal and diseased heart. This study investigates the possible roles of cardiac MG53 in regulation of KChIP2 expression and Ito,f, and the arrhythmogenic potential in hypertrophy...
February 14, 2019: Circulation
https://read.qxmd.com/read/30759864/tarbp2-enhanced-resistance-during-tamoxifen-treatment-in-breast-cancer
#20
Ming-Yang Wang, Hsin-Yi Huang, Yao-Lung Kuo, Chiao Lo, Hung-Yu Sun, Yu-Jhen Lyu, Bo-Rong Chen, Jie-Ning Li, Pai-Sheng Chen
Tamoxifen is the most widely used hormone therapy in estrogen receptor-positive (ER+) breast cancer, which accounts for approximately 70% of all breast cancers. Although patients who receive tamoxifen therapy benefit with respect to an improved overall prognosis, resistance and cancer recurrence still occur and remain important clinical challenges. A recent study identified TAR (HIV-1) RNA binding protein 2 (TARBP2) as an oncogene that promotes breast cancer metastasis. In this study, we showed that TARBP2 is overexpressed in hormone therapy-resistant cells and breast cancer tissues, where it enhances tamoxifen resistance...
February 12, 2019: Cancers
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