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Post-transcriptional

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https://www.readbyqxmd.com/read/29453323/rna-stabilization-factors-in-chloroplasts-of-vascular-plants
#1
REVIEW
Nikolay Manavski, Lisa-Marie Schmid, Jörg Meurer
In contrast to the cyanobacterial ancestor, chloroplast gene expression is predominantly governed on the post-transcriptional level such as modifications of the RNA sequence, decay rates, exo- and endonucleolytic processing as well as translational events. The concerted function of numerous chloroplast RNA-binding proteins plays a fundamental and often essential role in all these processes but our understanding of their impact in regulation of RNA degradation is only at the beginning. Moreover, metabolic processes and post-translational modifications are thought to affect the function of RNA protectors...
February 16, 2018: Essays in Biochemistry
https://www.readbyqxmd.com/read/29451902/an-artificial-mirna-system-reveals-that-relative-contribution-of-translational-inhibition-to-mirna-mediated-regulation-depends-on-environmental-and-developmental-factors-in-arabidopsis-thaliana
#2
Patrick von Born, Marti Bernardo-Faura, Ignacio Rubio-Somoza
Development and fitness of any organism rely on properly controlled gene expression. This is especially true for plants, as their development is determined by both internal and external cues. MicroRNAs (miRNAs) are embedded in the genetic cascades that integrate and translate those cues into developmental programs. miRNAs negatively regulate their target genes mainly post-transcriptionally through two co-existing mechanisms; mRNA cleavage and translational inhibition. Despite our increasing knowledge about the genetic and biochemical processes involved in those concurrent mechanisms, little is known about their relative contributions to the overall miRNA-mediated regulation...
2018: PloS One
https://www.readbyqxmd.com/read/29451334/microrna-profiling-between-bacillus-thuringiensis-cry1ab-susceptible-and-resistant-european-corn-borer-ostrinia-nubilalis-h%C3%A3-bner
#3
T Yu, X Li, B-S Coates, Q Zhang, B-D Siegfried, X Zhou
Transgenic maize hybrids that express insecticidal Bacillus thuringiensis (Bt) crystalline (Cry) protein toxins effectively protect against the European corn borer, Ostrinia nubilalis, a devastating maize pest. Field monitoring and laboratory selections have detected varying levels of O. nubilalis resistance to Cry1Ab toxin. MicroRNAs (miRNAs) are short noncoding RNAs that are involved in post-transcriptional gene regulation. Their potential roles in the evolution of Bt resistance, however, remain largely unknown...
February 16, 2018: Insect Molecular Biology
https://www.readbyqxmd.com/read/29449410/conserved-microrna-targeting-reveals-preexisting-gene-dosage-sensitivities-that-shaped-amniote-sex-chromosome-evolution
#4
Sahin Naqvi, Daniel W Bellott, Kathy S Lin, David C Page
Mammalian X and Y Chromosomes evolved from an ordinary autosomal pair. Genetic decay of the Y led to X Chromosome inactivation (XCI) in females, but some Y-linked genes were retained during the course of sex chromosome evolution, and many X-linked genes did not become subject to XCI. We reconstructed gene-by-gene dosage sensitivities on the ancestral autosomes through phylogenetic analysis of microRNA (miRNA) target sites and compared these preexisting characteristics to the current status of Y-linked and X-linked genes in mammals...
February 15, 2018: Genome Research
https://www.readbyqxmd.com/read/29448246/effect-of-mst1-on-endometriosis-apoptosis-and-migration-role-of-drp1-related-mitochondrial-fission-and-parkin-required-mitophagy
#5
Qingdong Zhao, Mingxia Ye, Wen Yang, Min Wang, Mingxia Li, Chenglei Gu, Luyang Zhao, Zhe Zhang, Weidong Han, Wensheng Fan, Yuanguang Meng
BACKGROUND/AIMS: Mitochondrial homeostasis is implicated in the development and progression of endometriosis through poorly defined mechanisms. Mst1 is the major growth suppressor related to cancer migration, apoptosis and proliferation. However, whether Mst1 is involved in endometriosis apoptosis and migration via regulating the mitochondrial function remains to be elucidated. METHODS: Expression of Mst1 in endometriosis was examined via western blots. Cellular apoptosis was detected via MTT and TUNEL assay...
February 9, 2018: Cellular Physiology and Biochemistry
https://www.readbyqxmd.com/read/29448039/development-of-sirna-mediated-rna-interference-and-functional-analysis-of-novel-parasitic-nematode-specific-protein-of-setaria-digitata
#6
M B C L Somarathne, Y I N S Gunawardena, N V Chandrasekharan, R S Dassanayake
Despite the differences of the host, parasitic nematodes may share commonalities in their parasitizing genes. Setaria digitata novel protein (SDNP) is such an entity which is parasitic nematode-specific and having sequence similarities with those of W. bancrofti, B. malayi, Loa loa and Onchocerca volvulus. Post-transcriptional gene silencing by siRNA mediated RNA interference (RNAi) is a widely used technique in functional genomics. Though the technique has been used in several free-living, plant and animal parasitic nematodes, it has not yet been tried out for the filarial worm S...
February 12, 2018: Experimental Parasitology
https://www.readbyqxmd.com/read/29447268/circulating-small-non-coding-rnas-reflect-ifn-status-and-b-cell-hyperactivity-in-patients-with-primary-sj%C3%A3-gren-s-syndrome
#7
Ana P Lopes, Maarten R Hillen, Eleni Chouri, Sofie L M Blokland, Cornelis P J Bekker, Aike A Kruize, Marzia Rossato, Joel A G van Roon, Timothy R D J Radstake
BACKGROUND: Considering the important role of miRNAs in the regulation of post-transcriptional expression of target genes, we investigated circulating small non-coding RNAs (snc)RNA levels in patients with primary Sjögren's syndrome (pSS). In addition we assessed if serum sncRNA levels can be used to differentiate patients with specific disease features. METHODS: Serum RNA was isolated from 37 pSS patients as well as 21 patients with incomplete Sjögren's Syndrome (iSS) and 17 healthy controls (HC) allocated to two independent cohorts: discovery and validation...
2018: PloS One
https://www.readbyqxmd.com/read/29447160/modeling-the-interactions-of-sense-and-antisense-period-transcripts-in-the-mammalian-circadian-clock-network
#8
Dorjsuren Battogtokh, Shihoko Kojima, John J Tyson
In recent years, it has become increasingly apparent that antisense transcription plays an important role in the regulation of gene expression. The circadian clock is no exception: an antisense transcript of the mammalian core-clock gene PERIOD2 (PER2), which we shall refer to as Per2AS RNA, oscillates with a circadian period and a nearly 12 h phase shift from the peak expression of Per2 mRNA. In this paper, we ask whether Per2AS plays a regulatory role in the mammalian circadian clock by studying in silico the potential effects of interactions between Per2 and Per2AS RNAs on circadian rhythms...
February 15, 2018: PLoS Computational Biology
https://www.readbyqxmd.com/read/29446735/epigenetic-regulation-of-regulatory-t-cells-in-kidney-disease-and-transplantation
#9
Yufeng Liu, Bo Peng, Shengdi Wu, Nuo Xu
Regulatory T (Treg) cells are a kind of immunosuppression cells, which have been used to treat autoimmune diseases and induce allograft tolerance in clinical trials. While Treg cells based therapy is a promising treatment for kidney diseases and an emerging concept for tolerance induction in renal transplantation, a better understanding of the functions and biology of Treg cells is needed to be able to optimally exploit them. Epigenetics regulation, which refers to potentially heritable alterations in gene expression without underlying changes of the nucleotide sequence, plays an important role in Treg cells induction and maintenance...
February 13, 2018: Current Gene Therapy
https://www.readbyqxmd.com/read/29446655/micrornas-as-molecular-targets-of-quercetin-and-its-derivatives-underlying-their-biological-effects-a-preclinical-strategy
#10
Dan Wang, Dongxiao Sun-Waterhouse, Feng Li, Li Xin, Dapeng Li
Quercetin is a well-known flavonoid naturally occurring in most of the plant foods and is often found in the human diet. It can act as a potent antioxidant and anti-inflammatory agent, and plays significant roles in the prevention of various chronic diseases. Recent findings revealed that quercetin could affect metabolic traits by regulating certain transcription factors or key proteins involved in cellular signal pathways and influencing the expression of functional genes along with related regulatory pathway(s), and that microRNAs (miRNAs) circulate in body fluids and are involved in post-transcriptional gene silencing and regulation of gene expression in various biological processes including development, proliferation, metabolism and inflammation...
February 15, 2018: Critical Reviews in Food Science and Nutrition
https://www.readbyqxmd.com/read/29444950/mirna-targeting-and-alternative-splicing-in-the-stress-response-events-hosted-by-membrane-less-compartments
#11
REVIEW
Mariya M Kucherenko, Halyna R Shcherbata
Stress can be temporary or chronic, and mild or acute. Depending on its extent and severity, cells either alter their metabolism, and adopt a new state, or die. Fluctuations in environmental conditions occur frequently, and such stress disturbs cellular homeostasis, but in general, stresses are reversible and last only a short time. There is increasing evidence that regulation of gene expression in response to temporal stress happens post-transcriptionally in specialized subcellular membrane-less compartments called ribonucleoprotein (RNP) granules...
February 14, 2018: Journal of Cell Science
https://www.readbyqxmd.com/read/29444662/a-systematic-approach-to-rna-associated-motif-discovery
#12
Tian Gao, Jiang Shu, Juan Cui
BACKGROUND: Sequencing-based large screening of RNA-protein and RNA-RNA interactions has enabled the mechanistic study of post-transcriptional RNA processing and sorting, including exosome-mediated RNA secretion. The downstream analysis of RNA binding sites has encouraged the investigation of novel sequence motifs, which resulted in exceptional new challenges for identifying motifs from very short sequences (e.g., small non-coding RNAs or truncated messenger RNAs), where conventional methods tend to be ineffective...
February 14, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29444437/mutations-in-cytosine-5-trna-methyltransferases-impact-mobile-element-expression-and-genome-stability-at-specific-dna-repeats
#13
Bianca Genenncher, Zeljko Durdevic, Katharina Hanna, Daniela Zinkl, Mehrpouya Balaghy Mobin, Nevcin Senturk, Bruno Da Silva, Carine Legrand, Clément Carré, Frank Lyko, Matthias Schaefer
The maintenance of eukaryotic genome stability is ensured by the interplay of transcriptional as well as post-transcriptional mechanisms that control recombination of repeat regions and the expression and mobility of transposable elements. We report here that mutations in two (cytosine-5) RNA methyltransferases, Dnmt2 and NSun2, impact the accumulation of mobile element-derived sequences and DNA repeat integrity in Drosophila. Loss of Dnmt2 function caused moderate effects under standard conditions, while heat shock exacerbated these effects...
February 13, 2018: Cell Reports
https://www.readbyqxmd.com/read/29443978/distinguishing-rna-modifications-from-noise-in-epitranscriptome-maps
#14
Anya V Grozhik, Samie R Jaffrey
Messenger RNA (mRNA) and long noncoding RNA (lncRNA) can be subjected to a variety of post-transcriptional modifications that markedly influence their fate and function. This concept of 'epitranscriptomic' modifications and the understanding of their function has been driven by new technologies for transcriptome-wide mapping of modified nucleotides using next-generation sequencing. Mapping technologies have successfully documented the location and prevalence of several modified nucleotides in the transcriptome...
February 14, 2018: Nature Chemical Biology
https://www.readbyqxmd.com/read/29442990/alteration-of-microrna-expression-profiles-by-surface-modified-gold-nanoparticles-in-human-lung-adenocarcinoma-cells
#15
Seon Young Choi, Pan Dong Ryu, Sang-Woo Joo, So Yeong Lee
MicroRNAs that bind to mRNA are important post-transcriptional regulators that control gene expression by degradation or suppressing translation of target mRNAs. Several studies indicate that nanoparticles (NPs) induce alterations in microRNA expression relating to cell processes including cell development and progressive diseases. However, the alteration of microRNA expression by surface-modified gold nanoparticles (AuNPs) in A549 cells has not been reported. In order to investigate the patterns of microRNA expression, we analyzed data from microRNA arrays using cells treated with citrate- or chitosan-AuNPs...
April 1, 2018: Journal of Nanoscience and Nanotechnology
https://www.readbyqxmd.com/read/29441447/transcriptional-mechanisms-of-secondary-fracture-healing
#16
REVIEW
Joseph L Roberts, David N Paglia, Hicham Drissi
PURPOSE OF REVIEW: Growing evidence supports the critical role of transcriptional mechanisms in promoting the spatial and temporal progression of bone healing. In this review, we evaluate and discuss new transcriptional and post-transcriptional regulatory mechanisms of secondary bone repair, along with emerging evidence for epigenetic regulation of fracture healing. RECENT FINDINGS: Using the candidate gene approach has identified new roles for several transcription factors in mediating the reactive, reparative, and remodeling phases of fracture repair...
February 13, 2018: Current Osteoporosis Reports
https://www.readbyqxmd.com/read/29440670/characterization-of-conserved-and-novel-micrornas-in-lilium-lancifolium-thunb-by-high-throughput-sequencing
#17
Xiangfeng He, Awraris Getachew Shenkute, Wenhe Wang, Shufa Xu
MicroRNAs (miRNAs) are among the class of noncoding small RNA molecules and play a crucial role in post-transcriptional regulation in plants. Although Lilium is one of the most popular ornamental flowers worldwide, however, there is no report on miRNAs identification. In the present study, therefore, miRNAs and their targets were identified from flower, leaf, bulblet and bulb of Lilium lancifolium Thunb. by high-throughput sequencing and bioinformatics analysis. In this study, a total of 38 conserved miRNAs belonging to 17 miRNA families and 44 novel miRNAs were identified...
February 13, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29440318/monitoring-the-5-methoxycarbonylmethyl-2-thiouridine-mcm5s2u-modification-in-eukaryotic-trnas-via-the-gamma-toxin-endonuclease
#18
Jenna M Lentini, Jillian Ramos, Dragony Fu
The post-transcriptional modification of tRNA at the wobble position is a universal process occurring in all domains of life. In eukaryotes, the wobble uridine of particular tRNAs is transformed to the 5-methoxycarbonylmethyl-2-thiouridine (mcm5s2U) modification which is critical for proper mRNA decoding and protein translation. However, current methods to detect mcm5s2U are technically challenging and/or require specialized instrumental expertise. Here, we show that gamma-toxin endonuclease from the yeast Kluyveromyces lactis can be used as a probe for assaying mcm5s2U status in the tRNA of diverse eukaryotic organisms ranging from protozoans to mammalian cells...
February 13, 2018: RNA
https://www.readbyqxmd.com/read/29440232/noncoding-rnas-long-non-coding-rnas-and-micrornas-in-endocrine-related-cancers
#19
Carolyn M Klinge
The human genome is 'pervasively transcribed' leading to a complex array of non-coding RNAs (ncRNAs) that far outnumber coding mRNAs. ncRNAs have regulatory roles in transcription and post-transcriptional processes as well numerous cellular functions that remain to be fully described. Best characterized of the 'expanding universe' of ncRNAs are the ~ 22 nucleotide microRNAs (miRNAs) that base-pair to target mRNA's 3' untranslated region within the RNA-induced silencing complex (RISC) and block translation and may stimulate mRNA transcript degradation...
February 12, 2018: Endocrine-related Cancer
https://www.readbyqxmd.com/read/29439213/a-genetic-network-for-systemic-rna-silencing-in-plants
#20
Wei Wei Chen, Xian Zhang, Yaya Fan, Bin Li, Eugene Ryabov, Nongnong Shi, Mei Zhao, Zhiming Yu, Cheng Qin, Qianqian Zheng, Pengcheng Zhang, Huizhong Wang, Stephen Jackson, Qi Cheng, Yule Liu, Philippe Gallusci, Yiguo Hong
Non-cell autonomous RNA silencing can spread from cell to cell and over long-distance in animals and plants. However, the genetic requirements and signals involved in plant mobile silencing remain poorly understood. Here, we identified a DICER-LIKE2 (DCL2)-dependent mechanism for systemic spread of post-transcriptional RNA silencing (also known as post-transcriptional gene silencing, PTGS) in Nicotiana benthamiana. Using a suite of transgenic DCL RNAi lines coupled with a GFP reporter, we demonstrated that N...
February 8, 2018: Plant Physiology
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