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https://www.readbyqxmd.com/read/29027959/radiation-induced-changes-of-microrna-expression-profiles-in-radiosensitive-and-radioresistant-leukemia-cell-lines-with-different-levels-of-chromosome-abnormalities
#1
Daria Liamina, Wladimir Sibirnyj, Anna Khokhlova, Viacheslav Saenko, Eugenia Rastorgueva, Aleksandr Fomin, Yury Saenko
In our study, we estimate an effect from chromosome aberrations and genome mutations on changes in microRNA expression profiles in cancer cell lines demonstrating different radiosensitivity. Here, cell viability and microRNA spectrum have been estimated 1, 4, and 24 h after irradiation. MiSeq high-throughput sequencing system (Illumina, San Diego, CA, USA) is employed to perform microRNA spectrum estimation. In the K562 cell line, the number of expressed microRNAs in chromosomes demonstrates a more pronounced variation...
October 13, 2017: Cancers
https://www.readbyqxmd.com/read/29025584/regulatory-mechanisms-of-long-noncoding-rnas-on-gene-expression-in-cancers
#2
REVIEW
Weiliang Sun, Yunben Yang, Chunjing Xu, Junming Guo
Long non-coding RNAs (lncRNAs) are a heterogeneous class of RNAs that are non-protein coding transcripts longer than 200 nucleotides. In this review, we introduce the mechanisms by which lncRNAs regulate gene expression in four parts, epigenetic regulation (genetic imprinting and chromatin remodeling), transcriptional regulation (molecular decoy), post-transcriptional regulation (splicing and mRNA decay), and translational regulation. H19, Xist, and others are involved in genomic imprinting. HOTAIR and ANRIL function in chromatin remodeling...
October 2017: Cancer Genetics
https://www.readbyqxmd.com/read/29024760/rna-processing-in-the-male-germline-mechanisms-and-implications-for-fertility
#3
REVIEW
Julien M D Legrand, Robin M Hobbs
Mammalian spermatogenesis is a tightly coordinated process that gives rise to mature spermatozoa capable of fertilising an ovum during sexual reproduction. A population of stem and progenitor cells known as undifferentiated spermatogonia enables continual spermatogenesis throughout life. A complex transcriptional network that balances self-renewal of spermatogonia with their timely differentiation in order to maintain constant fertility regulates this process. Importantly, post-transcriptional regulation of gene expression plays a critical role in spermatogenesis, necessitated by the profound genetic and morphological changes that occur during meiosis and sperm maturation...
October 9, 2017: Seminars in Cell & Developmental Biology
https://www.readbyqxmd.com/read/29024706/identification-of-circular-rnas-in-human-aortic-valves
#4
Jianle Chen, Jun Wang, Yun Jiang, Weidong Gu, Buqing Ni, Haoliang Sun, Wanjun Gu, Liang Chen, Yongfeng Shao
With the wide application of RNA-Seq technology, thousands of circular RNAs (circRNAs) have been identified in different type of tissues and cells in many organisms, but little is known on the human aortic valve expressed circRNAs. In this study, we identified all circRNAs in two calcified human aortic valves, and characterized the features of all circRNAs. A total of 5476 circRNAs were identified in human aortic valves, including 1412 (25.79%) aortic valve specific circRNAs. Next, we showed that most aortic valve specific circRNAs were derived from the exonic regions of their host genes, and majority of the host genes contained less than three circRNAs...
October 9, 2017: Gene
https://www.readbyqxmd.com/read/29024335/fifty-shades-of-sumo-its-role-in-immunity-and-at-the-fulcrum-of-growth-defense-balance
#5
Vivek Verma, Fenella Crolley, Ari Sadanandom
The sessile nature of plants requires them to cope with an ever changing environment. Effective adaptive responses require sophisticated cellular mechanisms at post-transcriptional and -translational levels. Post-translational modification by Small Ubiquitin-like Modifier (SUMO) proteins is emerging as a key player in these adaptive responses. SUMO conjugation can rapidly change the overall fate of target proteins by altering their stability or interaction with partner proteins or DNA. SUMOylation entails an enzyme cascade that leads to the activation, conjugation and ligation of SUMO to lysine residues of target proteins...
October 10, 2017: Molecular Plant Pathology
https://www.readbyqxmd.com/read/29023197/mutational-landscape-of-rna-binding-proteins-in-human-cancers
#6
Yaseswini Neelamraju, Abel Gonzalez-Perez, Poornima Bhat-Nakshatri, Harikrishna Nakshatri, Sarath Chandra Janga
RNA Binding Proteins (RBPs) are a class of post-transcriptional regulatory molecules which are increasingly documented to be dysfunctional in cancer genomes. However, our current understanding of these alterations is limited. Here, we delineate the mutational landscape of ∼1300 RBPs in ∼6000 cancer genomes. Our analysis revealed that RBPs have an average of ∼3 mutations per Mb across 26 cancer types. We identified 281 RBPs to be enriched for mutations (GEMs) in at least one cancer type. GEM RBPs were found to undergo frequent frameshift and inframe deletions as well as missense, nonsense and silent mutations when compared to those that are not enriched for mutations...
October 12, 2017: RNA Biology
https://www.readbyqxmd.com/read/29023006/expression-profile-of-stress-responsive-arabidopsis-thaliana-mirnas-and-their-target-genes-in-response-to-inoculation-with-pectobacterium-carotovorum-subsp-carotovorum
#7
A T Djami-Tchatchou, K Ntushelo
BACKGROUND: Pectobacterium carotovorum subsp. carotovorum (Pcc) is a soft rot bacterium which upon entry into the plant macerates plant tissues by producing plant cell wall degrading enzymes. It has a wide host range which includes carrot, potato, tomato, leafy greens, squash and other cucurbits, onion, green peppers and cassava. During plant-microbe interactions, one of the ways of plant response to pathogen infection is through the small RNA silencing mechanism. Under pathogen attack the plant utilizes microRNAs to regulate gene expression by means of mediating gene silencing at transcriptional and post-transcriptional level...
2017: Pakistan Journal of Biological Sciences: PJBS
https://www.readbyqxmd.com/read/29022589/dynamic-landscape-and-regulation-of-rna-editing-in-mammals
#8
Meng How Tan, Qin Li, Raghuvaran Shanmugam, Robert Piskol, Jennefer Kohler, Amy N Young, Kaiwen Ivy Liu, Rui Zhang, Gokul Ramaswami, Kentaro Ariyoshi, Ankita Gupte, Liam P Keegan, Cyril X George, Avinash Ramu, Ni Huang, Elizabeth A Pollina, Dena S Leeman, Alessandra Rustighi, Y P Sharon Goh, Ajay Chawla, Giannino Del Sal, Gary Peltz, Anne Brunet, Donald F Conrad, Charles E Samuel, Mary A O'Connell, Carl R Walkley, Kazuko Nishikura, Jin Billy Li
Adenosine-to-inosine (A-to-I) RNA editing is a conserved post-transcriptional mechanism mediated by ADAR enzymes that diversifies the transcriptome by altering selected nucleotides in RNA molecules. Although many editing sites have recently been discovered, the extent to which most sites are edited and how the editing is regulated in different biological contexts are not fully understood. Here we report dynamic spatiotemporal patterns and new regulators of RNA editing, discovered through an extensive profiling of A-to-I RNA editing in 8,551 human samples (representing 53 body sites from 552 individuals) from the Genotype-Tissue Expression (GTEx) project and in hundreds of other primate and mouse samples...
October 11, 2017: Nature
https://www.readbyqxmd.com/read/29022131/feedback-regulation-of-ribosome-assembly
#9
REVIEW
Jesús de la Cruz, Fernando Gómez-Herreros, Olga Rodríguez-Galán, Victoria Begley, María de la Cruz Muñoz-Centeno, Sebastián Chávez
Ribosome biogenesis is a crucial process for growth and constitutes the major consumer of cellular resources. This pathway is subjected to very stringent regulation to ensure correct ribosome manufacture with a wide variety of environmental and metabolic changes, and intracellular insults. Here we summarise our current knowledge on the regulation of ribosome biogenesis in Saccharomyces cerevisiae by particularly focusing on the feedback mechanisms that maintain ribosome homeostasis. Ribosome biogenesis in yeast is controlled mainly at the level of the production of both pre-rRNAs and ribosomal proteins through the transcriptional and post-transcriptional control of the TORC1 and protein kinase A signalling pathways...
October 11, 2017: Current Genetics
https://www.readbyqxmd.com/read/29021386/suppression-of-microrna-activity-in-kidney-collecting-ducts-induces-partial-loss-of-epithelial-phenotype-and-renal-fibrosis
#10
Sachin Hajarnis, Matanel Yheskel, Darren Williams, Thomas Brefort, Bob Glaudemans, Huguette Debaix, Michel Baum, Olivier Devuyst, Vishal Patel
microRNAs (miRNAs) are sequence-specific inhibitors of post-transcriptional gene expression. The physiologic function of these noncoding RNAs in postnatal renal tubules still remains unclear. Surprisingly, they appear to be dispensable for mammalian proximal tubule (PT) function. Here, we examined the effects of miRNA suppression in collecting ducts (CDs). To conclusively evaluate the role of miRNAs, we generated three mouse models with CD-specific inactivation of key miRNA pathway genes Dicer, Dgcr8, and the entire Argonaute gene family (Ago1, 2, 3, and 4)...
October 11, 2017: Journal of the American Society of Nephrology: JASN
https://www.readbyqxmd.com/read/29017967/non-coding-rnas-and-their-roles-in-stress-response-in-plants
#11
REVIEW
Jingjing Wang, Xianwen Meng, Oxana B Dobrovolskaya, Yuriy L Orlov, Ming Chen
Eukaryotic genomes encode thousands of non-coding RNAs (ncRNAs), which play crucial roles in transcriptional and post-transcriptional regulation of gene expression. Accumulating evidence indicates that ncRNAs, especially microRNAs (miRNAs) and long ncRNAs (lncRNAs), have emerged as key regulatory molecules in plant stress responses. In this review, we have summarized the current progress on the understanding of plant miRNA and lncRNA identification, characteristics, bioinformatics tools, and resources, and provided examples of mechanisms of miRNA- and lncRNA-mediated plant stress tolerance...
October 7, 2017: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/29016889/argonaute10-inhibits-in-vitro-shoot-regeneration-via-repression-of-mir165-166-in-arabidopsis-thaliana
#12
Tao Xue, Xuehuan Dai, Ruipu Wang, Junzhu Wang, Zhenhua Liu, Fengning Xiang
Many plant cells retain their totipotency when cultured in vitro. The regulation of shoot regeneration from in vitro culture involves a number of gene products, but the nature of the associated post-transcriptional events remains largely unknown. Here, the post transcriptional regulator ARGONAUTE10 (AGO10), a protein which is specifically expressed in the explant during the period when pro-SAMs are forming, has been known to inhibit shoot regeneration. In in vitro cultured explants of the loss-of-function mutant ago10, a much larger than normal number of shoot apical meristems was formed, and in these, the stem-cell marker genes WUS, CLV3 and STM were all strongly expressed...
August 21, 2017: Plant & Cell Physiology
https://www.readbyqxmd.com/read/28993932/genome-wide-identification-of-cd-responsive-nramp-transporter-genes-and-analyzing-expression-of-nramp-1-mediated-by-mir167-in-brassica-napus
#13
Jin Guo Meng, Xian Duo Zhang, Shang Kun Tan, Kai Xuan Zhao, Zhi Min Yang
In plants, metal transporters are responsible for metal uptake, translocation and homeostasis. These metals include essential nutrients such as zinc (Zn) and manganese (Mn) or non-essential metals like cadmium (Cd) and lead (Pb). Although a few metal transporters have been well characterized in model plants, little is known about their functionality in rapeseed (Brassica napus). In the study, 22 NRAMP transporter genes from B. napus genome were identified and annotated using bioinformatics and high-throughput RNA-sequencing (RNA-seq)...
October 9, 2017: Biometals: An International Journal on the Role of Metal Ions in Biology, Biochemistry, and Medicine
https://www.readbyqxmd.com/read/28993896/rcan1-mutation-and-functional-characterization-in-children-with-sporadic-congenital-heart-disease
#14
Xiaoyong Li, Lei Shi, Ming Xu, Xun Zheng, Yiwen Yu, Jing Jin
Congenital heart disease (CHD) is the most frequent birth defect. RCAN1 (regulator of calcineurin 1) contributes to CHD in Down syndrome. However, whether RCAN1 is also associated with nonsyndromic CHD remains unclear. This study sequenced the exons and flanking region of RCAN1 in 128 sporadic CHD patients and 150 normal controls. We identified six novel heterozygous mutations in CHD patients. Functional assay showed that the g.482G>T could obviously raise the promoter activity of RCAN1.4 in vitro; However, we failed to detect the expression of RCAN1 in the right auricle, which made it confused to evaluate the pathogenicity of this mutation...
October 9, 2017: Pediatric Cardiology
https://www.readbyqxmd.com/read/28993636/involvement-of-puf60-in-transcriptional-and-post-transcriptional-regulation-of-hepatitis-b-virus-pregenomic-rna-expression
#15
Suofeng Sun, Kenji Nakashima, Masahiko Ito, Yuan Li, Takeshi Chida, Hirotaka Takahashi, Koichi Watashi, Tatsuya Sawasaki, Takaji Wakita, Tetsuro Suzuki
Here we identified PUF60, a splicing factor and a U2 small nuclear ribonucleoprotein auxiliary factor, as a versatile regulator of transcriptional and post-transcriptional steps in expression of hepatitis B virus (HBV) 3.5 kb, precore plus pregenomic RNA. We demonstrate that PUF60 is involved in: 1) up-regulation of core promoter activity through its interaction with transcription factor TCF7L2, 2) promotion of 3.5 kb RNA degradation and 3) suppression of 3.5 kb RNA splicing. When the 1.24-fold HBV genome was introduced into cells with the PUF60-expression plasmid, the 3...
October 9, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28993448/aberrant-splicing-induced-by-dysregulated-rbfox2-produces-enhanced-function-of-cav1-2-calcium-channel-and-vascular-myogenic-tone-in-hypertension
#16
Yingying Zhou, Jia Fan, Huayuan Zhu, Li Ji, Wenyong Fan, Isha Kapoor, Yue Wang, Yuan Wang, Guoqing Zhu, Juejin Wang
Calcium influx from activated voltage-gated calcium channel CaV1.2 in vascular smooth muscle cells is indispensable for maintaining myogenic tone and blood pressure. The function of CaV1.2 channel can be optimized by alternative splicing, one of post-transcriptional modification mechanisms. The splicing factor Rbfox2 is known to regulate the CaV1.2 pre-mRNA alternative splicing events during neuronal development. However, Rbfox2's roles in modulating the key function of vascular CaV1.2 channel and in the pathogenesis of hypertension remain elusive...
October 9, 2017: Hypertension
https://www.readbyqxmd.com/read/28990926/irak2-directs-stimulus-dependent-nuclear-export-of-inflammatory-mrnas
#17
Hao Zhou, Katarzyna Bulek, Xiao Li, Tomasz Herjan, Minjia Yu, Wen Qian, Han Wang, Gao Zhou, Xing Chen, Hui Yang, Lingzi Hong, Junjie Zhao, Luke Qin, Koichi Fukuda, Annette Flotho, Ji Gao, Ashok Dongre, Julie A Carman, Zizhen Kang, Bing Su, Timothy S Kern, Jonathan D Smith, Thomas A Hamilton, Frauke Melchior, Paul L Fox, Xiaoxia Li
Expression of inflammatory genes is determined in part by post-transcriptional regulation of mRNA metabolism but how stimulus- and transcript-dependent nuclear export influence is poorly understood. Here we report a novel pathway in which LPS/TLR4 engagement promotes nuclear localization of IRAK2 to facilitate nuclear export of a specific subset of inflammation related mRNAs for translation in murine macrophages. IRAK2 kinase activity is required for LPS-induced RanBP2-mediated IRAK2 sumoylation and subsequent nuclear translocation...
October 9, 2017: ELife
https://www.readbyqxmd.com/read/28990842/microrna-655-3p-regulates-echinacea-purpurea-mediated-activation-of-abcg2
#18
Charles Awortwe, Meike Kaehler, Bernd Rosenkranz, Ingolf Cascorbi, Henrike Bruckmueller
The aim of this study was to investigate the regulatory effect of Echinacea purpurea (EP) on efflux transporters ABCB1 and ABCG2 and to identify specific microRNAs contributing to their post-transcriptional regulation. ABCB1 and ABCG2 levels were assessed in human hepatoblastoma HepG2 cells treated with 50 µg/mL methanolic extract of commercial EP capsules for different durations of time. The microRNA expression profile of HepG2 cells after EP treatment was evaluated and in silico target prediction was subsequently conducted to identify specific microRNAs with binding sites in the 3'-UTR of ABCB1 and ABCG2...
October 9, 2017: Xenobiotica; the Fate of Foreign Compounds in Biological Systems
https://www.readbyqxmd.com/read/28990296/association-between-mthfr-microrna-binding-site-polymorphisms-and-methotrexate-concentrations-in-chinese-pediatric-patients-with-acute-lymphoblastic-leukemia
#19
Shu-Mei Wang, Wei-Xin Zeng, Wan-Shui Wu, Lu-Lu Sun, Dan Yan
BACKGROUND: The pharmacokinetics and therapeutic response to methotrexate (MTX) display large variability in the treatment of acute lymphoblastic leukemia (ALL). The aim of the present study was to investigate the association of two microRNA (miRNA) binding site polymorphisms (rs3737966 G > A and rs35134728 DEL/TTC) in the 3'UTR of MTHFR with serum MTX concentrations, in a Chinese pediatric population with ALL. METHODS: Genotyping for MTHFR rs3737966 and rs35134728 in 144 children with ALL was performed using the Sequenom MassArray system...
October 9, 2017: Journal of Gene Medicine
https://www.readbyqxmd.com/read/28990243/micrornas-a-novel-potential-biomarker-for-diagnosis-and-therapy-in-patients-with-non-small-cell-lung-cancer
#20
REVIEW
Qun Zhou, Shao-Xin Huang, Feng Zhang, Shu-Jun Li, Cong Liu, Yong-Yong Xi, Liang Wang, Xin Wang, Qi-Qiang He, Cheng-Cao Sun, De-Jia Li
BACKGROUND: Lung cancer is still one of the most serious causes of cancer-related deaths all over the world. MicroRNAs (miRNAs) are defined as small non-coding RNAs which could play a pivotal role in post-transcriptional regulation of gene expression. Increasing evidence demonstrated dysregulation of miRNA expression associates with the development and progression of NSCLC. AIMS: To emphasize a variety of tissue-specific miRNAs, circulating miRNAs and miRNA-derived exosomes could be used as potential diagnostic and therapeutic biomarkers in NSCLC patients...
October 8, 2017: Cell Proliferation
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