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MicroRNA sequencing

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https://www.readbyqxmd.com/read/28813447/the-use-of-high-throughput-small-rna-sequencing-reveals-differentially-expressed-micrornas-in-response-to-aster-yellows-phytoplasma-infection-in-vitis-vinifera-cv-chardonnay
#1
Marius C Snyman, Marie-Chrystine Solofoharivelo, Rose Souza-Richards, Dirk Stephan, Shane Murray, Johan T Burger
Phytoplasmas are cell wall-less plant pathogenic bacteria responsible for major crop losses throughout the world. In grapevine they cause grapevine yellows, a detrimental disease associated with a variety of symptoms. The high economic impact of this disease has sparked considerable interest among researchers to understand molecular mechanisms related to pathogenesis. Increasing evidence exist that a class of small non-coding endogenous RNAs, known as microRNAs (miRNAs), play an important role in post-transcriptional gene regulation during plant development and responses to biotic and abiotic stresses...
2017: PloS One
https://www.readbyqxmd.com/read/28812395/current-research-on-circular-rnas-associated-with-colorectal-cancer
#2
Penghui Wang, Xiaodong He
Representing a novel type of endogenous noncoding RNAs, circular RNAs (circRNAs) have recently gained much attention for their involvement in multiple biological processes. CircRNAs are ubiquitously expressed in eukaryotic cells and modulate gene expression by acting as sponges of microRNAs (miRNAs) or other proteins, such as RNA-binding proteins (RBPs). Due to their unique structure, circRNAs are more stable than linear RNAs. Expression profiles of circRNAs are associated with clinicopathological characteristics of colorectal cancer patients, such as differentiation, TNM classification and distant metastasis...
August 16, 2017: Scandinavian Journal of Gastroenterology
https://www.readbyqxmd.com/read/28811555/identification-of-novel-micrornas-in-the-sheep-heart-and-their-regulation-in-heart-failure
#3
Lee Lee Wong, Miriam T Rademaker, Eng Leng Saw, Kar Sheng Lew, Leigh J Ellmers, Christopher J Charles, Arthur Mark Richards, Peipei Wang
Study of microRNA (miRNAs) using sheep models is limited due to lack of miRNA information. We therefore investigated oar-miRNAs and their regulation in an ovine model of heart failure (HF). Left ventricular (LV) tissue was collected from normal (Cont), HF (LV pacing @ ~220bpm for 13-days) and HF-recovery sheep (HF-R, 26-days after pacing cessation). MiRNA expression was profiled using next-generation sequencing (NGS) and miRNA array, and validated by stem-loop qPCR. Detected sequences were mapped against the ovine genome (Oar v4...
August 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28811264/protein-coding-genes-as-hosts-for-noncoding-rna-expression
#4
REVIEW
Vincent Boivin, Gabrielle Deschamps-Francoeur, Michelle S Scott
With the emergence of high-throughput sequence characterization methods and the subsequent improvements in gene annotations, it is becoming increasingly clear that a large proportion of eukaryotic protein-coding genes (as many as 50% in human) serve as host genes for non-coding RNA genes. Amongst the most extensively characterized embedded non-coding RNA genes, small nucleolar RNAs and microRNAs represent abundant families. Encoded individually or clustered, in sense or antisense orientation with respect to their host and independently expressed or dependent on host expression, the genomic characteristics of embedded genes determine their biogenesis and the extent of their relationship with their host gene...
August 12, 2017: Seminars in Cell & Developmental Biology
https://www.readbyqxmd.com/read/28810930/sex-differences-in-microrna-mrna-networks-examination-of-novel-epigenetic-programming-mechanisms-in-the-sexually-dimorphic-neonatal-hypothalamus
#5
Christopher P Morgan, Tracy L Bale
BACKGROUND: Sexual differentiation of the male brain, and specifically the stress circuitry in the hypothalamus, is primarily driven by estrogen exposure during the perinatal period. Surprisingly, this single hormone promotes diverse programs of sex-specific development that vary widely between different cell types and across the developing male brain. The complexity of this phenomenon suggests that additional layers of gene regulation, including microRNAs (miRNAs), must act downstream of estrogen to mediate this specificity...
August 15, 2017: Biology of Sex Differences
https://www.readbyqxmd.com/read/28809941/analysis-of-agoshrna-maturation-and-loading-into-ago2
#6
Alex Harwig, Zita Kruize, Zhenhuang Yang, Tobias Restle, Ben Berkhout
The RNA interference (RNAi) pathway was recently expanded by the discovery of multiple alternative pathways for processing of natural microRNA (miRNA) and man-made short hairpin RNA (shRNA) molecules. One non-canonical pathway bypasses Dicer cleavage and requires instead processing by Argonaute2 (Ago2), which also executes the subsequent silencing step. We named these molecules AgoshRNA, which generate only a single active RNA strand and thus avoid off-target effects that can be induced by the passenger strand of a regular shRNA...
2017: PloS One
https://www.readbyqxmd.com/read/28809475/a-dna-fueled-and-catalytic-molecule-machine-lights-up-trace-under-expressed-micrornas-in-living-cells
#7
Daxiu Li, Wenjiao Zhou, Ruo Yuan, Yun Xiang
The detection of specific intracellular microRNAs (miRNAs) in living cells can potentially provide insight into the causal mechanism of cancer metastasis and invasion. However, due to the characteristic nature of miRNAs in terms of small sizes, low abundance and similarity among family members, it is of great challenge to monitor miRNAs in living cells, especially those with much lower expression levels. In this work, we describe the establishment of a DNA-fueled and catalytic molecule machinery in cell signal amplification approach for monitoring trace and under-expressed miRNAs in living cells...
August 15, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28808963/extraction-and-qpcr-based-detection-of-mirnas-from-cultured-pbmcs-of-bubaline-origin
#8
Chandra S Mukhopadhyay, Ramneek Verma, Jasdeep Singh
MicroRNAs are small noncoding but functionally important RNA molecules that are involved in regulating diverse cellular, metabolic, and immune processes. Their small size necessitates modification in traditional acid phenol-chloroform based RNA isolation procedures to get highly enriched fraction of small RNA that includes miRNAs and siRNAs . Further, of the different methods available, real-time PCR is a powerful tool for precise and specific detection and quantification of miRNA. Moreover, real-time PCR is used to validate the screening or expression of miRNAs that are discovered during high-throughput sequencing, or microarray analysis...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28808767/identification-and-expression-analysis-of-micrornas-during-ovule-development-in-rice-oryza-sativa-by-deep-sequencing
#9
Ya Wu, Liyu Yang, Meiling Yu, Jianbo Wang
MicroRNA (miRNA) expression profiles during rice ovule development revealed the possible miRNA-mediated regulation between ovule sporophytic tissue and female gametophyte and the involvement of miRNAs in programmed cell death. MiRNAs are 20-24-nucleotide small RNAs that play key roles in the regulation of many growth and developmental processes in plants. Rice ovule development comprises a series of biological events, which are regulated by complex molecular mechanisms. To gain insight into miRNA-mediated regulation of rice ovule development, Illumina sequencing was used to examine the expression of miRNAs from the megaspore mother cell meiosis stage to the fertilized ovule stage...
August 14, 2017: Plant Cell Reports
https://www.readbyqxmd.com/read/28808643/polymorphism-rs16917496-at-the-mir-502-binding-site-of-the-lysine-methyltransferase-5a-set8-and-its-correlation-with-colorectal-cancer-in-iranians
#10
Meysam Mosallayi, Miganoosh Simonian, Sharifeh Khosravi, Ahmad Reza Salehi, Mahsa Khodadoostan, Vahid Sebghatollahi, Azar Baradaran, Rasoul Salehi
BACKGROUND: One of the gene expression regulatory mechanisms is mediated by small noncoding RNAs called microRNA (miRNA). They interact with a recognition sequence located mostly in 3'-untranslated regions (3'-UTRs) of mRNAs. Polymorphisms in miRNAs recognition sequences could affect gene expression which in turn may alter disease susceptibility. SET8, a member of the SET domain-containing methyltransferase, acts in a variety of biological processes such as genomic stability. Here, we report correlation of rs16917496 polymorphism, located in the recognition sequence of miR-502 within 3'-UTR of SET8, with colorectal cancer (CRC) in Iranians...
2017: Advanced Biomedical Research
https://www.readbyqxmd.com/read/28808237/coding-and-small-non-coding-transcriptional-landscape-of-tuberous-sclerosis-complex-cortical-tubers-implications-for-pathophysiology-and-treatment
#11
James D Mills, Anand M Iyer, Jackelien van Scheppingen, Anika Bongaarts, Jasper J Anink, Bart Janssen, Till S Zimmer, Wim G Spliet, Peter C van Rijen, Floor E Jansen, Martha Feucht, Johannes A Hainfellner, Pavel Krsek, Josef Zamecnik, Katarzyna Kotulska, Sergiusz Jozwiak, Anna Jansen, Lieven Lagae, Paolo Curatolo, David J Kwiatkowski, R Jeroen Pasterkamp, Ketharini Senthilkumar, Lars von Oerthel, Marco F Hoekman, Jan A Gorter, Peter B Crino, Angelika Mühlebner, Brendon P Scicluna, Eleonora Aronica
Tuberous Sclerosis Complex (TSC) is a rare genetic disorder that results from a mutation in the TSC1 or TSC2 genes leading to constitutive activation of the mechanistic target of rapamycin complex 1 (mTORC1). TSC is associated with autism, intellectual disability and severe epilepsy. Cortical tubers are believed to represent the neuropathological substrates of these disabling manifestations in TSC. In the presented study we used high-throughput RNA sequencing in combination with systems-based computational approaches to investigate the complexity of the TSC molecular network...
August 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28805722/estrogen-repression-of-micrornas-is-associated-with-high-guanine-content-in-the-terminal-loop-sequences-of-their-precursors
#12
Amit Cohen, Mario Alberto Burgos-Aceves, Tamar Kahan, Yoav Smith
Widespread microRNA (miRNA) repression is a phenomenon observed in mammals after exposure to cigarette smoke and in many types of cancer. A comprehensive reduction in miRNA expression after treatment with the hormone estrogen has also previously been described. Here, we reveal a conserved association of miRNA downregulation after estrogen exposure in zebrafish, mouse, and human breast cancer cell line, with a high guanine content in the terminal loop sequences of their precursors, and offer a possible link between estrogen-related miRNA-adducts formation and carcinogenesis...
August 14, 2017: Biomedicines
https://www.readbyqxmd.com/read/28804724/microrna-regulation-of-glycolytic-metabolism-in-glioblastoma
#13
REVIEW
Huda Alfardus, Alan McIntyre, Stuart Smith
Glioblastoma (GBM) is the most aggressive and common malignant brain tumour in adults. A well-known hallmark of GMB and many other tumours is aerobic glycolysis. MicroRNAs (miRNAs) are a class of short nonprotein coding sequences that exert posttranscriptional controls on gene expression and represent critical regulators of aerobic glycolysis in GBM. In GBM, miRNAs regulate the expression of glycolytic genes directly and via the regulation of metabolism-associated tumour suppressors and oncogenic signalling pathways...
2017: BioMed Research International
https://www.readbyqxmd.com/read/28803958/identification-and-characterization-of-lymph-organ-micrornas-in-red-swamp-crayfish-procambarus-clarkii-infected-with-white-spot-syndrome-virus
#14
Zhi-Qiang Du, Xiao-Yun Leng, Xiu-Li Shen, Yan-Hui Jin, Xin-Cang Li
MicroRNAs (miRNAs) were important post-transcriptional regulators and played vital roles in innate immunity system of invertebrates, especially in the aspect of antivirus. In this study, using high-throughput small RNAs Illumina sequencing system, differently expressed miRNAs (DEMs) from lymph organs in red swamp crayfish, Procambarus clarkii, infected with white spot syndrome virus, were identified. As a result, 32 known miRNAs and 7 novel miRNAs were identified in crayfish lymph organ small RNAs library of NG and WG...
August 10, 2017: Fish & Shellfish Immunology
https://www.readbyqxmd.com/read/28803886/a-method-for-extracting-and-characterizing-rna-from-urine-for-downstream-pcr-and-rnaseq-analysis
#15
Kun Zhou, Monique A Spillman, Kian Behbakht, Julia M Komatsu, Juan E Abrahante, Douglas Hicks, Brent Schotl, Evan Odean, Kenneth L Jones, Michael W Graner, Lynne T Bemis
Readily accessible samples such as urine or blood are seemingly ideal for differentiating and stratifying patients; however, it has proven a daunting task to identify reliable biomarkers in such samples. Noncoding RNA holds great promise as a source of biomarkers distinguishing physiologic wellbeing or illness. Current methods to isolate and characterize RNA molecules in urine are limited. In this proof of concept study, we present a method to extract and identify small noncoding RNAs in urine. Initially, quantitative reverse transcription PCR was applied to confirm the presence of microRNAs in total RNA extracted from urine...
August 10, 2017: Analytical Biochemistry
https://www.readbyqxmd.com/read/28803540/preparation-of-highly-multiplexed-small-rna-sequencing-libraries
#16
Helena Persson, Rolf Søkilde, Anna Chiara Pirona, Carlos Rovira
MicroRNAs (miRNAs) are ~22-nucleotide-long small non-coding RNAs that regulate the expression of protein-coding genes by base pairing to partially complementary target sites, preferentially located in the 3´ untranslated region (UTR) of target mRNAs. The expression and function of miRNAs have been extensively studied in human disease, as well as the possibility of using these molecules as biomarkers for prognostication and treatment guidance. To identify and validate miRNAs as biomarkers, their expression must be screened in large collections of patient samples...
August 1, 2017: BioTechniques
https://www.readbyqxmd.com/read/28802563/metabolic-circuit-involving-free-fatty-acids-microrna-122-and-triglyceride-synthesis-in-liver-and-muscle-tissues
#17
Chofit Chai, Mila Rivkin, Liav Berkovits, Alina Simerzin, Elina Zorde-Khvalevsky, Nofar Rosenberg, Shiri Klein, Dayana Yaish, Ronen Durst, Shoshana Shpitzen, Shiran Udi, Joseph Tam, Joerg Heeren, Anna Worthmann, Christoph Schramm, Johannes Kluwe, Revital Ravid, Eran Hornstein, Hilla Giladi, Eithan Galun
BACKGROUND & AIMS: Effective treatments are needed for hepatic steatosis characterized by accumulation of triglycerides in hepatocytes, which leads to hepatocellular carcinoma. MicroRNA 122 (MIR122) is expressed only in the liver, where it regulates lipid metabolism. We investigated the mechanism by which free fatty acids (FFAs) regulate MIR122 expression and the effect of MIR122 on triglyceride synthesis. METHODS: We analyzed MIR122 promoter activity and validated its target mRNAs by transfection of luciferase reporter plasmids into Huh7, BNL-1ME, and HEK293 cultured cell lines...
August 9, 2017: Gastroenterology
https://www.readbyqxmd.com/read/28802262/small-noncoding-rna-expression-during-extreme-anoxia-tolerance-of-annual-killifish-austrofundulus-limnaeus-embryos
#18
Claire Louise Riggs, Jason E Podrabsky
Small noncoding RNAs (sncRNA) have recently emerged as specific and rapid regulators of gene expression, involved in a myriad of cellular and organismal processes. MicroRNAs, a class of sncRNAs, are differentially expressed in diverse taxa in response to environmental stress, including anoxia. In most vertebrates, a brief period of oxygen deprivation results in severe tissue damage or death. Studies on sncRNA and anoxia have focused on these anoxia-sensitive species. Studying sncRNAs in anoxia-tolerant organisms may provide insight into adaptive mechanisms supporting anoxia tolerance...
August 11, 2017: Physiological Genomics
https://www.readbyqxmd.com/read/28801229/immunomodulation-a-definitive-role-of-microrna-142
#19
REVIEW
Salil Sharma
Majority of microRNAs are evolutionarily conserved in vertebrates. This is suggestive of their similar roles in regulation of gene networks. In addition to their conserved mature sequences and regulatory roles, a few microRNAs show very cell or tissue specific expression. These microRNAs are highly enriched in some cell types or organs. One such microRNA is microRNA-142 (miR-142). The classical stem-loop structure of miR142 encodes for two species of mature microRNAs; miR142-5p and miR142-3p. MiR-142 is abundant in cells of hematopoietic origin, and therefore, aptly plays a role in lineage differentiation of hematopoietic cells...
August 9, 2017: Developmental and Comparative Immunology
https://www.readbyqxmd.com/read/28800319/mir-503-3p-induces-apoptosis-of-lung-cancer-cells-by-regulating-p21-and-cdk4-expression
#20
Yi Sun, Li Li, Shigang Xing, Yinghua Pan, Yunxiang Shi, Linghua Zhang, Qiang Shen
Studies have shown that microRNAs (miRNAs) can promote or suppress tumor growth and therefore act as targets for cancer therapy. Hsa-miR-503-5p, a mature miRNA derived from 5' ends of pre-miR-503, has been proved to regulate cell proliferation, transformation, migration and invasion. However, the biological function of miR-503-3p derived from 3' ends of pre-miR-503 has never been reported. In current study, we found that miR-503-3p inhibits lung cancer cell viability and induces cell apoptosis. To better understand the molecular mechanism underlying the miR-503-3p participating in this process, PCR array and RNA-sequencing (RNA-seq) were performed and some differential expression genes were discovered between NC and miR-503-3p treated groups...
July 28, 2017: Cancer Biomarkers: Section A of Disease Markers
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