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miRNA biogenesis

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https://www.readbyqxmd.com/read/29327403/biogenesis-and-regulatory-hierarchy-of-phased-small-interfering-rnas-in-plants
#1
REVIEW
Pingchuan Deng, Sajid Muhammad, Min Cao, Liang Wu
Several varieties of small RNAs including microRNAs (miRNAs) and small interfering RNAs (siRNAs) are generated in plants to regulate development, genome stability, and response to adverse environments. Phased siRNA (phasiRNA) is a type of secondary siRNA that is processed from a miRNA-mediated cleavage of RNA transcripts, increasing silencing efficiency or simultaneously suppressing multiple target genes. Trans-acting siRNAs (ta-siRNAs) are a particular class of phasiRNA produced from non-coding transcripts that silence targets in trans...
January 11, 2018: Plant Biotechnology Journal
https://www.readbyqxmd.com/read/29322448/characterization-of-circular-rnas-circrna-associated-with-the-translation-machinery
#2
Deniz Bartsch, Anne Zirkel, Leo Kurian
A substantial proportion of the currently annotated genes in eukaryotes are proposed to function as RNA molecules (>200 bp) with no significant protein coding potential, currently classified as long noncoding RNAs (lncRNA). A distinct subgroup of lncRNAs is circular RNAs (circRNAs), which can be easily identified by unique junction reads, resulting from their biogenesis. CircRNAs are largely cytosolic and thought to either code for micro-peptides or facilitate gene regulation by sequestering microRNAs (miRNAs) or RNA-binding proteins (RBPs) from their targets...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29317340/the-microrna-landscape-of-cutaneous-squamous-cell-carcinoma
#3
REVIEW
Kathryn Konicke, Argelia Lopez, José Luis Muñoz, Luis Steven Servin, Armando Flores, Edit Olasz, Zelmira Lazarova
Cutaneous squamous cell carcinoma (cSCC) is a keratinocyte-derived skin tumor. It is the second-most-common cancer affecting the Caucasian population and is responsible for >20% of all skin-cancer-related deaths. The estimated incidence of non-melanoma skin cancer in the USA is >1000000 cases per year, of which roughly 20-30% are squamous cell carcinoma. To better understand and treat this challenging cancer, current research focuses on development of novel strategies to improve the understanding of tumor biogenesis on an individual basis...
January 6, 2018: Drug Discovery Today
https://www.readbyqxmd.com/read/29301498/pcaf-mediated-acetylation-of-lin28b-increases-let-7-biogenesis-in-lung-adenocarcinoma-h1299-cells
#4
Ting-Ting Qu, Fei Chen, Jing Wang, Yan-Jun Zhang, Mo-Bin Cheng, Wen-Zheng Sun, Yu-Fei Shen, Ye Zhang
BACKGROUND: Lin28B and its paralog Lin28A are small RNA binding proteins that have similar inhibitory effects, although they target separate steps in the maturation of let-7 miRNAs in mammalian cells. Because Lin28B participates in the promotion and development of tumors mostly by blocking the let-7 tumor suppressor family members, we sought to explore the associated mechanisms to gain insights into how Lin28B might be decreased in human cancer cells to increase let-7 levels and reverse malignancy...
January 4, 2018: BMC Cancer
https://www.readbyqxmd.com/read/29281264/piwi-interacting-rna-in-drosophila-biogenesis-transposon-regulation-and-beyond
#5
Haruna Yamashiro, Mikiko C Siomi
PIWI-interacting RNAs (piRNAs) are germline-enriched small RNAs that control transposons to maintain genome integrity. To achieve this, upon being processed from piRNA precursors, most of which are transcripts of intergenic piRNA clusters, piRNAs bind PIWI proteins, germline-specific Argonaute proteins, to form effector complexes. The mechanism of this piRNA-mediated transposon silencing pathway is fundamentally similar to that of siRNA/miRNA-dependent gene silencing in that a small RNA guides its partner Argonaute protein to target gene transcripts for repression via RNA-RNA base pairing...
December 27, 2017: Chemical Reviews
https://www.readbyqxmd.com/read/29280958/development-of-novel-therapeutic-agents-by-inhibition-of-oncogenic-micrornas
#6
REVIEW
Dinh-Duc Nguyen, Suhwan Chang
MicroRNAs (miRs, miRNAs) are regulatory small noncoding RNAs, with their roles already confirmed to be important for post-transcriptional regulation of gene expression affecting cell physiology and disease development. Upregulation of a cancer-causing miRNA, known as oncogenic miRNA, has been found in many types of cancers and, therefore, represents a potential new class of targets for therapeutic inhibition. Several strategies have been developed in recent years to inhibit oncogenic miRNAs. Among them is a direct approach that targets mature oncogenic miRNA with an antisense sequence known as antimiR, which could be an oligonucleotide or miRNA sponge...
December 27, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29276984/genetic-polymorphisms-offer-insight-into-the-causal-role-of-microrna-in-coronary-artery-disease
#7
REVIEW
Andrea Borghini, Maria Grazia Andreassi
There is growing interest in the potential of circulating microRNAs (miRNAs), a class of small and noncoding RNA molecules, as diagnostic and/or prognostic biomarkers in coronary artery disease (CAD). Despite this promising role, there are still widespread inconsistencies among studies, and important obstacles must be overcome before miRNAs can enter clinical practice. The study of single nucleotide polymorphisms (SNPs) in the miRNA regulatory network could help shed light on the causality of associations as well as validate the value of cardiovascular miRNAs...
December 15, 2017: Atherosclerosis
https://www.readbyqxmd.com/read/29260525/-the-association-between-the-polymorphisms-of-mirna-biogenesis-related-genes-dicer-drosha-and-ran-and-unexplained-recurrent-spontaneous-abortion-in-chinese-women
#8
Mei Fu, Wen-Ming Xu, Tai-Zhou Qin, Ke-Hui Xu
OBJECTIVE: To explore the association between polymorphisms of miRNA biogenesis related gene DICER,DROSHA,RAN and unexplained recurrent spontaneous abortion (URSA) in Chinese women. METHODS: We recruited 217 patients with URSA (URSA group) and 390 healthy controls who were fertile women with history of more than one successful pregnancy outcome (control group) from June 2013 to December 2015 in the West China Second University Hospital of Sichuan University. The control group was recruited from regular physical examination and prepregnancy check for women of childbearing age during the same period...
November 2017: Sichuan da Xue Xue Bao. Yi Xue Ban, Journal of Sichuan University. Medical Science Edition
https://www.readbyqxmd.com/read/29258963/secretory-micrornas-as-biomarkers-of-cancer
#9
REVIEW
Kazuharu Kai, Rachel L Dittmar, Subrata Sen
MicroRNAs (miRNAs) are small, non-coding RNAs that regulate gene expression predominantly by inhibiting transcription and/or promoting degradation of target mRNAs also in addition to being involved in non-canonical mechanisms regulating transcription, translation and cell signaling processes. Extracellular secretory miRNAs, either in complex with specific proteins or encapsulated in microvesicles called exosomes, are transported between cells as means of intercellular communication. Secretory miRNAs in circulation remain functional after delivery to recipient cells, regulating target genes and their corresponding signaling pathways...
December 16, 2017: Seminars in Cell & Developmental Biology
https://www.readbyqxmd.com/read/29246022/tumor-derived-exosomes-in-colorectal-cancer-progression-and-their-clinical-applications
#10
REVIEW
Jianbiao Zhou, Xiao-Lan Li, Zhi-Rong Chen, Wee-Joo Chng
Colorectal cancer (CRC) ranks as the third leading cause of cancer mortality in both of men and women worldwide due to its metastatic properties and resistance to current treatment. Recent studies have shown that tumor-derived exosomes play emerging roles in the development of cancer. Exosomes are nano-sized extracellular vesicles (EVs) that contain lipids, proteins, DNAs, and RNA species (mRNA, miRNA, long non-coding RNA). These exosomal cargos can be transferred locally and systemically, after taken by recipient cells, so exosomes represent a new form of intercellular communication...
November 21, 2017: Oncotarget
https://www.readbyqxmd.com/read/29244865/the-arabidopsis-thaliana-f-box-gene-hawaiian-skirt-is-a-new-player-in-the-microrna-pathway
#11
Xuebin Zhang, Dasuni Jayaweera, Janny L Peters, Judit Szecsi, Mohammed Bendahmane, Jeremy A Roberts, Zinnia H González-Carranza
In Arabidopsis, the F-box HAWAIIAN SKIRT (HWS) protein is important for organ growth. Loss of function of HWS exhibits pleiotropic phenotypes including sepal fusion. To dissect the HWS role, we EMS-mutagenized hws-1 seeds and screened for mutations that suppress hws-1 associated phenotypes. We identified shs-2 and shs-3 (suppressor of hws-2 and 3) mutants in which the sepal fusion phenotype of hws-1 was suppressed. shs-2 and shs-3 (renamed hst-23/hws-1 and hst-24/hws-1) carry transition mutations that result in premature terminations in the plant homolog of Exportin-5 HASTY (HST), known to be important in miRNA biogenesis, function and transport...
2017: PloS One
https://www.readbyqxmd.com/read/29236291/dysregulation-of-microrna-biogenesis-machinery-and-microrna-rna-ratio-in-skeletal-muscle-of-amyotrophic-lateral-sclerosis-mice
#12
Aaron P Russell, Lobna Ghobrial, Shyuan Ngo, Justin Yerbury, Evelyn Zacharewicz, Roger Chung, Séverine Lamon
INTRODUCTION: The pathology of amyotrophic lateral sclerosis (ALS) is associated with impaired RNA processing and microRNA (miRNA) dysregulation. Here we investigate the regulation of the members of the miRNA biogenesis pathways and total miRNA levels at different stages of the disease. METHODS: Muscle, brain, and spinal cord tissue were obtained from presymptomatic, symptomatic, and end-stage superoxide dismutase 1 (SOD1)G93A mice. miRNA and transcript levels were measured by quantitative polymerase chain reaction...
December 13, 2017: Muscle & Nerve
https://www.readbyqxmd.com/read/29233923/the-landscape-of-mirna-editing-in-animals-and-its-impact-on-mirna-biogenesis-and-targeting
#13
Lishi Li, Yulong Song, Xinrui Shi, Jianheng Liu, Shaolei Xiong, Wanying Chen, Qiang Fu, Zichao Huang, Nannan Gu, Rui Zhang
Adenosine-to-inosine (A-to-I) RNA editing regulates miRNA biogenesis and function. To date, fewer than 160 miRNA editing sites have been identified. Here, we present a quantitative atlas of miRNA A-to-I editing through the profiling of 201 pri-miRNA samples and 4694 mature miRNA samples in human, mouse, and Drosophila. We identified 4162 sites present in ∼80% of the pri-miRNAs and 574 sites in mature miRNAs. miRNA editing is prevalent in many tissue types in human. However, high-level editing is mostly found in neuronal tissues in mouse and Drosophila Interestingly, the edited miRNAs in neuronal and non-neuronal tissues in human gain two distinct sets of new targets, which are significantly associated with cognitive and organ developmental functions, respectively...
December 12, 2017: Genome Research
https://www.readbyqxmd.com/read/29233922/deep-experimental-profiling-of-microrna-diversity-deployment-and-evolution-across-the-drosophila-genus
#14
Jaaved Mohammed, Alex S Flynt, Alexandra M Panzarino, Md Mosharrof Hussein Mondal, Matthew DeCruz, Adam Siepel, Eric C Lai
To assess miRNA evolution across the Drosophila genus, we analyzed several billion small RNA reads across 12 fruit fly species. These data permit comprehensive curation of species- and clade-specific variation in miRNA identity, abundance, and processing. Among well-conserved miRNAs, we observed unexpected cases of clade-specific variation in 5' end precision, occasional antisense loci, and putatively noncanonical loci. We also used strict criteria to identify a large set (649) of novel, evolutionarily restricted miRNAs...
December 12, 2017: Genome Research
https://www.readbyqxmd.com/read/29230098/circular-rnas-a-novel-type-of-non-coding-rna-and-their-potential-implications-in-antiviral-immunity
#15
REVIEW
Man Wang, Fei Yu, Wei Wu, Yuan Zhang, Wenguang Chang, Murugavel Ponnusamy, Kun Wang, Peifeng Li
Circular RNAs (circRNAs), a novel type of non-coding RNAs (ncRNAs), are ubiquitously expressed in eukaryotic cells during post-transcriptional processes. Unlike linear RNAs, circRNAs form covalent-closed continuous loops without 5' to 3' polarities and poly (A) tails. With advances in high-throughput sequencing technology, numerous circRNAs have been identified in plants, animals and humans. Notably, circRNAs display cell-type, tissue-type and developmental-stage specific expression patterns in eukaryotic transcriptome, which reveals their significant regulatory functions in gene expression...
2017: International Journal of Biological Sciences
https://www.readbyqxmd.com/read/29219950/exosomes-new-molecular-targets-of-diseases
#16
REVIEW
Saheli Samanta, Sheeja Rajasingh, Nicholas Drosos, Zhigang Zhou, Buddhadeb Dawn, Johnson Rajasingh
Extracellular vesicles (EVs) comprise apoptotic bodies, microvesicles and exosomes, and they perform as key regulators in cell-to-cell communication in normal as well as diseased states. EVs contain natural cargo molecules, such as miRNA, mRNA and proteins, and transfer these functional cargos to neighboring cells or more distant cells through circulation. These functionally active molecules then affect distinct signaling cascades. The message conveyed to the recipient cells is dependent upon the composition of the EV, which is determined by the parent cell and the EV biogenesis...
December 7, 2017: Acta Pharmacologica Sinica
https://www.readbyqxmd.com/read/29215721/the-biological-roles-and-clinical-implications-of-micrornas-in-clear-cell-renal-cell-carcinoma
#17
REVIEW
Ying-Hua He, Chen Chen, Zheng Shi
Clear cell renal cell carcinoma (ccRCC) accounts for about 3% of tumors in adults as well as 85% of all primary renal carcinoma. And it is the third most predominant urological carcinoma, but it has the maximum mortality rate. Early diagnosis and proper follow-up of ccRCC patients may improve the prognosis of the illness. Thus, it is imperative to understand the new biomarkers of ccRCC and study new method for the modern therapy of this deadly disease. Furthermore, a large number of microRNAs (miRNAs), small non-coding RNAs, have been relevant to tumor type, stage, or survival and miRNAs might be progressed as the markers of diagnosis or prognosis in ccRCC...
December 7, 2017: Journal of Cellular Physiology
https://www.readbyqxmd.com/read/29197026/an-expression-atlas-of-mirnas-in-arabidopsis-thaliana
#18
Le Xu, Yugang Hu, Ying Cao, Jingrui Li, Ligeng Ma, Yan Li, Yijun Qi
MicroRNAs (miRNAs) are small non-coding RNAs that regulate a variety of biological processes. MiRNA expression often exhibits spatial and temporal specificity. However, genome-wide miRNA expression patterns in different organs during development of Arabidopsis thaliana have not yet been systemically investigated. In this study, we sequenced small RNA libraries generated from 27 different organ/tissue types, which cover the entire life cycle of Arabidopsis. Analysis of the sequencing data revealed that most miRNAs are ubiquitously expressed, whereas a small set of miRNAs display highly specific expression patterns...
November 29, 2017: Science China. Life Sciences
https://www.readbyqxmd.com/read/29187591/microrna-dynamics-at-the-onset-of-primordial-germ-and-somatic-cells-sex-differentiation-during-mouse-embryonic-gonad-development
#19
Daniel Fernandez-Perez, Miguel Angel Brieño-Enriquez, Javier Isoler-Alcaraz, Eduardo Larriba, Jesus Del Mazo
IIn mammals, commitment and specification of germ cell lines implies involves complex programs that include sex differentiation, control of proliferation and meiotic initiation. Regulation of these processes is genetically controlled by fine-tuned mechanisms of gene regulation in which microRNAs (miRNAs) are involved. We have characterized, by small-RNAseq and bioinformatics analyses, the miRNA expression patterns of male and female mouse Primordial Germ Cells (PGCs) and gonadal somatic cells at embryonic stages: E11...
November 29, 2017: RNA
https://www.readbyqxmd.com/read/29171334/g-quadruplexes-influence-pri-microrna-processing
#20
Samuel G Rouleau, Jean-Michel Garant, François Bolduc, Martin Bisaillon, Jean-Pierre Perreault
RNA G-Quadruplexes (G4) have been shown to possess many biological functions, including the regulation of microRNA (miRNA) biogenesis and function. However, their impact on pri-miRNA processing remains unknown. We identified G4 located near the Drosha cleavage site in three distinct pri-miRNAs: pri-mir200c, pri-mir451a, and pri-mir497. The folding of the potential G4 motifs was determined in solution. Subsequently, mutations disrupting G4 folding led to important changes in the mature miRNAs levels in cells...
December 11, 2017: RNA Biology
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