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microRNA biogenesis

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https://www.readbyqxmd.com/read/28087842/novel-determinants-of-mammalian-primary-microrna-processing-revealed-by-systematic-evaluation-of-hairpin-containing-transcripts-and-human-genetic-variation
#1
Christine Anne Roden, Jonathan Gaillard, Shaveta Kanoria, William Rennie, Syndi Barish, Jijun Cheng, Wen Pan, Jun Liu, Chris Cotsapas, Ye Ding, Jun Lu
Mature microRNAs (miRNAs) are processed from hairpin-containing primary miRNAs (pri-miRNAs). However, rules that distinguish pri-miRNAs from other hairpin-containing transcripts in the genome are incompletely understood. By developing a computational pipeline to systematically evaluate 30 structural and sequence features of mammalian RNA hairpins, we report several new rules that are preferentially utilized in miRNA hairpins and govern efficient pri-miRNA processing. We propose that a hairpin stem length of 36+/-3nt is optimal for pri-miRNA processing...
January 13, 2017: Genome Research
https://www.readbyqxmd.com/read/28087411/aspirin-prevents-tnf-%C3%AE-induced-endothelial-cell-dysfunction-by-regulating-the-nf-%C3%AE%C2%BAb-dependent-mir-155-enos-pathway-role-of-a-mir-155-enos-axis-in-preeclampsia
#2
Joohwan Kim, Kyu-Sun Lee, Ji-Hee Kim, Dong-Keon Lee, Minsik Park, Seunghwan Choi, Wonjin Park, Suji Kim, Yoon Kyoung Choi, Jong Yun Hwang, Jongseon Choe, Moo-Ho Won, Dooil Jeoung, Hansoo Lee, Sungwoo Ryoo, Kwon-Soo Ha, Young-Guen Kwon, Young-Myeong Kim
Preeclampsia is an inflammatory disease with endothelial cell dysfunction that occurs via decreased endothelial nitric oxide synthase/nitric oxide (eNOS/NO) activity. Aspirin reduces the incidence of hypertensive pregnancy complications. However, the underlying mechanism has not been clearly explained. Here, we found that tumor necrosis factor (TNF)-α, microRNA (miR)-155, and eNOS levels as well as endothelial redox phenotype were differentially regulated in preeclamptic patients, implying the involvement of TNF-α- and redox signal-mediated miR-155 biogenesis and eNOS downregulation in the pathogenesis of preeclampsia...
January 10, 2017: Free Radical Biology & Medicine
https://www.readbyqxmd.com/read/28074552/validation-of-microrna-pathway-polymorphisms-in-esophageal-adenocarcinoma-survival
#3
Olusola O Faluyi, Lawson Eng, Xin Qiu, Jiahua Che, Qihuang Zhang, Dangxiao Cheng, Nanjiao Ying, Alvina Tse, Qin Kuang, Lorin Dodbiba, Daniel J Renouf, Sharon Marsh, Sevtap Savas, Helen J Mackay, Jennifer J Knox, Gail E Darling, Rebecca K S Wong, Wei Xu, Abul Kalam Azad, Geoffrey Liu
Polymorphisms in miRNA and miRNA pathway genes have been previously associated with cancer risk and outcome, but have not been studied in esophageal adenocarcinoma outcomes. Here, we evaluate candidate miRNA pathway polymorphisms in esophageal adenocarcinoma prognosis and attempt to validate them in an independent cohort of esophageal adenocarcinoma patients. Among 231 esophageal adenocarcinoma patients of all stages/treatment plans, 38 candidate genetic polymorphisms (17 biogenesis, 9 miRNA targets, 5 pri-miRNA, 7 pre-miRNA) were genotyped and analyzed...
January 11, 2017: Cancer Medicine
https://www.readbyqxmd.com/read/28072411/the-early-growth-response-protein-1-mir-30a-5p-neurogenic-differentiation-factor-1-axis-as-a-novel-biomarker-for-schizophrenia-diagnosis-and-treatment-monitoring
#4
S Liu, F Zhang, Y Y Shugart, L Yang, X Li, Z Liu, N Sun, C Yang, X Guo, J Shi, L Wang, L Cheng, K Zhang, T Yang, Y Xu
To date, diagnosis of schizophrenia is still based on clinical interviews and careful observations, which is subjective and variable, and can lead to misdiagnosis and/or delay in diagnosis. As early intervention in schizophrenia is important in improving outcomes, objective tests that can be used for schizophrenia diagnosis or treatment monitoring are thus in great need. MicroRNAs (miRNAs) negatively regulate target gene expression and their biogenesis is tightly controlled by various factors including transcription factors (TFs)...
January 10, 2017: Translational Psychiatry
https://www.readbyqxmd.com/read/28049499/circular-rnas-in-cancer-an-emerging-key-player
#5
REVIEW
Yeping Dong, Dan He, Zhenzi Peng, Wei Peng, Wenwen Shi, Jun Wang, Bin Li, Chunfang Zhang, Chaojun Duan
Circular RNAs (circRNAs) are a class of endogendous RNAs that form a covalently closed continuous loop and exist extensively in mammalian cells. Majority of circRNAs are conserved across species and often show tissue/developmental stage-specific expression. CircRNAs were first thought to be the result of splicing error; however, subsequent research shows that circRNAs can function as microRNA (miRNA) sponges and regulate splicing and transcription. Emerging evidence shows that circRNAs possess closely associated with human diseases, especially cancers, and may serve as better biomarkers...
January 3, 2017: Journal of Hematology & Oncology
https://www.readbyqxmd.com/read/28025059/microrna-206-prevents-hepatosteatosis-and-hyperglycemia-by-facilitating-insulin-signaling-and-impairing-lipogenesis
#6
Heng Wu, Tianpeng Zhang, Fei Pan, Clifford J Steer, Zhuoyu Li, Xin Chen, Guisheng Song
BACKGROUND & AIMS: The paradox of selective hepatic insulin resistance, wherein the insulin-resistant liver fails to suppress glucose production but continues to produce lipids, has been central to the pathophysiology of hepatosteatosis and hyperglycemia. Our study was designed to investigate the mechanism(s) by which microRNA-206 alleviates the pathogenesis of hepatosteatosis and hyperglycemia. METHODS: Dietary obese mice induced by a high fat diet were used to study the role of microRNA-206 in the pathogenesis of hepatosteatosis and hyperglycemia...
December 23, 2016: Journal of Hepatology
https://www.readbyqxmd.com/read/28018143/emerging-functions-of-circular-rnas
#7
REVIEW
Mariela Cortés-López, Pedro Miura
Many thousands of Circular RNAs (circRNAs) have recently been identified in metazoan genomes by transcriptome-wide sequencing. Most circRNAs are generated by back-splicing events from exons of protein-coding genes. A great deal of progress has recently been made in understanding the genome-wide expression patterns, biogenesis, and regulation of circRNAs. To date, however, few functions of circRNAs have been identified. CircRNAs are preferentially expressed in neural tissues and some are found at synapses, suggesting possible functions in the nervous system...
December 2016: Yale Journal of Biology and Medicine
https://www.readbyqxmd.com/read/28010188/the-in-vivo-genetic-toolkit-for-studying-expression-and-functions-of-drosophila-melanogaster-micrornas
#8
Hina Iftikhar, Janna N Schultzhaus, Chloe J Bennett, Ginger E Carney
Since the initial reports that a group of small RNAs, now known as microRNAs (miRNAs), regulates gene expression without being translated into proteins, there has been an explosion of studies on these important expression modulators. Drosophila melanogaster has proven to be one of the most amenable animal models for investigations of miRNA biogenesis and gene regulatory activities. Here, we highlight the publicly available genetic tools and strategies for in vivo functional studies of miRNA activity in D. melanogaster...
December 23, 2016: RNA Biology
https://www.readbyqxmd.com/read/28006752/regulation-of-mirnas-by-herbal-medicine-an-emerging-field-in-cancer-therapies
#9
REVIEW
Ali Mohammadi, Behzad Mansoori, Behzad Baradaran
MicroRNAs' expression profiles have recently gained major attention as far as cancer research is concerned. MicroRNAs are able to inhibit target gene expression via binding to the 3' UTR of target mRNA, resulting in target mRNA cleavage or translation inhibition. MicroRNAs play significant parts in a myriad of biological processes; studies have proven, on the other hand, that aberrant microRNA expression is, more often than not, associated with the growth and progression of cancers. MicroRNAs could act as oncogenes (oncomir) or tumor suppressors and can also be utilized as biomarkers for diagnosis, prognosis, and cancer therapy...
December 19, 2016: Biomedicine & Pharmacotherapy, Biomédecine & Pharmacothérapie
https://www.readbyqxmd.com/read/27999330/dysregulated-microrna-expression-profiles-and-potential-cellular-circulating-and-polymorphic-biomarkers-in-non-hodgkin-lymphoma
#10
REVIEW
Gabrielle Bradshaw, Heidi G Sutherland, Larisa M Haupt, Lyn R Griffiths
A large number of studies have focused on identifying molecular biomarkers, including microRNAs (miRNAs) to aid in the diagnosis and prognosis of the most common subtypes of non-Hodgkin lymphoma (NHL), Diffuse Large B-cell Lymphoma and Follicular Lymphoma. NHL is difficult to diagnose and treat with many cases becoming resistant to chemotherapy, hence the need to identify improved biomarkers to aid in both diagnosis and treatment modalities. This review summarises more recent research on the dysregulated miRNA expression profiles found in NHL, as well as the regulatory role and biomarker potential of cellular and circulating miRNAs found in tissue and serum, respectively...
December 17, 2016: Genes
https://www.readbyqxmd.com/read/27994142/regulatory-module-involving-fgf13-mir-504-and-p53-regulates-ribosomal-biogenesis-and-supports-cancer-cell-survival
#11
Débora R Bublik, Slađana Bursać, Michal Sheffer, Ines Oršolić, Tali Shalit, Ohad Tarcic, Eran Kotler, Odelia Mouhadeb, Yonit Hoffman, Gilad Fuchs, Yishai Levin, Siniša Volarević, Moshe Oren
The microRNA miR-504 targets TP53 mRNA encoding the p53 tumor suppressor. miR-504 resides within the fibroblast growth factor 13 (FGF13) gene, which is overexpressed in various cancers. We report that the FGF13 locus, comprising FGF13 and miR-504, is transcriptionally repressed by p53, defining an additional negative feedback loop in the p53 network. Furthermore, we show that FGF13 1A is a nucleolar protein that represses ribosomal RNA transcription and attenuates protein synthesis. Importantly, in cancer cells expressing high levels of FGF13, the depletion of FGF13 elicits increased proteostasis stress, associated with the accumulation of reactive oxygen species and apoptosis...
December 19, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27992407/lin28-phosphorylation-by-mapk-erk-couples-signalling-to-the-post-transcriptional-control-of%C3%A2-pluripotency
#12
Kaloyan M Tsanov, Daniel S Pearson, Zhaoting Wu, Areum Han, Robinson Triboulet, Marc T Seligson, John T Powers, Jihan K Osborne, Susan Kane, Steven P Gygi, Richard I Gregory, George Q Daley
Signalling and post-transcriptional gene control are both critical for the regulation of pluripotency, yet how they are integrated to influence cell identity remains poorly understood. LIN28 (also known as LIN28A), a highly conserved RNA-binding protein, has emerged as a central post-transcriptional regulator of cell fate through blockade of let-7 microRNA biogenesis and direct modulation of mRNA translation. Here we show that LIN28 is phosphorylated by MAPK/ERK in pluripotent stem cells, which increases its levels via post-translational stabilization...
January 2017: Nature Cell Biology
https://www.readbyqxmd.com/read/27973704/crosstalk-between-hippo-signalling-and-mirnas-in-tumour-progression
#13
REVIEW
Nianshuang Li, Chuan Xie, Nonghua Lu
The Hippo signalling pathway co-ordinately modulates cell regeneration and organ size, and its deregulation contributes to tumourigenesis through many cellular processes, including over-proliferation, apoptosis resistance, and cell migration. Recent discoveries have shed new light on how microRNAs (miRNAs) are closely linked to the Hippo pathway in tumour progression. Hippo signalling has been reported to affect widespread miRNA biogenesis. In turn, several miRNAs regulate Hippo signalling, which contributes to carcinogenesis...
December 14, 2016: FEBS Journal
https://www.readbyqxmd.com/read/27957388/microrna-biogenesis-pathway-genes-polymorphisms-and-cancer-risk-a-systematic-review-and-meta-analysis
#14
Jieyu He, Jun Zhao, Wenbo Zhu, Daxun Qi, Lina Wang, Jinfang Sun, Bei Wang, Xu Ma, Qiaoyun Dai, Xiaojin Yu
MicroRNAs (miRNAs) may promote the development and progression of human cancers. Therefore, components of the miRNA biogenesis pathway may play critical roles in human cancer. Single nucleotide polymorphisms (SNPs) or mutations in genes involved in the miRNA biogenesis pathway may alter levels of gene expression, affecting disease susceptibility. Results of previous studies on genetic variants in the miRNA biogenesis pathway and cancer risk were inconsistent. Therefore, a meta-analysis is needed to assess the associations of these genetic variants with human cancer risk...
2016: PeerJ
https://www.readbyqxmd.com/read/27943457/the-functions-of-plant-small-rnas-in-development-and-in-stress-responses
#15
Shengjun Li, Claudia Castillo-Gonzalez, Bin Yu, Xiuren Zhang
Like metazoans, plants use small regulatory RNAs (sRNAs) to direct gene expression. Several classes of sRNAs, which are distinguished by their origin and biogenesis, exist in plants. Among them, microRNAs (miRNAs) and trans-acting small interfering RNAs (ta-siRNAs) mainly inhibit gene expression at post-transcriptional levels. In the past decades, plant miRNAs and ta-siRNAs have been shown to be essential for numerous developmental processes, including growth and development of shoots, leaves, flowers, roots, and seeds among others...
December 10, 2016: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/27941687/low-dose-methylmercury-induced-genes-regulate-mitochondrial-biogenesis-via-mir-25-in-immortalized-human-embryonic-neural-progenitor-cells
#16
Xinjin Wang, Mengling Yan, Lina Zhao, Qing Wu, Chunhua Wu, Xiuli Chang, Zhijun Zhou
Mitochondria are essential organelles and important targets for environmental pollutants. The detection of mitochondrial biogenesis and generation of reactive oxygen species (ROS) and p53 levels following low-dose methylmercury (MeHg) exposure could expand our understanding of underlying mechanisms. Here, the sensitivity of immortalized human neural progenitor cells (ihNPCs) upon exposure to MeHg was investigated. We found that MeHg altered cell viability and the number of 5-ethynyl-2'-deoxyuridine (EdU)-positive cells...
December 9, 2016: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/27938667/biogenesis-of-phased-sirnas-on-membrane-bound-polysomes-in-arabidopsis
#17
Shengben Li, Brandon Le, Xuan Ma, Shaofang Li, Chenjiang You, Yu Yu, Bailong Zhang, Lin Liu, Lei Gao, Ting Shi, Yonghui Zhao, Beixin Mo, Xiaofeng Cao, Xuemei Chen
Small RNAs are central players in RNA silencing, yet their cytoplasmic compartmentalization and the effects it may have on their activities have not been studied at the genomic scale. Here we report that Arabidopsis microRNAs (miRNAs) and small interfering RNAs (siRNAs) are distinctly partitioned between the endoplasmic reticulum (ER) and cytosol. All miRNAs are associated with membrane-bound polysomes (MBPs) as opposed to polysomes in general. The MBP association is functionally linked to a deeply conserved and tightly regulated activity of miRNAs - production of phased siRNAs (phasiRNAs) from select target RNAs...
December 12, 2016: ELife
https://www.readbyqxmd.com/read/27935420/the-epigenetic-regulation-of-dicer-and-microrna-biogenesis-by-panobinostat
#18
Nicholas C Hoffend, William J Magner, Thomas B Tomasi
microRNAs (miRs) are small noncoding RNAs that regulate/fine tune many cellular protein networks by targeting mRNAs for either degradation or translational inhibition. Dicer, a type III endoribonuclease, is a critical component in miR biogenesis and is required for mature mRNA production. Abnormal Dicer expression occurs in numerous cancer types and correlates with poor patient prognosis. Recent reports have demonstrated that epigenetic agents, including histone deacetylase inhibitors (HDACi), may regulate Dicer and miR expression...
December 9, 2016: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/27934859/trbp-ensures-efficient-dicer-processing-of-precursor-microrna-in-rna-crowded-environments
#19
Mohamed Fareh, Kyu-Hyeon Yeom, Anna C Haagsma, Sweeny Chauhan, Inha Heo, Chirlmin Joo
The RNA-binding protein TRBP is a central component of the Dicer complex. Despite a decade of biochemical and structural studies, the essential functionality of TRBP in microRNA (miRNA) biogenesis remains unknown. Here we show that TRBP is an integral cofactor for time-efficient Dicer processing in RNA-crowded environments. We competed for Dicer processing of pre-miRNA with a large amount of cellular RNA species and found that Dicer-TRBP, but not Dicer alone, remains resilient. To apprehend the mechanism of this substrate selectivity, we use single-molecule fluorescence...
December 9, 2016: Nature Communications
https://www.readbyqxmd.com/read/27929436/comparison-of-small-rna-profiles-of-glycine-max-and-glycine-soja-at-early-developmental-stages
#20
Yuzhe Sun, Zeta Mui, Xuan Liu, Aldrin Kay-Yuen Yim, Hao Qin, Fuk-Ling Wong, Ting-Fung Chan, Siu-Ming Yiu, Hon-Ming Lam, Boon Leong Lim
Small RNAs, including microRNAs (miRNAs) and phased small interfering RNAs (phasiRNAs; from PHAS loci), play key roles in plant development. Cultivated soybean, Glycine max, contributes a great deal to food production, but, compared to its wild kin, Glycine soja, it may lose some genetic information during domestication. In this work, we analyzed the sRNA profiles of different tissues in both cultivated (C08) and wild soybeans (W05) at three stages of development. A total of 443 known miRNAs and 15 novel miRNAs showed varying abundances between different samples, but the miRNA profiles were generally similar in both accessions...
December 6, 2016: International Journal of Molecular Sciences
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