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microRNA biogenesis pathway

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https://www.readbyqxmd.com/read/29777751/evaluating-the-susceptibility-of-ago2-loaded-micrornas-to-degradation-by-nucleases-in-vitro
#1
Reyad Elbarbary, Lynne E Maquat
MicroRNAs (miRNAs) comprise a class of small non-coding RNAs that regulate the stability and/or translatability of most protein-coding transcripts. Steady-state levels of mature miRNAs can be controlled through mechanisms that influence their biogenesis and/or decay rates. Pathways that mediate mature miRNA decay are less well understood than those that mediate miRNA biogenesis. We recently described Tudor-staphylococcal/micrococcal-like nuclease (TSN)-mediated miRNA decay (TumiD) as a cellular pathway that promotes the sequence-specific endonucleolytic decay of miRNAs that harbor a CA and/or UA dinucleotide...
May 16, 2018: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/29765080/distinguishing-mirtrons-from-canonical-mirnas-with-data-exploration-and-machine-learning-methods
#2
Grzegorz Rorbach, Olgierd Unold, Bogumil M Konopka
Mirtrons are non-canonical microRNAs encoded in introns the biogenesis of which starts with splicing. They are not processed by Drosha and enter the canonical pathway at the Exportin-5 level. Mirtrons are much less evolutionary conserved than canonical miRNAs. Due to the differences, canonical miRNA predictors are not applicable to mirtron prediction. Identification of differences is important for designing mirtron prediction algorithms and may help to improve the understanding of mirtron functioning. So far, only simple, single-feature comparisons were reported...
May 15, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29764990/ire1%C3%AE-prevents-hepatic-steatosis-by-processing-and-promoting-the-degradation-of-select-micrornas
#3
Jie-Mei Wang, Yining Qiu, Zhao Yang, Hyunbae Kim, Qingwen Qian, Qinghua Sun, Chunbin Zhang, Lei Yin, Deyu Fang, Sung Hong Back, Randal J Kaufman, Ling Yang, Kezhong Zhang
Obesity or a high-fat diet represses the endoribonuclease activity of inositol-requiring enzyme 1α (IRE1α), a transducer of the unfolded protein response (UPR) in cells under endoplasmic reticulum (ER) stress. An impaired UPR is associated with hepatic steatosis and nonalcoholic fatty liver disease (NAFLD), which is caused by lipid accumulation in the liver. We found that IRE1α was critical to maintaining lipid homeostasis in the liver by repressing the biogenesis of microRNAs (miRNAs) that regulate lipid mobilization...
May 15, 2018: Science Signaling
https://www.readbyqxmd.com/read/29749606/interactions-between-short-and-long-noncoding-rnas
#4
REVIEW
Igor Ulitsky
It is now evident that noncoding RNAs play key roles in regulatory networks determining cell fate and behavior, in a myriad of different conditions, and across all species. Among these noncoding RNAs are short RNAs, such as microRNAs, snoRNAs, and piRNAs, and the functions of those are relatively well understood. Other noncoding RNAs are longer, and their modes of action and functions are also increasingly explored and deciphered. Short RNAs and long noncoding RNAs (lncRNAs) interact with each other with reciprocal consequences for their fates and functions...
May 10, 2018: FEBS Letters
https://www.readbyqxmd.com/read/29718424/psrnatarget-a-plant-small-rna-target-analysis-server-2017-release
#5
Xinbin Dai, Zhaohong Zhuang, Patrick Xuechun Zhao
Plant regulatory small RNAs (sRNAs), which include most microRNAs (miRNAs) and a subset of small interfering RNAs (siRNAs), such as the phased siRNAs (phasiRNAs), play important roles in regulating gene expression. Although generated from genetically distinct biogenesis pathways, these regulatory sRNAs share the same mechanisms for post-translational gene silencing and translational inhibition. psRNATarget was developed to identify plant sRNA targets by (i) analyzing complementary matching between the sRNA sequence and target mRNA sequence using a predefined scoring schema and (ii) by evaluating target site accessibility...
April 30, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29706542/cryo-em-structure-of-human-dicer-and-its-complexes-with-a-pre-mirna-substrate
#6
Zhongmin Liu, Jia Wang, Hang Cheng, Xin Ke, Lei Sun, Qiangfeng Cliff Zhang, Hong-Wei Wang
Human Dicer (hDicer) is a multi-domain protein belonging to the RNase III family. It plays pivotal roles in small RNA biogenesis during the RNA interference (RNAi) pathway by processing a diverse range of double-stranded RNA (dsRNA) precursors to generate ∼22 nt microRNA (miRNA) or small interfering RNA (siRNA) products for sequence-directed gene silencing. In this work, we solved the cryoelectron microscopy (cryo-EM) structure of hDicer in complex with its cofactor protein TRBP and revealed the precise spatial arrangement of hDicer's multiple domains...
April 20, 2018: Cell
https://www.readbyqxmd.com/read/29697794/non-coding-rnas-in-endometriosis-a-narrative-review
#7
Kavita Panir, John E Schjenken, Sarah A Robertson, M Louise Hull
BACKGROUND: Endometriosis is a benign gynaecological disorder, which affects 10% of reproductive-aged women and is characterized by endometrial cells from the lining of the uterus being found outside the uterine cavity. However, the pathophysiological mechanisms causing the development of this heterogeneous disease remain enigmatic, and a lack of effective biomarkers necessitates surgical intervention for diagnosis. There is international recognition that accurate non-invasive diagnostic tests and more effective therapies are urgently needed...
April 25, 2018: Human Reproduction Update
https://www.readbyqxmd.com/read/29697284/biological-and-immunological-aspects-of-iron-deficiency-anemia-in-cancer-development-a-narrative-review
#8
Fatema Zohora, Katayoon Bidad, Zahra Pourpak, Mostafa Moin
Iron Deficiency Anemia (IDA) is a universal health problem and a risk factor for the development of cancer. IDA changes the microenvironment of the human body by affecting both the biological and immunological systems. It increases DNA damage and genomic instability by different mechanisms. IDA is one of the leading causes of the imbalance between different antioxidant enzymes as well as enzymes involved in DNA damage and DNA repair systems of the body. It can affect the biogenesis/expression of microRNAs. IDA interrupts the oxidative phosphorylation energy metabolism and intestinal Cytochrome-P450 systems...
April 26, 2018: Nutrition and Cancer
https://www.readbyqxmd.com/read/29694248/adar1-attenuates-allogeneic-graft-rejection-by-suppressing-mir-21-biogenesis-in-macrophages-and-promoting-m2-polarization
#9
Junjie Li, Jiangang Xie, Shanshou Liu, Xiao Li, Dongliang Zhang, Xianqi Wang, Jinquan Jiang, Wei Hu, Yuan Zhang, Boquan Jin, Ran Zhuang, Wen Yin
ADAR1 (adenosine deaminase acting on double-stranded RNA 1) is an RNA-editing enzyme that mediates adenosine-to-inosine RNA editing events, an important post-transcriptional modification mechanism that can alter the coding properties of mRNA or regulate microRNA biogenesis. ADAR1 also regulates the innate immune response. Here, we have demonstrated that ADAR1 expression increased in LPS-stimulated macrophages. Silencing ADAR1 by using small interfering RNA in macrophages resulted in the pronounced polarization of macrophages to M1, whereas ADAR1 overexpression promoted M2 polarization, which indicated that ADAR1 can inhibit macrophage hyperpolarization and prevent immune hyperactivity...
April 25, 2018: FASEB Journal: Official Publication of the Federation of American Societies for Experimental Biology
https://www.readbyqxmd.com/read/29683487/regulation-of-primary-microrna-processing
#10
REVIEW
Antoine Creugny, Aurélie Fender, Sébastien Pfeffer
MicroRNAs (miRNAs) are evolutionarily conserved small regulatory RNAs that participate in the fine-tuning of many, if not all, fundamental biological processes. Molecular mechanisms involved in miRNA biogenesis and mode of action have been elucidated in the past two decades. Similar to many cellular pathways, miRNA processing and function can be globally or specifically regulated at several levels and by numerous proteins and RNAs. Given their role as fine-tuning molecules, it is essential for miRNA expression to be tightly regulated in order to maintain cellular homeostasis...
April 23, 2018: FEBS Letters
https://www.readbyqxmd.com/read/29674166/microrna-hsa-mir-19b-2-5p-targets-key-mitochondrial-biogenesis-genes-a-bioinformatics-analysis
#11
Sunil Kumar Saini, Ponnusamy Kalaiarasan, Rajnish Kumar Singh, Siddharth Manvati, R N K Bamezai
The present study on the basis of a detailed bioinformatics analysis proposed a potential role of a miRNA, hsa-miR-19b-2-5p, in regulating the mitochondrial biogenesis. The miRNA has shown to be involved in important biological processes of cellular metabolic, cellular macromolecule biosynthetic processes and gene expression pathways. The miRNA, hsa-miR-19b-2-5p, was predicted to regulate the molecular function of nucleic acid, organic/heterocyclic compound, nucleic acid binding transcription factor activity...
April 16, 2018: Mitochondrion
https://www.readbyqxmd.com/read/29615475/micrornas-crucial-regulators-of-placental-development
#12
Heyam Hayder, Jacob O'Brien, Uzma Nadeem, Chun Peng
MicroRNAs (miRNAs) are small non-coding single-stranded RNA that are integral to a wide range of cellular processes mainly through the regulation of translation and mRNA stability of their target genes. The placenta is a transient organ that exists throughout gestation in mammals, facilitating nutrient and gas exchange and waste removal between the mother and the fetus. MiRNAs are expressed in the placenta and many studies have shown that miRNAs play an important role in regulating trophoblast differentiation, migration, invasion, proliferation, apoptosis, vasculogenesis/angiogenesis, and cellular metabolism...
April 3, 2018: Reproduction: the Official Journal of the Society for the Study of Fertility
https://www.readbyqxmd.com/read/29606147/baseline-antibody-profiles-predict-toxicity-in-melanoma-patients-treated-with-immune-checkpoint-inhibitors
#13
Michael F Gowen, Keith M Giles, Danny Simpson, Jeremy Tchack, Hua Zhou, Una Moran, Zarmeena Dawood, Anna C Pavlick, Shaohui Hu, Melissa A Wilson, Hua Zhong, Michelle Krogsgaard, Tomas Kirchhoff, Iman Osman
BACKGROUND: Immune checkpoint inhibitors (anti-CTLA-4, anti-PD-1, or the combination) enhance anti-tumor immune responses, yielding durable clinical benefit in several cancer types, including melanoma. However, a subset of patients experience immune-related adverse events (irAEs), which can be severe and result in treatment termination. To date, no biomarker exists that can predict development of irAEs. METHODS: We hypothesized that pre-treatment antibody profiles identify a subset of patients who possess a sub-clinical autoimmune phenotype that predisposes them to develop severe irAEs following immune system disinhibition...
April 2, 2018: Journal of Translational Medicine
https://www.readbyqxmd.com/read/29599909/rna-binding-protein-auf1-suppresses-mir-122-biogenesis-by-down-regulating-dicer1-in-hepatocellular-carcinoma
#14
Xia Wu, Yingzhuo Yang, Yike Huang, Yang Chen, Tianying Wang, Shuo Wu, Lei Tong, Yan Wang, Lexun Lin, Meili Hao, Zhao-Hua Zhong, Fengmin Zhang, Wenran Zhao
Hepatocellular carcinoma (HCC) is one of the common cancers worldwide, especially in developing countries. Although the chronic infections of hepatitis B and C viruses have been established as the etiological factors of HCC, the mechanism for the tumorigenesis and development of HCC is still unclear. The liver-specific microRNA-122 (miR-122), an established tumor-suppressor miRNA, is often down-regulated in HCC, while the underlying mechanism is not well understood. Here we report that the AU-rich element-binding factor AUF1 suppresses the expression of Dicer1, the type III RNase that is required for microRNA maturation, leading to the inhibited biogenesis of miR-122...
March 13, 2018: Oncotarget
https://www.readbyqxmd.com/read/29530052/exosomal-microrna-32-5p-induces-multidrug-resistance-in-hepatocellular-carcinoma-via-the-pi3k-akt-pathway
#15
Xiao Fu, Mengjie Liu, Shengyang Qu, Jiequn Ma, Yamin Zhang, Tingting Shi, Hongqing Wen, Yujuan Yang, Shuhong Wang, Jing Wang, Kejun Nan, Yu Yao, Tao Tian
BACKGROUND: Multidrug resistance is the main obstacle for hepatocellular carcinoma (HCC) treatment. miR-32-5p is involved in HCC progression but its function in multidrug resistance is still unclear. Here we aim to find out the function of miR-32-5p in inducing multidrug resistance and its underlying mechanisms of transforming sensitive cell to resistant cell. METHODS: We detected the expression of miR-32-5p and PTEN in the multidrug-resistant cell line (Bel/5-FU) and the sensitive cell line (Bel7402), HCC and para-carcinoma liver tissues through real-time PCR...
March 12, 2018: Journal of Experimental & Clinical Cancer Research: CR
https://www.readbyqxmd.com/read/29527542/immunoprecipitation-of-tri-methylated-capped-rna
#16
Karen E Hayes, Jamie A Barr, Mingyi Xie, Joan A Steitz, Ivan Martinez
Cellular quiescence (also known as G0 arrest) is characterized by reduced DNA replication, increased autophagy, and increased expression of cyclin-dependent kinase p27Kip1 . Quiescence is essential for wound healing, organ regeneration, and preventing neoplasia. Previous findings indicate that microRNAs (miRNAs) play an important role in regulating cellular quiescence. Our recent publication demonstrated the existence of an alternative miRNA biogenesis pathway in primary human foreskin fibroblast (HFF) cells during quiescence...
February 5, 2018: Bio-protocol
https://www.readbyqxmd.com/read/29523774/the-multiple-lives-of-dead-box-rna-helicase-dp103-ddx20-gemin3
#17
REVIEW
Frank Curmi, Ruben J Cauchi
Gemin3, also known as DDX20 or DP103, is a DEAD-box RNA helicase which is involved in more than one cellular process. Though RNA unwinding has been determined in vitro , it is surprisingly not required for all of its activities in cellular metabolism. Gemin3 is an essential gene, present in Amoeba and Metazoa. The highly conserved N-terminus hosts the helicase core, formed of the helicase- and DEAD-domains, which, based on crystal structure determination, have key roles in RNA binding. The C-terminus of Gemin3 is highly divergent between species and serves as the interaction site for several accessory factors that could recruit Gemin3 to its target substrates and/or modulate its function...
April 17, 2018: Biochemical Society Transactions
https://www.readbyqxmd.com/read/29522510/coordinated-regulation-of-arabidopsis-microrna-biogenesis-and-red-light-signaling-through-dicer-like-1-and-phytochrome-interacting-factor-4
#18
Zhenfei Sun, Min Li, Ying Zhou, Tongtong Guo, Yin Liu, Hui Zhang, Yuda Fang
Light and microRNAs (miRNAs) are key external and internal signals for plant development, respectively. However, the relationship between the light signaling and miRNA biogenesis pathways remains unknown. Here we found that miRNA processer proteins DCL1 and HYL1 interact with a basic helix-loop-helix (bHLH) transcription factor, phytochrome-interacting factor 4 (PIF4), which mediates the destabilization of DCL1 during dark-to-red-light transition. PIF4 acts as a transcription factor for some miRNA genes and is necessary for the proper accumulation of miRNAs...
March 2018: PLoS Genetics
https://www.readbyqxmd.com/read/29509898/tsc2-regulates-microrna-biogenesis-via-mtorc1-and-gsk3%C3%AE
#19
Barbara Ogórek, Hilaire C Lam, Damir Khabibullin, Heng-Jia Liu, Julie Nijmeh, Robinson Triboulet, David J Kwiatkowski, Richard I Gregory, Elizabeth P Henske
Tuberous sclerosis complex (TSC) is an autosomal dominant disease caused by germline inactivating mutations of TSC1 or TSC2. In TSC-associated tumors of the brain, heart, skin, kidney and lung, inactivation of both alleles of TSC1 or TSC2 leads to hyperactivation of the mTORC1 pathway. The TSC/mTORC1 pathway is a key regulator of cellular processes related to growth, proliferation and autophagy. We and others have previously found that mTORC1 regulates microRNA biogenesis, but the mechanisms are not fully understood...
May 1, 2018: Human Molecular Genetics
https://www.readbyqxmd.com/read/29506672/microrna-based-drugs-for-brain-tumors
#20
REVIEW
Shubaash Anthiya, Audrey Griveau, Claire Loussouarn, Patrick Baril, Martin Garnett, Jean-Paul Issartel, Emmanuel Garcion
MicroRNAs (miRNAs) are key regulatory elements encoded by the genome. A single miRNA can downregulate the expression of multiple genes involved in diverse functions. Because cancer is a disease with multiple gene aberrations, developing novel approaches to identify and modulate miRNA pathways may result in a breakthrough for cancer treatment. With a special focus on glioblastoma (GBM), this review provides an up-to-date summary of miRNA biogenesis, the role of miRNA in cancer resistance, and essential tools for modulating miRNA expression, as well as of clinically promising RNAi delivery systems and how they can be adapted for therapy...
March 2018: Trends in Cancer
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