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https://www.readbyqxmd.com/read/29144434/the-role-of-non-coding-rnas-in-cytoplasmic-male-sterility-in-flowering-plants
#1
REVIEW
Helena Štorchová
The interactions between mitochondria and nucleus substantially influence plant development, stress response and morphological features. The prominent example of a mitochondrial-nuclear interaction is cytoplasmic male sterility (CMS), when plants produce aborted anthers or inviable pollen. The genes responsible for CMS are located in mitochondrial genome, but their expression is controlled by nuclear genes, called fertility restorers. Recent explosion of high-throughput sequencing methods enabled to study transcriptomic alterations in the level of non-coding RNAs under CMS biogenesis...
November 16, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29138420/expression-of-both-poly-r-c-binding-protein-1-pcbp1-and-mirna-3978-is-suppressed-in-peritoneal-gastric-cancer-metastasis
#2
Fu-Jian Ji, Yuan-Yu Wu, Zhe An, Xue-Song Liu, Jun-Nan Jiang, Fang-Fang Chen, Xue-Dong Fang
The expression of legumain which has been shown overexpressed in patients with metastatic gastric cancer is positively correlated to both disease progression and outcome, and negatively correlated to microRNA (miR)-3978 expression. The RNA-binding protein, poly r(C) binding protein 1 (PCBP1) was the most downregulated protein in the metastatic tissue specimens. Quantitative real-time PCR showed that PCBP1 expression is transcriptionally downregulated in peritoneal metastasis tissues. RNA immunoprecipitation experiments showed that PCBP1 and miR-3978 are sequestered in normal peritoneal tissue, but the complex is disrupted following metastatic progression...
November 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29126230/a-survey-of-software-tools-for-microrna-discovery-and-characterization-using-rna-seq
#3
Michele Bortolomeazzi, Enrico Gaffo, Stefania Bortoluzzi
Since the small RNA-sequencing (sRNA-seq) technology became available, it allowed the discovery of thousands new microRNAs (miRNAs) in humans and many other species, providing new data on these small RNAs (sRNAs) of high biological and translational relevance. MiRNA discovery has not yet reached saturation, even in the most studied model organisms, and many researchers are using sRNA-seq in studies with different aims in biomedicine, fundamental research and in applied animal sciences. We review several miRNA discovery and characterization software tools that implement different strategies, providing a useful guide for researchers to select the programs best suiting their study objectives and data...
November 6, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/29115582/passenger-strand-of-mir-145-3p-acts-as-a-tumor-suppressor-by-targeting-myo1b-in-head-and-neck-squamous-cell-carcinoma
#4
Yasutaka Yamada, Keiichi Koshizuka, Toyoyuki Hanazawa, Naoko Kikkawa, Atsushi Okato, Tetsuya Idichi, Takayuki Arai, Sho Sugawara, Koji Katada, Yoshitaka Okamoto, Naohiko Seki
Analysis of the microRNA (miRNA) expression signature of head and neck squamous cell carcinoma (HNSCC) based on RNA sequencing showed that dual strands of pre‑miR‑145 (miR‑145‑5p, guide strand; and miR‑145‑3p, passenger strand) were significantly reduced in cancer tissues. In miRNA biogenesis, passenger strands of miRNAs are degraded and have no biological activities in cells. The aims of this study were to investigate the functional significance of the passenger strand of miR‑145 and to identify miR‑145‑3p‑regulated oncogenic genes in HNSCC cells...
November 6, 2017: International Journal of Oncology
https://www.readbyqxmd.com/read/29114080/a-role-for-the-f-box-protein-hawaiian-skirt-in-plant-microrna-function
#5
Patricia L M Lang, Michael D Christie, Ezgi S Dogan, Rebecca Schwab, Jörg Hagmann, Anna-Lena Van de Weyer, Detlef Weigel, Emanuele Scacchi
As regulators of gene expression in multicellular organisms, microRNAs (miRNAs) are crucial for growth and development. While a plethora of factors involved in their biogenesis and action in Arabidopsis thaliana has been described, these processes and their fine-tuning are not fully understood. Here, we used plants expressing an artificial miRNA target mimic (MIM) to screen for negative regulators of miR156. We identified a new mutant allele of the F-box gene HAWAIIAN SKIRT (HWS; At3G61590), hws-5, as a suppressor of the MIM156-induced developmental and molecular phenotypes...
November 7, 2017: Plant Physiology
https://www.readbyqxmd.com/read/29114017/a-microrna-feedback-loop-regulates-global-microrna-abundance-during-aging
#6
Sachi Inukai, Zachary Pincus, Alexandre de Lencastre, Frank J Slack
Expression levels of many microRNAs (miRNAs) change during aging, notably declining globally in a number of organisms and tissues across taxa. However, little is known about the mechanisms or the biological relevance for this change. We investigated the network of genes that controls miRNA transcription and processing during C. elegans aging. We found that miRNA biogenesis genes are highly networked with transcription factors and aging-associated miRNAs. In particular, miR-71, known to influence lifespan and itself upregulated during aging, represses alg-1/Argonaute expression post-transcriptionally during aging...
November 7, 2017: RNA
https://www.readbyqxmd.com/read/29109687/low-intensity-ultrasound-induced-anti-inflammatory-effects-are-mediated-by-several-new-mechanisms-including-gene-induction-immunosuppressor-cell-promotion-and-enhancement-of-exosome-biogenesis-and-docking
#7
Qian Yang, Gayani K Nanayakkara, Charles Drummer, Yu Sun, Candice Johnson, Ramon Cueto, Hangfei Fu, Ying Shao, Luqiao Wang, William Y Yang, Peng Tang, Li-Wen Liu, Shuping Ge, Xiao-Dong Zhou, Mohsin Khan, Hong Wang, Xiaofeng Yang
Background: Low-intensity ultrasound (LIUS) was shown to be beneficial in mitigating inflammation and facilitating tissue repair in various pathologies. Determination of the molecular mechanisms underlying the anti-inflammatory effects of LIUS allows to optimize this technique as a therapy for the treatment of malignancies and aseptic inflammatory disorders. Methods: We conducted cutting-edge database mining approaches to determine the anti-inflammatory mechanisms exerted by LIUS. Results: Our data revealed following interesting findings: (1) LIUS anti-inflammatory effects are mediated by upregulating anti-inflammatory gene expression; (2) LIUS induces the upregulation of the markers and master regulators of immunosuppressor cells including MDSCs (myeloid-derived suppressor cells), MSCs (mesenchymal stem cells), B1-B cells and Treg (regulatory T cells); (3) LIUS not only can be used as a therapeutic approach to deliver drugs packed in various structures such as nanobeads, nanospheres, polymer microspheres, and lipidosomes, but also can make use of natural membrane vesicles as small as exosomes derived from immunosuppressor cells as a novel mechanism to fulfill its anti-inflammatory effects; (4) LIUS upregulates the expression of extracellular vesicle/exosome biogenesis mediators and docking mediators; (5) Exosome-carried anti-inflammatory cytokines and anti-inflammatory microRNAs inhibit inflammation of target cells via multiple shared and specific pathways, suggesting exosome-mediated anti-inflammatory effect of LIUS feasible; and (6) LIUS-mediated physical effects on tissues may activate specific cellular sensors that activate downstream transcription factors and signaling pathways...
2017: Frontiers in Physiology
https://www.readbyqxmd.com/read/29109067/the-insertion-in-the-double-stranded-rna-binding-domain-of-human-drosha-is-important-for-its-function
#8
Xiaoxiao Zhang, Peng Li, Jian Lin, Haochu Huang, Bin Yin, Yan Zeng
microRNAs (miRNAs) are first transcribed as long, primary transcripts, which are then processed by multiple enzymes and proteins to generate the single-stranded, approximately 22-nucleotide (nt)-long mature miRNAs. A critical step in animal miRNA biogenesis is the cleavage of primary miRNA transcripts (pri-miRNAs) to produce precursor miRNAs (pre-miRNAs) by the enzyme Drosha. How Drosha recognizes its substrates remains incompletely understood. In this study we constructed a series of human Drosha mutants and examined their enzymatic activities and interaction with RNAs...
November 3, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/29107738/extracellular-vesicles-released-from-mesenchymal-stromal-cells-stimulate-bone-growth-in-osteogenesis-imperfecta
#9
Satoru Otsuru, Laura Desbourdes, Adam J Guess, Ted J Hofmann, Theresa Relation, Takashi Kaito, Massimo Dominici, Masahiro Iwamoto, Edwin M Horwitz
BACKGROUND: Systemic infusion of mesenchymal stromal cells (MSCs) has been shown to induce acute acceleration of growth velocity in children with osteogenesis imperfecta (OI) despite minimal engraftment of infused MSCs in bones. Using an animal model of OI we have previously shown that MSC infusion stimulates chondrocyte proliferation in the growth plate and that this enhanced proliferation is also observed with infusion of MSC conditioned medium in lieu of MSCs, suggesting that bone growth is due to trophic effects of MSCs...
October 26, 2017: Cytotherapy
https://www.readbyqxmd.com/read/29107112/the-emerging-role-of-exosome-derived-non-coding-rnas-in-cancer-biology
#10
Qing Fan, Liang Yang, Xiaodong Zhang, Xueqiang Peng, Shibo Wei, Dongming Su, Zhenhua Zhai, Xiangdong Hua, Hangyu Li
Exosomes are a new means of intercellular information exchange that have aroused great research interest. Long neglected in research, exosomes were deemed nonfunctional cellular components to be discarded. However, it has been gradually revealed that exosomes are an important tool for the exchange of intercellular information and material. Exosomes contain specific repertoires of non-coding RNAs (ncRNAs, including microRNA and lncRNA), indicating that a specific RNA sorting mechanism may exist. Correspondingly, intracellular multivesicular bodies (MVBs) are produced after fusion with the cell membrane to release exosomes rather than inducing autophagy, which reveals that there may be a specific regulatory mechanism for MVB secretion...
October 26, 2017: Cancer Letters
https://www.readbyqxmd.com/read/29098629/exosomes-mediate-the-beneficial-effects-of-exercise
#11
Yangxin Li, Chaoshan Han, Juanjuan Wang, Jin Zhou, Chun Liang, Kasturi Ranganna, Yao-Hua Song
It is known that moderate exercise can prevent the development of cardiovascular diseases, but the exact molecular mechanisms mediating cardioprotective effect of exercise remain unknown. Emerging evidence suggests that exercise has great impact on the biogenesis of exosomes, which have been found in both interstitial fluid and circulation, and play important roles in cellular communication. Exosomes carry functional molecules such as mRNAs, microRNA, and specific proteins, which can be used in the early diagnosis and targeted therapy of a variety of diseases...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/29074849/the-circular-rna-circbirc6-participates-in-the-molecular-circuitry-controlling-human-pluripotency
#12
Chun-Ying Yu, Tung-Cheng Li, Yi-Ying Wu, Chan-Hsien Yeh, Wei Chiang, Ching-Yu Chuang, Hung-Chih Kuo
Accumulating evidence indicates that circular RNAs (circRNAs) are abundant in the human transcriptome. However, their involvement in biological processes, including pluripotency, remains mostly undescribed. We identified a subset of circRNAs that are enriched in undifferentiated human embryonic stem cells (hESCs) and demonstrated that two, circBIRC6 and circCORO1C, are functionally associated with the pluripotent state. Mechanistically, we found that circBIRC6 is enriched in the AGO2 complex and directly interacts with microRNAs, miR-34a, and miR-145, which are known to modulate target genes that maintain pluripotency...
October 27, 2017: Nature Communications
https://www.readbyqxmd.com/read/29063445/il-17-exerts-anti-apoptotic-effect-via-mir-155-5p-downregulation-in-experimental-autoimmune-encephalomyelitis
#13
Dominika Ksiazek-Winiarek, Piotr Szpakowski, Malgorzata Turniak, Janusz Szemraj, Andrzej Glabinski
Multiple sclerosis is an autoimmune, neurodegenerative disease, affecting mostly young adults and resulting in progressive disability. It is a multifactorial disorder, with important involvement of both cellular and epigenetic components. Among the epigenetic factors, microRNAs are currently intensively investigated in the context of multiple sclerosis. It has been shown that their biogenesis and function may be regulated by various cytokines. IL-17, a hallmark cytokine of Th17 cells, has been thought to function predominantly as a pro-inflammatory factor, leading to increased disease symptoms...
October 23, 2017: Journal of Molecular Neuroscience: MN
https://www.readbyqxmd.com/read/29050335/evidence-for-the-association-of-chromatin-and-microrna-regulation-in-the-human-genome
#14
Bang-Bao Tao, Xi-Qiang Liu, Wenhao Zhang, Shu Li, Dong Dong, Mang Xiao, Jun Zhong
Both microRNAs (miRNAs) and chromatin regulation play important roles in cellular processes and they function at different regulatory levels of transcription. Although efforts have been devoted to the investigation of miRNA and chromatin regulation, there's still no comprehensive work to illustrate their relationships due tothe lack of whole-genome wide datasets in different human cellular contexts. Based on the recently published large-scale epigenetic data, we examined the association between miRNA and epigenetic machinery...
September 19, 2017: Oncotarget
https://www.readbyqxmd.com/read/29049738/a-genome-wide-scan-for-microrna-related-genetic-variants-associated-with-primary-open-angle-glaucoma
#15
Mohsen Ghanbari, Adriana I Iglesias, Henriët Springelkamp, Cornelia M van Duijn, M Arfan Ikram, Abbas Dehghan, Stefan J Erkeland, Caroline C W Klaver, Magda A Meester-Smoor
Purpose: To identify microRNAs (miRNAs) involved in primary open-angle glaucoma (POAG), using genetic data. MiRNAs are small noncoding RNAs that posttranscriptionally regulate gene expression. Genetic variants in miRNAs or miRNA-binding sites within gene 3'-untranslated regions (3'UTRs) are expected to affect miRNA function and contribute to disease risk. Methods: Data from the recent genome-wide association studies on intraocular pressure, vertical cup-to-disc ratio (VCDR), cupa area and disc area were used to investigate the association of miRNAs with POAG endophenotypes...
October 1, 2017: Investigative Ophthalmology & Visual Science
https://www.readbyqxmd.com/read/29048752/the-how-and-where-of-plant-micrornas
#16
REVIEW
Yu Yu, Tianran Jia, Xuemei Chen
Contents Summary I. II. III. IV. References SUMMARY: MicroRNAs (miRNAs) are small non-coding RNAs, of typically 20-24 nt, that regulate gene expression post-transcriptionally through sequence complementarity. Since the identification of the first miRNA, lin-4, in the nematode Caenorhabditis elegans in 1993, thousands of miRNAs have been discovered in animals and plants, and their regulatory roles in numerous biological processes have been uncovered. In plants, research efforts have established the major molecular framework of miRNA biogenesis and modes of action, and are beginning to elucidate the mechanisms of miRNA degradation...
October 19, 2017: New Phytologist
https://www.readbyqxmd.com/read/29045748/conserved-asymmetry-underpins-homodimerization-of-dicer-associated-double-stranded-rna-binding-proteins
#17
Alex Heyam, Claire E Coupland, Clément Dégut, Ruth A Haley, Nicola J Baxter, Leonhard Jakob, Pedro M Aguiar, Gunter Meister, Michael P Williamson, Dimitris Lagos, Michael J Plevin
Double-stranded RNA-binding domains (dsRBDs) are commonly found in modular proteins that interact with RNA. Two varieties of dsRBD exist: canonical Type A dsRBDs interact with dsRNA, while non-canonical Type B dsRBDs lack RNA-binding residues and instead interact with other proteins. In higher eukaryotes, the microRNA biogenesis enzyme Dicer forms a 1:1 association with a dsRNA-binding protein (dsRBP). Human Dicer associates with HIV TAR RNA-binding protein (TRBP) or protein activator of PKR (PACT), while Drosophila Dicer-1 associates with Loquacious (Loqs)...
October 17, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29042235/splicing-factors-as-regulators-of-mirna-biogenesis-links-to-human-disease
#18
REVIEW
Madara Ratnadiwakara, Monika Mohenska, Minna-Liisa Änkö
MicroRNAs (miRNAs) are small non-coding RNAs that regulate gene expression post-transcriptionally by fine-tuning mRNA levels and translation during development and in adult tissues. miRNAs are transcribed as parts of longer precursors that undergo multiple processing steps before the mature miRNAs reach their target mRNAs in the cytoplasm. In addition to Drosha/DGCR8 and Dicer that are the essential components of the miRNA processing pathway, a range of other RNA binding proteins have recently been implicated in miRNA biogenesis...
October 19, 2017: Seminars in Cell & Developmental Biology
https://www.readbyqxmd.com/read/29036314/mirnovo-genome-free-prediction-of-micrornas-from-small-rna-sequencing-data-and-single-cells-using-decision-forests
#19
Dimitrios M Vitsios, Elissavet Kentepozidou, Leonor Quintais, Elia Benito-Gutiérrez, Stijn van Dongen, Matthew P Davis, Anton J Enright
The discovery of microRNAs (miRNAs) remains an important problem, particularly given the growth of high-throughput sequencing, cell sorting and single cell biology. While a large number of miRNAs have already been annotated, there may well be large numbers of miRNAs that are expressed in very particular cell types and remain elusive. Sequencing allows us to quickly and accurately identify the expression of known miRNAs from small RNA-Seq data. The biogenesis of miRNAs leads to very specific characteristics observed in their sequences...
September 25, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29032146/microrna-single-polynucleotide-polymorphism-influences-on-microrna-biogenesis-and-mrna-target-specificity
#20
REVIEW
Jarosław Króliczewski, Aleksandra Sobolewska, Dawid Lejnowski, James F Collawn, Rafał Bartoszewski
microRNAs (miRNAs) are nowadays recognized as an essential component of gene regulatory networks. Furthermore, deregulation of miRNAs expression often contributes to human pathologies. Recently, a substantial number of single nucleotide polymorphism (SNPs) and rare mutations within pri-, pre- and mature miRNA sequences have been reported. These miRNA SNPs have often been associated with human disease. However, due to the complexity of miRNA biogenesis and the genome-wide functional effects of miRNAs, the determination of biological consequences of these miRNA SNPs remains challenging...
January 15, 2018: Gene
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