scholarly journals A non-canonical microRNA derived from the snaR-A non-coding RNA targets a metastasis inhibitor

2021 ◽  
Author(s):  
Daniel Stribling ◽  
Yi Lei ◽  
Casey M Guardia ◽  
Lu Li ◽  
Christopher J Fields ◽  
...  
Keyword(s):  
Bioinformatic Analysis ◽  
Biological Processes ◽  
Analysis Method ◽  
Functional Link ◽  
Small Noncoding Rnas ◽  
Novel Mirna ◽  
Non Coding Rna ◽  
Rna Targets ◽  
Dicer Cleavage ◽  
Metastasis Inhibitor

MicroRNAs (miRNAs) are small noncoding RNAs that function as critical post-transcriptional regulators in various biological processes. While most miRNAs are generated from processing of long primary transcripts via sequential Drosha and Dicer cleavage, some miRNAs that bypass Drosha cleavage can be transcribed as part of another small non-coding RNA. Here, we develop the Target-Oriented miRNA Discovery (TOMiD) bioinformatic analysis method to identify Drosha-independent miRNAs from Argonaute crosslinking and sequencing of hybrids (Ago-CLASH) datasets. Using this technique, we discovered a novel miRNA derived from a primate specific non-coding RNA, the small NF90 associated RNA A (snaR-A). The miRNA derived from snaR-A (miR-snaR) arises independent of Drosha processing, but requires Exportin-5 and Dicer for biogenesis. We identify that miR-snaR is concurrently upregulated with the full snaR-A transcript in cancer cells. Functionally, miR-snaR associates with Ago proteins and targets NME1, a key metastasis inhibitor, contributing to snaR-A's role in promoting cancer cell migration. Our findings suggest a functional link between a novel miRNA and its precursor non-coding RNA.

scholarly journals A non-canonical microRNA derived from the snaR-A non-coding RNA targets a metastasis inhibitor

RNA ◽  
2021 ◽  
pp. rna.078694.121
Author(s):  
Daniel Stribling ◽  
Yi Lei ◽  
Casey M. Guardia ◽  
Lu Li ◽  
Christopher J. Fields ◽  
...  
Keyword(s):  
Non Coding Rna ◽  
Rna Targets ◽  
Metastasis Inhibitor

CASC15：A tumor-associated long non-coding RNA

2020 ◽  
Vol 26 ◽  
Author(s):  
Bei Wang ◽  
Wen Xu ◽  
Yuxuan Cai ◽  
Chong Guo ◽  
Gang Zhou ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Therapeutic Target ◽  
Cancer Colorectal ◽  
Tumor Development ◽  
Pathophysiological Mechanism ◽  
Biological Processes ◽  
Non Coding Rna ◽  
Cancer Côlon ◽  
The Relationship ◽  
Long Non Coding Rna

Background: CASC15, one of long non-coding RNA, is involved in the regulation of many tumor biological processes, and is expected to become a new biological therapeutic target. This paper aims to elucidate the pathophysiological function of CASC15 in various tumors. Methods: The relationship between CASC15 and tumors was analyzed by searching references, and summarizes the specific pathophysiological mechanism of CASC15. Results: LncRNA CASC15 is closely related to tumor development, and has been shown to be abnormally high expressed in all kinds of tumors, including breast cancer, cervical cancer, lung cancer, hepatocellular carcinoma, gastric cancer, bladder cancer, colon cancer, colorectal cancer, cardiac hypertrophy, intrahepatic cholangiocarcinoma, leukemia, melanoma, tongue squamous cell carcinoma, nasopharyngeal carcinoma. However, CASC15 has been found to be downexpressed abnormally in ovarian cancer, glioma and neuroblastoma. Besides, it is identified that CASC15 can affect the proliferation, invasion and apoptosis of tumors. Conclusion: LncRNA CASC15 has the potential to become a new therapeutic target or marker for a variety of tumors.

scholarly journals The Role of Extracellular Vesicles as Shuttles of RNA and Their Clinical Significance as Biomarkers in Hepatocellular Carcinoma

Genes ◽  
2021 ◽  
Vol 12 (6) ◽  
pp. 902
Author(s):  
Eva Costanzi ◽  
Carolina Simioni ◽  
Gabriele Varano ◽  
Cinzia Brenna ◽  
Ilaria Conti ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Extracellular Vesicles ◽  
Tumor Metastasis ◽  
Biological Processes ◽  
Rna Molecules ◽  
Expression Of Genes ◽  
Non Coding Rna ◽  
Donor Cells ◽  
Relevant Role

Extracellular vesicles (EVs) have attracted interest as mediators of intercellular communication following the discovery that EVs contain RNA molecules, including non-coding RNA (ncRNA). Growing evidence for the enrichment of peculiar RNA species in specific EV subtypes has been demonstrated. ncRNAs, transferred from donor cells to recipient cells, confer to EVs the feature to regulate the expression of genes involved in differentiation, proliferation, apoptosis, and other biological processes. These multiple actions require accuracy in the isolation of RNA content from EVs and the methodologies used play a relevant role. In liver, EVs play a crucial role in regulating cell–cell communications and several pathophysiological events in the heterogeneous liver class of cells via horizontal transfer of their cargo. This review aims to discuss the rising role of EVs and their ncRNAs content in regulating specific aspects of hepatocellular carcinoma development, including tumorigenesis, angiogenesis, and tumor metastasis. We analyze the progress in EV-ncRNAs’ potential clinical applications as important diagnostic and prognostic biomarkers for liver conditions.

scholarly journals Molecular Signature of Extracellular Vesicular Small Non-Coding RNAs Derived from Cerebrospinal Fluid of Leptomeningeal Metastasis Patients: Functional Implication of miR-21 and Other Small RNAs in Cancer Malignancy

Cancers ◽  
2021 ◽  
Vol 13 (2) ◽  
pp. 209
Author(s):  
Kyue-Yim Lee ◽  
Yoona Seo ◽  
Ji Hye Im ◽  
Jiho Rhim ◽  
Woosun Baek ◽  
...  
Keyword(s):  
Cerebrospinal Fluid ◽  
Rare Complication ◽  
Leptomeningeal Metastasis ◽  
Molecular Signature ◽  
Definitive Treatment ◽  
Small Nuclear Rna ◽  
Diagnostic Strategies ◽  
Novel Mirna ◽  
Non Coding Rna ◽  
Sequencing Method

Leptomeningeal metastasis (LM) is a fatal and rare complication of cancer in which the cancer spreads via the cerebrospinal fluid (CSF). At present, there is no definitive treatment or diagnosis for this deleterious disease. In this study, we systemically and quantitatively investigated biased expression of key small non-coding RNA (smRNA) subpopulations from LM CSF extracellular vesicles (EVs) via a unique smRNA sequencing method. The analyzed subpopulations included microRNA (miRNA), Piwi-interacting RNA (piRNA), Y RNA, small nuclear RNA (snRNA), small nucleolar RNAs (snoRNA), vault RNA (vtRNA), novel miRNA, etc. Here, among identified miRNAs, miR-21, which was already known to play an essential oncogenic role in tumorigenesis, was thoroughly investigated via systemic biochemical, miR-21 sensor, and physiological cell-based approaches, with the goal of confirming its functionality and potential as a biomarker for the pathogenesis and diagnosis of LM. We herein uncovered LM CSF extravesicular smRNAs that may be associated with LM-related complications and elucidated plausible pathways that may mechanistically contribute to LM progression. In sum, the analyzed smRNA subpopulations will be useful as targets for the development of therapeutic and diagnostic strategies for LM and LM-related complications.

scholarly journals Aberrant activation of non-coding RNA targets of transcriptional elongation complexes contributes to TDP-43 toxicity

2018 ◽  
Vol 9 (1) ◽  
Author(s):  
Chia-Yu Chung ◽  
Amit Berson ◽  
Jason R. Kennerdell ◽  
Ashley Sartoris ◽  
Travis Unger ◽  
...  
Keyword(s):  
Transcriptional Elongation ◽  
Non Coding Rna ◽  
Rna Targets

scholarly journals Consistent global structures of complex RNA states through multidimensional chemical mapping

eLife ◽  
2015 ◽  
Vol 4 ◽  
Author(s):  
Clarence Yu Cheng ◽  
Fang-Chieh Chou ◽  
Wipapat Kladwang ◽  
Siqi Tian ◽  
Pablo Cordero ◽  
...  
Keyword(s):  
Secondary Structure ◽  
3D Structure ◽  
Three Dimensions ◽  
Biological Processes ◽  
Chemical Mapping ◽  
Entry Site ◽  
Tertiary Structures ◽  
Internal Ribosome Entry ◽  
Non Coding Rna ◽  
Paired End Sequencing

Accelerating discoveries of non-coding RNA (ncRNA) in myriad biological processes pose major challenges to structural and functional analysis. Despite progress in secondary structure modeling, high-throughput methods have generally failed to determine ncRNA tertiary structures, even at the 1-nm resolution that enables visualization of how helices and functional motifs are positioned in three dimensions. We report that integrating a new method called MOHCA-seq (Multiplexed •OH Cleavage Analysis with paired-end sequencing) with mutate-and-map secondary structure inference guides Rosetta 3D modeling to consistent 1-nm accuracy for intricately folded ncRNAs with lengths up to 188 nucleotides, including a blind RNA-puzzle challenge, the lariat-capping ribozyme. This multidimensional chemical mapping (MCM) pipeline resolves unexpected tertiary proximities for cyclic-di-GMP, glycine, and adenosylcobalamin riboswitch aptamers without their ligands and a loose structure for the recently discovered human HoxA9D internal ribosome entry site regulon. MCM offers a sequencing-based route to uncovering ncRNA 3D structure, applicable to functionally important but potentially heterogeneous states.

scholarly journals Identification and Characterization of MicroRNAs inMacaca fascicularisby EST Analysis

2012 ◽  
Vol 2012 ◽  
pp. 1-9 ◽  
Author(s):  
Hao Yang ◽  
Haiyang Zhang ◽  
Lin Zhu ◽  
Chenyu Zhang ◽  
Donghai Li
Keyword(s):  
Macaca Fascicularis ◽  
Expressed Sequence Tag ◽  
Est Analysis ◽  
Small Noncoding Rnas ◽  
Novel Mirna ◽  
Medical Experiments ◽  
Alternative Approach ◽  
Model Animal ◽  
Identification And Characterization

MicroRNAs (miRNAs) are small noncoding RNAs which repress gene expression at the posttranscriptional level. In this study, an expressed sequence tag (EST)-based combined method was applied for the detection of miRNAs inMacaca fasciculariswhich is used as a model animal extensively in medical experiments, particularly those involved with neuroscience and disease. Initially, previously known miRNA sequences from metazoans were used to blast with the EST databases ofMacaca fascicularis, and then a range of filtering criteria was conducted to remove some pseudo ones. At last a total of 8 novel conserved miRNAs were identified; their functions were further predicted and analyzed. Together, our study provides insight into miRNAs and their functions inMacaca fascicularis, indicating that the EST analysis is an efficient and affordable alternative approach for identifying novel miRNA candidates.

scholarly journals MISIM v2.0: a web server for inferring microRNA functional similarity based on microRNA-disease associations

2019 ◽  
Vol 47 (W1) ◽  
pp. W536-W541 ◽  
Author(s):  
Jianwei Li ◽  
Shan Zhang ◽  
Yanping Wan ◽  
Yingshu Zhao ◽  
Jiangcheng Shi ◽  
...  
Keyword(s):  
Web Server ◽  
Enrichment Analysis ◽  
Fold Increase ◽  
Functional Enrichment Analysis ◽  
Functional Enrichment ◽  
Rna Molecules ◽  
Novel Mirna ◽  
Non Coding Rna ◽  
Disease Associations ◽  
Data Content

Abstract MicroRNAs (miRNAs) are one class of important small non-coding RNA molecules and play critical roles in health and disease. Therefore, it is important and necessary to evaluate the functional relationship of miRNAs and then predict novel miRNA-disease associations. For this purpose, here we developed the updated web server MISIM (miRNA similarity) v2.0. Besides a 3-fold increase in data content compared with MISIM v1.0, MISIM v2.0 improved the original MISIM algorithm by implementing both positive and negative miRNA-disease associations. That is, the MISIM v2.0 scores could be positive or negative, whereas MISIM v1.0 only produced positive scores. Moreover, MISIM v2.0 achieved an algorithm for novel miRNA-disease prediction based on MISIM v2.0 scores. Finally, MISIM v2.0 provided network visualization and functional enrichment analysis for functionally paired miRNAs. The MISIM v2.0 web server is freely accessible at http://www.lirmed.com/misim/.

scholarly journals Functional Analysis of Three miRNAs in Agropyron mongolicum Keng under Drought Stress

Agronomy ◽  
2019 ◽  
Vol 9 (10) ◽  
pp. 661 ◽  
Author(s):  
Xuting Zhang ◽  
Bobo Fan ◽  
Zhuo Yu ◽  
Lizhen Nie ◽  
Yan Zhao ◽  
...  
Keyword(s):  
Drought Stress ◽  
Drought Tolerance ◽  
High Throughput Sequencing ◽  
Target Genes ◽  
Northern China ◽  
Bioinformatic Analysis ◽  
Pcr Analysis ◽  
Rna Molecules ◽  
Natural Pasture ◽  
Non Coding Rna

Agropyron mongolicum Keng, a perennial diploid grass with high drought tolerance, belongs to the genus Agropyron, tribe Triticeae. It has made tremendous contributions toward reseeding natural pasture and seeding artificial grassland in China, especially in the arid and semi-arid area of northern China. As a wild relative of wheat, A. mongolicum is also a valuable resource for the genetic improvement of wheat crops. MicroRNAs are small non-coding RNA molecules ubiquitous in plants, which have been involved in responses to a wide variety of stresses including drought, salinity, chilling temperature. To date, little research has been done on drought-responsive miRNAs in A. mongolicum. In this study, two miRNA libraries of A. mongolicum under drought and normal conditions were constructed, and drought-responsive miRNAs were screened via Solexa high throughput sequencing and bioinformatic analysis. A total of 114 new miRNAs were identified in A. mongolicum including 53 conservative and 61 unconservative miRNAs, and 1393 target genes of 98 miRNAs were predicted. Seventeen miRNAs were found to be differentially expressed under drought stress, seven (amo-miR21, amo-miR62, amo-miR82, amo-miR5, amo-miR77, amo-miR44 and amo-miR17) of which were predicted to target on genes involved in drought tolerance. QRT-PCR analysis confirmed the expression changes of the seven drought related miRNAs in A. mongolicum. We then transformed the seven miRNAs into Arabidopsis thaliana plants, and three of them (amo-miR21, amo-miR5 and amo-miR62) were genetically stable. The three miRNAs demonstrated the same expression pattern in A. thaliana as that in A. mongolicum under drought stress. Findings from this study will better our understanding of the molecular mechanism of miRNAs in drought tolerance and promote molecular breeding of forage grass with improved adaption to drought.

MicroRNA: Potential biomarker and target of therapy in acute lung injury

2020 ◽  
Vol 39 (11) ◽  
pp. 1429-1442
Author(s):  
Z-F Jiang ◽  
L Zhang ◽  
J Shen
Keyword(s):  
Acute Lung Injury ◽  
Lung Injury ◽  
Respiratory Diseases ◽  
Current Evidence ◽  
Biological Processes ◽  
Fatal Disease ◽  
Small Noncoding Rnas ◽  
Potential Biomarker ◽  
Indirect Injury

MicroRNAs (miRNAs) are small noncoding RNAs stretching over 18–22 nucleotides and considered to be modifiers of many respiratory diseases. They are highly evolutionary conserved and have been implicated in several biological processes, including cell proliferation, apoptosis, differentiation, among others. Acute lung injury (ALI) is a fatal disease commonly caused by direct or indirect injury factors and has a high mortality rate in intensive care unit. Changes in expression of several types of miRNAs have been reported in patients with ALI. Some miRNAs suppress cellular injury and accelerate the recovery of ALI by targeting specific molecules and decreasing excessive immune response. For this reason, miRNAs are proposed as potential biomarkers for ALI and as therapeutic targets for this disease. This review summarizes current evidence supporting the role of miRNAs in ALI.

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