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Journal articles on the topic 'Pre-miRNA'

Author: Grafiati

Published: 4 June 2021

Last updated: 26 July 2025

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1

TITOV, IGOR I., and PAVEL S. VOROZHEYKIN. "AB INITIO HUMAN miRNA AND PRE-miRNA PREDICTION." Journal of Bioinformatics and Computational Biology 11, no. 06 (2013): 1343009. http://dx.doi.org/10.1142/s0219720013430099.

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MicroRNAs (miRNAs) are small single-stranded noncoding RNAs that play an important role in post-transcriptional regulation of gene expression. In this paper, we present a web server for ab initio prediction of the human miRNAs and their precursors. The prediction methods are based on the hidden Markov Models and the context-structural characteristics. By taking into account the identified patterns of primary and secondary structures of the pre-miRNAs, a new HMM model is proposed and the existing context-structural Markov model is modified. The evaluation of the method performance has shown tha

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Ferrarelli, Leslie K. "ERK blocks pre-miRNA export." Science Signaling 9, no. 456 (2016): ec280-ec280. http://dx.doi.org/10.1126/scisignal.aal4588.

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Kurzynska-Kokorniak, Anna, Natalia Koralewska, Agata Tyczewska, Tomasz Twardowski, and Marek Figlerowicz. "RNA oligomers as microRNA production process regulators." BioTechnologia 95, no. 4 (2015): 272–75. https://doi.org/10.5114/bta.2014.56600.

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The present invention relates to an RNA oligomer, methods for regulating’a microRNA (miRNA) production process and RNA oligomers used as miRNA production process regulators. More precisely, the present invention relates to use of RNA oligomers disrupting a pre- iRNA structure as miRNA production process regulators. Oligomer interactions with a miRNA precursor (pre-miRNA) change the precursor’s secondary and tertiary structure. In consequence, the pre-miRNA is not specifically recognised and cleaved by the Dicer ribonuclease, and the specific miRNA is not produced

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Wang, Hsiuying, and Ching Ho. "The Human Pre-miRNA Distance Distribution for Exploring Disease Association." International Journal of Molecular Sciences 24, no. 2 (2023): 1009. http://dx.doi.org/10.3390/ijms24021009.

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MicroRNAs (miRNAs), playing an important role in cell differentiation, development, gene regulation, and apoptosis, have attracted much attention in recent years. miRNAs were shown to be involved in the mechanisms of various diseases, and certainly, they can be employed as useful disease biomarkers. The phylogenetic tree analysis of miRNA biomarkers is a useful tool to investigate the association between various diseases as well as the association between viruses and disease. In addition to the phylogenetic tree analysis, a more advanced study is to use the miRNA distance distribution to evalu

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O'Hara, Andrea J., Wolfgang Vahrson, and Dirk P. Dittmer. "Gene alteration and precursor and mature microRNA transcription changes contribute to the miRNA signature of primary effusion lymphoma." Blood 111, no. 4 (2008): 2347–53. http://dx.doi.org/10.1182/blood-2007-08-104463.

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MicroRNAs are regulated by gene alteration, transcription, and processing. Thus far, few studies have simultaneously assessed all 3 levels of regulation. Using real-time quantitative polymerase chain reaction (QPCR)–based arrays, we determined changes in gene copy number, pre-miRNA, and mature miRNA levels for the largest set of primary effusion lymphomas (PELs) to date. We detected PEL-specific miRNA gene amplifications, and concordant changes in pre-miRNA and mature miRNA. We identified 68 PEL-specific miRNAs. This defines the miRNA signature of PEL and shows that transcriptional regulation

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Jiang, Shuai, and Wei Yan. "Current View of microRNA Processing." Signal Transduction Insights 5 (January 2016): STI.S12317. http://dx.doi.org/10.4137/sti.s12317.

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Small evolutionarily conserved noncoding RNAs, microRNAs (miRNAs), regulate gene expression either by translational repression or by mRNA degradation in mammals. miRNAs play functional roles in diverse physiological and pathological processes. miRNA processing is accurately regulated through multifarious factors. The canonical miRNA processing pathway consists of four sequential steps: (a) miRNA gene is transcribed into primary miRNA (pri-miRNA) mainly by RNA polymerase II; (b) pri-miRNA is processed into precursor miRNA (pre-miRNA) through microprocessor complex; (c) pre-miRNA is exported fro

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Kamiya, Yukiko, Hiroshi Kamimoto, Hongyu Zhu, and Hiroyuki Asanuma. "Development and Modification of Pre-miRNAs with a FRET Dye Pair for the Intracellular Visualization of Processing Intermediates That Are Generated in Cells." Sensors 21, no. 5 (2021): 1785. http://dx.doi.org/10.3390/s21051785.

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microRNAs (miRNAs) are small non-coding ribonucleic acids (RNAs), which regulate gene expression via the RNA interference (RNAi) system. miRNAs have attracted enormous interest because of their biological significance and disease relationship. In cell systems, the generation of miRNA is regulated by multiple steps: the transfer of primary miRNA from the nucleus to the cytosol, the generation of the precursor-miRNA (pre-miRNA), the production of double-stranded RNA from pre-miRNA by the Dicer, the interaction with protein argonaute-2 (AGO2), and the subsequent release of one strand to form miRI

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Petković, Marko, and Vlado Menkovski. "Description Generation Using Variational Auto-Encoders for Precursor microRNA." Entropy 26, no. 11 (2024): 921. http://dx.doi.org/10.3390/e26110921.

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Micro RNAs (miRNA) are a type of non-coding RNA involved in gene regulation and can be associated with diseases such as cancer, cardiovascular, and neurological diseases. As such, identifying the entire genome of miRNA can be of great relevance. Since experimental methods for novel precursor miRNA (pre-miRNA) detection are complex and expensive, computational detection using Machine Learning (ML) could be useful. Existing ML methods are often complex black boxes that do not create an interpretable structural description of pre-miRNA. In this paper, we propose a novel framework that makes use o

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Sperber, Henrik, Alan Beem, Sandra Shannon, et al. "miRNA sensitivity to Drosha levels correlates with pre-miRNA secondary structure." RNA 20, no. 5 (2014): 621–31. http://dx.doi.org/10.1261/rna.043943.113.

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10

Neubacher, Saskia, Claudine M. Dojahn, and Christoph Arenz. "A Rapid Assay for miRNA Maturation by Using Unmodified pre-miRNA." ChemBioChem 12, no. 15 (2011): 2302–5. http://dx.doi.org/10.1002/cbic.201100445.

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Kim, Won-Je, JiYeon Shin, Kyeongmi Bang, Hyun Kyu Song, and Nak-Kyoon Kim. "Structural Characterization of pre-miRNA 155." Journal of the Korean Magnetic Resonance Society 20, no. 2 (2016): 46–49. http://dx.doi.org/10.6564/jkmrs.2016.20.2.046.

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Becker, Nils, and Christina M. Lockwood. "Pre-analytical variables in miRNA analysis." Clinical Biochemistry 46, no. 10-11 (2013): 861–68. http://dx.doi.org/10.1016/j.clinbiochem.2013.02.015.

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Wang, Ying, Jidong Ru, Xianglian Meng, et al. "Role of SNPs in the Biogenesis of Mature miRNAs." BioMed Research International 2021 (June 17, 2021): 1–13. http://dx.doi.org/10.1155/2021/2403418.

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Single nucleotide polymorphisms (SNPs) play a significant role in microRNA (miRNA) generation, processing, and function and contribute to multiple phenotypes and diseases. Therefore, whole-genome analysis of how SNPs affect miRNA maturation mechanisms is important for precision medicine. The present study established an SNP-associated pre-miRNA (SNP-pre-miRNA) database, named miRSNPBase, and constructed SNP-pre-miRNA sequences. We also identified phenotypes and disease biomarker-associated isoform miRNA (isomiR) based on miRFind, which was developed in our previous study. We identified functio

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HASHEMI, MOHAMMAD, EBRAHIM ESKANDARI-NASAB, ZAHRA ZAKERI, et al. "Association of pre-miRNA-146a rs2910164 and pre-miRNA-499 rs3746444 polymorphisms and susceptibility to rheumatoid arthritis." Molecular Medicine Reports 7, no. 1 (2012): 287–91. http://dx.doi.org/10.3892/mmr.2012.1176.

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Oner, Tuba, Guven Yenmis, Kubra Tombulturk, et al. "Association of Pre-miRNA-499 rs3746444 and Pre-miRNA-146a rs2910164 Polymorphisms and Susceptibility to Behcet's Disease." Genetic Testing and Molecular Biomarkers 19, no. 8 (2015): 424–30. http://dx.doi.org/10.1089/gtmb.2015.0016.

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Abaturov, A. E., and V. L. Babуch. "MiRNA biogenesis. Part 1. Maturation of pre-miRNA. Maturation of canonical miRNAs." CHILD`S HEALTH 16, no. 2 (2021): 200–207. http://dx.doi.org/10.22141/2224-0551.16.2.2021.229886.

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The scientific review presents the biogenesis of miRNAs. To write the article, information was searched using databases Scopus, Web of Science, MedLine, PubMed, Google Scholar, EMBASE, Global Health, The Cochrane Library, CyberLeninka. The article presents a brief description of the RNA sequence encoding miRNAs. It is emphasized that microRNAs, depending on the location of the sequence encoding them in the genome, are divided into two major groups: canonical and non-canonical miRNAs. It has been found that a single locus of a sequence encoding a miRNA can generate a series of non-coding matur

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Meher, Prabina Kumar, Shbana Begam, Tanmaya Kumar Sahu, et al. "ASRmiRNA: Abiotic Stress-Responsive miRNA Prediction in Plants by Using Machine Learning Algorithms with Pseudo K-Tuple Nucleotide Compositional Features." International Journal of Molecular Sciences 23, no. 3 (2022): 1612. http://dx.doi.org/10.3390/ijms23031612.

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MicroRNAs (miRNAs) play a significant role in plant response to different abiotic stresses. Thus, identification of abiotic stress-responsive miRNAs holds immense importance in crop breeding programmes to develop cultivars resistant to abiotic stresses. In this study, we developed a machine learning-based computational method for prediction of miRNAs associated with abiotic stresses. Three types of datasets were used for prediction, i.e., miRNA, Pre-miRNA, and Pre-miRNA + miRNA. The pseudo K-tuple nucleotide compositional features were generated for each sequence to transform the sequence data

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Li, Jin, Ying Wang, Lei Wang, et al. "MatPred: Computational Identification of Mature MicroRNAs within Novel Pre-MicroRNAs." BioMed Research International 2015 (2015): 1–9. http://dx.doi.org/10.1155/2015/546763.

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Background.MicroRNAs (miRNAs) are short noncoding RNAs integral for regulating gene expression at the posttranscriptional level. However, experimental methods often fall short in finding miRNAs expressed at low levels or in specific tissues. While several computational methods have been developed for predicting the localization of mature miRNAs within the precursor transcript, the prediction accuracy requires significant improvement.Methodology/Principal Findings.Here, we present MatPred, which predicts mature miRNA candidates within novel pre-miRNA transcripts. In addition to the relative loc

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Kataoka, Naoyuki, Megumi Fujita, and Mutsuhito Ohno. "Functional Association of the Microprocessor Complex with the Spliceosome." Molecular and Cellular Biology 29, no. 12 (2009): 3243–54. http://dx.doi.org/10.1128/mcb.00360-09.

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ABSTRACT The majority of human microRNAs (miRNAs) are located in the introns of other genes (A. Rodriguez, S. Griffiths-Jones, J. L. Ashurst, and A. Bradley, Genome Res. 14:1902-1910, 2004). Based on the discovery that artificial insertion of pre-miRNAs in introns did not hamper mRNA production and that the miRNA-harboring introns were spliced more slowly than the adjacent introns, a model was previously proposed in which Drosha crops the pre-miRNA and the two cropped fragments from the pre-mRNA are subsequently trans spliced (Y. K. Kim and V. N. Kim, EMBO J. 26:775-783, 2007). However, the mo

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Okada, Chimari, Eiki Yamashita, Soo Jae Lee, et al. "A High-Resolution Structure of the Pre-microRNA Nuclear Export Machinery." Science 326, no. 5957 (2009): 1275–79. http://dx.doi.org/10.1126/science.1178705.

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Nuclear export of microRNAs (miRNAs) by exportin-5 (Exp-5) is an essential step in miRNA biogenesis. Here, we present the 2.9 angstrom structure of the pre-miRNA nuclear export machinery formed by pre-miRNA complexed with Exp-5 and a guanine triphosphate (GTP)–bound form of the small nuclear guanine triphosphatase (GTPase) Ran (RanGTP). The x-ray structure shows that Exp-5:RanGTP recognizes the 2-nucleotide 3′ overhang structure and the double-stranded stem of the pre-miRNA. Exp-5:RanGTP shields the pre-miRNA stem from degradation in a baseball mitt–like structure where it is held by broadly d

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Allen-Coyle, Taylor J., Berta Capella Roca, Alan Costello, et al. "miRNA- and Cell Line-Specific Constraints on Precursor miRNA Processing of Stably Transfected Pancreatic Cancer and Other Mammalian Cells." International Journal of Molecular Sciences 25, no. 11 (2024): 5666. http://dx.doi.org/10.3390/ijms25115666.

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MicroRNAs (miRNAs) regulate approximately one-third of all human genes. The dysregulation of miRNAs has been implicated in the development of numerous human diseases, including cancers. In our investigation focusing on altering specific miRNA expression in human pancreatic cancer cells, we encountered an interesting finding. While two expression vector designs effectively enhanced miR-708 levels, they were unable to elevate mature forms of miR-29b, -1290, -2467, and -6831 in pancreatic cancer cell lines. This finding was also observed in a panel of other non-pancreatic cancer cell lines, sugge

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Zyrianova, I. M., and S. N. Koval’chuk. "Bovine leukemia virus pre-miRNA genes’ polymorphism." RNA Biology 15, no. 12 (2018): 1440–47. http://dx.doi.org/10.1080/15476286.2018.1555406.

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23

Avitabile, Concetta, Michele Saviano, Luca D'Andrea, et al. "Targeting pre-miRNA by Peptide Nucleic Acids." Artificial DNA: PNA & XNA 3, no. 2 (2012): 88–96. http://dx.doi.org/10.4161/adna.20911.

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Liu, Chun-Jie, Xin Fu, Mengxuan Xia, Qiong Zhang, Zhifeng Gu, and An-Yuan Guo. "miRNASNP-v3: a comprehensive database for SNPs and disease-related variations in miRNAs and miRNA targets." Nucleic Acids Research 49, no. D1 (2020): D1276—D1281. http://dx.doi.org/10.1093/nar/gkaa783.

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Abstract MicroRNAs (miRNAs) related single-nucleotide variations (SNVs), including single-nucleotide polymorphisms (SNPs) and disease-related variations (DRVs) in miRNAs and miRNA-target binding sites, can affect miRNA functions and/or biogenesis, thus to impact on phenotypes. miRNASNP is a widely used database for miRNA-related SNPs and their effects. Here, we updated it to miRNASNP-v3 (http://bioinfo.life.hust.edu.cn/miRNASNP/) with tremendous number of SNVs and new features, especially the DRVs data. We analyzed the effects of 7 161 741 SNPs and 505 417 DRVs on 1897 pre-miRNAs (2630 mature

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Yu, Lei, Yu Liu, Xuan Jiang, Enyi Shi, and Tianxiang Gu. "Overexpression of MicroRNA-106b-5p Attenuates Kidney Injuries after Deep Hypothermic Circulatory Arrest in Rats." Thoracic and Cardiovascular Surgeon 66, no. 01 (2017): 109–15. http://dx.doi.org/10.1055/s-0037-1604429.

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Background MicroRNAs (miRNA) have been identified to exert a wide range of biological functions in acute kidney injury (AKI) after deep hypothermic circulatory arrest (DHCA). We sought to investigate the renoprotection of miRNA-106b-5p in a rat model of DHCA by targeting phosphatase and tensin homolog (PTEN). Methods Overexpression of miRNA-106b-5p in vivo was conducted by directly injection of lentivirus vectors containing pre-miRNA-106b-5p into the renal parenchyma of the animals under the ultrasound guidance 7 days before DHCA. The vehicle or control lentivirus vectors were given to the con

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Teune, Jan-Hendrik, and Gerhard Steger. "NOVOMIR: De Novo Prediction of MicroRNA-Coding Regions in a Single Plant-Genome." Journal of Nucleic Acids 2010 (2010): 1–10. http://dx.doi.org/10.4061/2010/495904.

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MicroRNAs (miRNA) are small regulatory, noncoding RNA molecules that are transcribed as primary miRNAs (pri-miRNA) from eukaryotic genomes. At least in plants, their regulatory activity is mediated through base-pairing with protein-coding messenger RNAs (mRNA) followed by mRNA degradation or translation repression. We describeNOVOMIR, a program for the identification of miRNA genes in plant genomes. It uses a series of filter steps and a statistical model to discriminate a pre-miRNA from other RNAs and does rely neither on prior knowledge of a miRNA target nor on comparative genomics. The sens

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Kim, Young-Kook, Boseon Kim, and V. Narry Kim. "Re-evaluation of the roles of DROSHA, Exportin 5, and DICER in microRNA biogenesis." Proceedings of the National Academy of Sciences 113, no. 13 (2016): E1881—E1889. http://dx.doi.org/10.1073/pnas.1602532113.

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Biogenesis of canonical microRNAs (miRNAs) involves multiple steps: nuclear processing of primary miRNA (pri-miRNA) by DROSHA, nuclear export of precursor miRNA (pre-miRNA) by Exportin 5 (XPO5), and cytoplasmic processing of pre-miRNA by DICER. To gain a deeper understanding of the contribution of each of these maturation steps, we deleted DROSHA, XPO5, and DICER in the same human cell line, and analyzed their effects on miRNA biogenesis. Canonical miRNA production was completely abolished in DROSHA-deleted cells, whereas we detected a few DROSHA-independent miRNAs including three previously u

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AL-ZAMILY, Aqeel Meer. "Effect of GLP-1 Receptor Agonists (Liraglutide) on Glycemic Parameters and Circulating miRNA Expression in Type 2 Diabetes Mellitus." Medicina Moderna - Modern Medicine 32, no. 2 (2025): 143–50. https://doi.org/10.31689/rmm.2025.32.2.143.

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Background: Circulating miRNA modulates a variety of cellular activities including the pathogenesis of many diseases. In type 2 diabetes mellitus (T2DM), alteration in miRNA profiles can have a significant effect on insulin signaling, β-cell function, and inflammation. It has been suggested that antidiabetic therapies can normalize circulating miRNA levels and improve metabolic parameters, rendering miRNA as potential biomarkers for T2DM monitoring and treatment response. Aim: To examine the impact of GLP-1 receptor agonists on the glycemic profile and on circulating levels of miRNA-146a, miRN

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Biswas, Manosh Kumar, Dhiman Biswas, Mita Bagchi, Ganjun Yi, and Guiming Deng. "A Comprehensive Plant microRNA Simple Sequence Repeat Marker Database to Accelerate Genetic Improvements in Crops." Agronomy 11, no. 11 (2021): 2298. http://dx.doi.org/10.3390/agronomy11112298.

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Microsatellites, or simple sequences repeat (SSRs), are distributed in genes, intergenic regions and transposable elements in the genome. SSRs were identified for developing markers from draft genome assemblies, transcriptome sequences and genome survey sequences in plant and animals. The identification, distribution, and density of microsatellites in pre-microRNAs (miRNAs) are not well documented in plants. In this study, SSRs were identified in 16,892 pre-miRNA sequences from 292 plant species in six taxonomic groups (algae to dicots). Fifty-one percent of pre-miRNA sequences contained SSRs.

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Steeman, Tomás J., Andrea M. J. Weiner, Aldana P. David, Andrés Binolfi, Nora B. Calcaterra, and Pablo Armas. "G-Quadruplexes Regulate miRNA Biogenesis in Live Zebrafish Embryos." International Journal of Molecular Sciences 24, no. 5 (2023): 4828. http://dx.doi.org/10.3390/ijms24054828.

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RNA guanine quadruplexes (G4s) regulate RNA functions, metabolism, and processing. G4s formed within precursors of microRNAs (pre-miRNAs) may impair pre-miRNAs maturation by Dicer, thus repressing mature miRNA biogenesis. As miRNAs are essential for proper embryonic development, we studied the role of G4s on miRNA biogenesis in vivo during zebrafish embryogenesis. We performed a computational analysis on zebrafish pre-miRNAs to find putative G4 forming sequences (PQSs). The precursor of the miRNA 150 (pre-miR-150) was found to contain an evolutionarily conserved PQS formed by three G-tetrads a

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Yoshida, Toyotaka, Yoshimasa Asano, and Kumiko Ui-Tei. "Modulation of MicroRNA Processing by Dicer via Its Associated dsRNA Binding Proteins." Non-Coding RNA 7, no. 3 (2021): 57. http://dx.doi.org/10.3390/ncrna7030057.

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MicroRNAs (miRNAs) are small non-coding RNAs that are about 22 nucleotides in length. They regulate gene expression post-transcriptionally by guiding the effector protein Argonaute to its target mRNA in a sequence-dependent manner, causing the translational repression and destabilization of the target mRNAs. Both Drosha and Dicer, members of the RNase III family proteins, are essential components in the canonical miRNA biogenesis pathway. miRNA is transcribed into primary-miRNA (pri-miRNA) from genomic DNA. Drosha then cleaves the flanking regions of pri-miRNA into precursor-miRNA (pre-miRNA),

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James, Amanda Marie, Meredith B. Baker, Gang Bao, and Charles D. Searles. "MicroRNA Detection Using a Double Molecular Beacon Approach: Distinguishing Between miRNA and Pre-miRNA." Theranostics 7, no. 3 (2017): 634–46. http://dx.doi.org/10.7150/thno.16840.

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Imperatore, Joshua A., McKenna L. Then, Keefe B. McDougal, and Mihaela Rita Mihailescu. "Characterization of a G-Quadruplex Structure in Pre-miRNA-1229 and in Its Alzheimer’s Disease-Associated Variant rs2291418: Implications for miRNA-1229 Maturation." International Journal of Molecular Sciences 21, no. 3 (2020): 767. http://dx.doi.org/10.3390/ijms21030767.

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Alzheimer’s disease (AD), the most common age-related neurodegenerative disease, is associated with various forms of cognitive and functional impairment that worsen with disease progression. AD is typically characterized as a protein misfolding disease, in which abnormal plaques form due to accumulation of tau and β-amyloid (Aβ) proteins. An assortment of proteins is responsible for the processing and trafficking of Aβ, including sortilin-related receptor 1 (SORL1). Recently, a genome-wide association study of microRNA-related variants found that a single nucleotide polymorphism (SNP) rs229141

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Choudhury, Nila Roy, and Gracjan Michlewski. "Terminal loop-mediated control of microRNA biogenesis." Biochemical Society Transactions 40, no. 4 (2012): 789–93. http://dx.doi.org/10.1042/bst20120053.

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Regulation of miRNA (microRNA) biogenesis shapes the profiles of miRNAs in the living cell, contributing to cell identity and function. Importantly, aberrant miRNA levels have been linked to a variety of human pathological states. In recent years, a number of proteins have been shown to regulate the miRNA biogenesis at the level of Drosha and Dicer cleavage. A large proportion of these factors regulate miRNA production through binding to the TL (terminal loop) regions of miRNA progenitors. In the present paper, we review the current knowledge about pri-miRNA (primary miRNA) and pre-miRNA (prec

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Baky, Fady, Richard Matulewicz, Andrea Knezevic, et al. "Pre-orchiectomy serum miRNA-371a-3p and 372-3p levels in men with clinically localized testicular masses." Journal of Clinical Oncology 42, no. 4_suppl (2024): 519. http://dx.doi.org/10.1200/jco.2024.42.4_suppl.519.

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519 Background: MicroRNA (miRNA) are short noncoding RNAs involved in regulation of gene expression and have shown promise as novel biomarkers in the diagnosis and management of testicular germ cell tumors (GCT). We report the accuracy of our combined miRNA assay in men with Clinical Stage I (CSI) GCTs. We also sought to explore the relationship between miRNA levels and patient and oncologic variables to better understand how these factors may influence miRNA results. Methods: We retrospectively identified patients at Memorial Sloan Kettering (MSK) with a newly identified testicular mass conce

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Kandhavelu, Meenakshisundaram, and Jeyalakshumi Kandhavelu. "pre-piRNA biogenesis mimics the pathway of miRNA." Biochemical Systematics and Ecology 43 (August 2012): 200–204. http://dx.doi.org/10.1016/j.bse.2012.03.012.

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Zhang, Huiyu, Hua Wang, Yuangen Yao, and Ming Yi. "PlantMirP-Rice: An Efficient Program for Rice Pre-miRNA Prediction." Genes 11, no. 6 (2020): 662. http://dx.doi.org/10.3390/genes11060662.

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Rice microRNAs (miRNAs) are important post-transcriptional regulation factors and play vital roles in many biological processes, such as growth, development, and stress resistance. Identification of these molecules is the basis of dissecting their regulatory functions. Various machine learning techniques have been developed to identify precursor miRNAs (pre-miRNAs). However, no tool is implemented specifically for rice pre-miRNAs. This study aims at improving prediction performance of rice pre-miRNAs by constructing novel features with high discriminatory power and developing a training model

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Wypijewska del Nogal, Anna, Vinoth Sundar Rajan, Fredrik Westerlund, and L. Marcus Wilhelmsson. "Complex Conformational Dynamics of the Heart Failure-Associated Pre-miRNA-377 Hairpin Revealed by Single-Molecule Optical Tweezers." International Journal of Molecular Sciences 22, no. 16 (2021): 9008. http://dx.doi.org/10.3390/ijms22169008.

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Pre-miRNA-377 is a hairpin-shaped regulatory RNA associated with heart failure. Here, we use single-molecule optical tweezers to unzip pre-miRNA-377 and study its stability and dynamics. We show that magnesium ions have a strong stabilizing effect, and that sodium ions stabilize the hairpin more than potassium ions. The hairpin unfolds in a single step, regardless of buffer composition. Interestingly, hairpin folding occurs either in a single step (type 1) or through the formation of intermediates, in multiple steps (type 2) or gradually (type 3). Type 3 occurs only in the presence of both sod

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Shinde, Santosh, and Utpal Bhadra. "A Complex Genome-MicroRNA Interplay in Human Mitochondria." BioMed Research International 2015 (2015): 1–13. http://dx.doi.org/10.1155/2015/206382.

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Small noncoding regulatory RNA exist in wide spectrum of organisms ranging from prokaryote bacteria to humans. In human, a systematic search for noncoding RNA is mainly limited to the nuclear and cytosolic compartments. To investigate whether endogenous small regulatory RNA are present in cell organelles, human mitochondrial genome was also explored for prediction of precursor microRNA (pre-miRNA) and mature miRNA (miRNA) sequences. Six novel miRNA were predicted from the organelle genome by bioinformatics analysis. The structures are conserved in other five mammals including chimp, orangutan,

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Zeinali, Fahime, Seyed Mohsen Aghaei Zarch, Alireza Jahan-Mihan, et al. "Circulating microRNA-122, microRNA-126-3p and microRNA-146a are associated with inflammation in patients with pre-diabetes and type 2 diabetes mellitus: A case control study." PLOS ONE 16, no. 6 (2021): e0251697. http://dx.doi.org/10.1371/journal.pone.0251697.

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The prevalence of type 2 diabetes mellitus (T2DM) is increasing dramatically worldwide. Dysregulation of microRNA (miRNA) as key regulators of gene expression, has been reported in numerous diseases including diabetes. The aim of this study was to investigate the expression levels of miRNA-122, miRNA-126-3p and miRNA-146a in diabetic and pre-diabetic patients and in healthy individuals, and to determine whether the changes in the level of these miRNAs are reliable biomarkers in diagnosis, prognosis, and pathogenesis of T2DM. Additionally, we examined the relationship between miRNA levels and p

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Esposito, Salvatore, Riccardo Aversano, Pasquale Tripodi, and Domenico Carputo. "Whole-Genome Doubling Affects Pre-miRNA Expression in Plants." Plants 10, no. 5 (2021): 1004. http://dx.doi.org/10.3390/plants10051004.

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Whole-genome doubling (polyploidy) is common in angiosperms. Several studies have indicated that it is often associated with molecular, physiological, and phenotypic changes. Mounting evidence has pointed out that micro-RNAs (miRNAs) may have an important role in whole-genome doubling. However, an integrative approach that compares miRNA expression in polyploids is still lacking. Here, a re-analysis of already published RNAseq datasets was performed to identify microRNAs’ precursors (pre-miRNAs) in diploids (2x) and tetraploids (4x) of five species (Arabidopsis thaliana L., Morus alba L., Bras

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Lorenz, Daniel A., Steve Vander Roest, Martha J. Larsen, and Amanda L. Garner. "Development and Implementation of an HTS-Compatible Assay for the Discovery of Selective Small-Molecule Ligands for Pre-microRNAs." SLAS DISCOVERY: Advancing the Science of Drug Discovery 23, no. 1 (2017): 47–54. http://dx.doi.org/10.1177/2472555217717944.

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microRNAs (miRNAs) are small gene regulatory RNAs, and their expression has been found to be dysregulated in a number of human diseases. To facilitate the discovery of small molecules capable of selectively modulating the activity of a specific miRNA, we have utilized new high-throughput screening technology targeting Dicer-mediated pre-miRNA maturation. Pilot screening of ~50,000 small molecules and ~33,000 natural product extract libraries against pre-miR-21 processing indicated the potential of our assay for this goal, yielding a campaign Z′ factor of 0.52 and an average plate signal-to-bac

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Sin, Onsam, Prudence Mabiala, Ye Liu та ін. "Gene Silencing Efficiency and INF-β Induction Effects of Splicing miRNA 155-Based Artificial miRNA with Pre-miRNA Stem-Loop Structures". Biochemical Genetics 50, № 1-2 (2011): 112–21. http://dx.doi.org/10.1007/s10528-011-9476-y.

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Qi, Yong-Li, Liang-Jiao Xue, Yousry A. El-Kassaby, and Ying Guo. "Identification and Comparative Analysis of Conserved and Species-Specific microRNAs in Four Populus Sections." Forests 13, no. 6 (2022): 873. http://dx.doi.org/10.3390/f13060873.

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The conservation and diversity of microRNA (miRNA) families provide insights into the evolution of miRNA genes. However, there are few studies to explore the miRNA genes at the genus level in plants. Here, we identified 1194 miRNA loci in four Populus species P. deltoides, P. euphratica, P. tremula, and P. trichocarpa from Aigeiros, Turanga, Populus, and Tacamahaca sections, respectively, by combining de novo and homolog-based approaches. Our results indicated that a similar number of miRNA loci exist in each species (296–301 miRNA loci). Among the identified 143 miRNA families, 68 families ar

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Fan, Dashuai, Yuangen Yao, and Ming Yi. "PlantMirP2: An Accurate, Fast and Easy-To-Use Program for Plant Pre-miRNA and miRNA Prediction." Genes 12, no. 8 (2021): 1280. http://dx.doi.org/10.3390/genes12081280.

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MicroRNAs (miRNAs) are a kind of short non-coding ribonucleic acid molecules that can regulate gene expression. The computational identification of plant miRNAs is of great significance to understanding biological functions. In our previous studies, we have put firstly forward and further developed a set of knowledge-based energy features to construct two plant pre-miRNA prediction tools (plantMirP and riceMirP). However, these two tools cannot be used for miRNA prediction from NGS (Next-Generation Sequencing) data. In addition, for further improving the prediction performance and accessibilit

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Mertens, Daniel, Danilo Allegra, Angela Philippen, Thorsten Zenz, Hartmut Döhner, and Stephan Stilgenbauer. "Maturation of the miR15a/miR16-1 Family Is Impaired In Chronic Lymphocytic Leukaemia." Blood 116, no. 21 (2010): 53. http://dx.doi.org/10.1182/blood.v116.21.53.53.

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Abstract Abstract 53 A role as tumor suppressor has been proposed for the miR15a/miR-16-1 family of miRNA genes localized in a critical region in 13q14 that is deleted in more than 50% of CLL patients. These two miRNA genes regulate cell cycle progression and apoptosis in cell lines and in vivo, and knockout of the syntenic region in mice results in the development of a CLL-like phenotype. We measured by qRT-PCR mir15a and miR-16 in CLL samples (n=38) and normal B-cells (n=14) and observed reduced levels in CLL independent of the 13q deletion status. We then assessed the levels of the primary

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Sebastian, Bram, and Samuel E. Aggrey. "Specificity and Sensitivity of PROMIR, ERPIN and MIR-ABELA in Predicting Pre-MicroRNAs in the Chicken Genome." In Silico Biology: Journal of Biological Systems Modeling and Multi-Scale Simulation 8, no. 5-6 (2008): 377–81. https://doi.org/10.3233/isb-00366.

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MicroRNAs (miRNAs) are endogenous 21–23 nucleotide molecules that are known to regulate about 30% of protein-coding genes through the RNAi pathway. Low level expression of some miRNA has limited their in-situ discovery. Such limitations could be ameliorated by in-silico methodologies. The efficacies of three major programs (ERPIN, ProMir and miR-abela) in detecting known pre-miRNA were evaluated using chicken pre-miRNA data. The sensitivity of ProMir, miR-abela and ERPIN were 53%, 57% and 93%, respectively. The specificity of the three algorithms using 5,000 random sequences was 98.94%, 99.46%

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Sathyamurthy, Ganesh, and N. Ramachandra Swamy. "Computational Identification of Putative miRNAs from Felis Catus." Biomedical Engineering and Computational Biology 2 (January 2010): BECB.S5233. http://dx.doi.org/10.4137/becb.s5233.

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microRNAs represent a class of noncoding small RNAs of approximately 20–23 nt length, which are evolutionarily conserved and play a vital role in various biological processes by either degrading or repressing mRNA translation. The Felis catus (cat) genome sequence has been published, and just revealed the number of miRNAs in the genome–-without mention of any further details on these miRNAs. This paper discusses an in silico comparative approach using all known sequences of vertebrate pre-miRNA as query sequence, and report 405 putative miRNAs from cat genome. We determine the identity values

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Jaszczuk, Ilona, Dorota Koczkodaj, Adrianna Kondracka, Anna Kwaśniewska, Izabela Winkler, and Agata Filip. "The role of miRNA-210 in pre-eclampsia development." Annals of Medicine 54, no. 1 (2022): 1350–56. http://dx.doi.org/10.1080/07853890.2022.2071459.

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Terasawa, Kazuya, Kazuharu Shimizu, and Gozoh Tsujimoto. "Synthetic Pre-miRNA-Based shRNA as Potent RNAi Triggers." Journal of Nucleic Acids 2011 (2011): 1–6. http://dx.doi.org/10.4061/2011/131579.

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RNA interference (RNAi) is a powerful tool for studying gene function owing to the ease with which it can selectively silence genes of interest, and it has also attracted attention because of its potential for therapeutic applications. Chemically synthesized small interfering RNAs (siRNAs) and DNA vector-based short hairpin RNAs (shRNAs) are now widely used as RNAi triggers. In contrast to expressed shRNAs, the use of synthetic shRNAs is limited. Here we designed shRNAs modeled on a precursor microRNA (pre-miRNA) and evaluated their biological activity. We demonstrated that chemically syntheti

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