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Identification of a long non‑coding RNA‑mediated competitive endogenous RNA network in hepatocellular carcinoma

Hui He, Di Chen, Shimeng Cui, Hailong Piao, Haibo Tang, Xun Wang, Peng Ye, Shi Jin
2019 Oncology Reports  
Then, a competitive endogenous (ce)RNA network was constructed from these interactions, and network topology and Gene Ontology enrichment analyses were conducted to mine potential functions of ceRNAs.  ...  The present study was designed to identify the endogenous RNA regulatory networks involved in hepatocellular carcinoma (HCC) by bioinformatic analysis.  ...  Funding The present study was supported in part by the National Natural Science Foundation of China (NSFC 81702526).  ... 
doi:10.3892/or.2019.7181 pmid:31173261 fatcat:pjlztb2nrrer3j4hsty3tsje7i

Abnormal expression of lncRNA UCA1 disturbed cell apoptosis through mediating mitochondrial dynamics in PDAC

BuWei Teng, Tao Feng, Wei Li, Zhong Wang
2020 Neoplasma (Bratislava)  
In this research, data mining revealed that upregulated UCA1 occurred in PDAC patients, which meant a high likelihood of a poor prognosis.  ...  Meanwhile, the morphological analysis showed significantly enhanced mitochondrial fragmentation presented in UCA1 knockdown cells, coupled with increased expression of Drp1 and Fis1, together with an activation  ...  What's more, data mining showed that an unsatisfactory outcome was presented in patients with a higher UCA1 expression than those with a lower expression.  ... 
doi:10.4149/neo_2020_200629n671 fatcat:axzohej6krg2lizto3nlpf6gjq

The Neat Dance of COVID-19: NEAT1, DANCR, and Co-Modulated Cholinergic RNAs Link to Inflammation

Chanan Meydan, Nimrod Madrer, Hermona Soreq
2020 Frontiers in Immunology  
We selected inflammation-prone men and women of diverse ages among the cohort of Genome Tissue expression (GTEx) by mining RNA-seq datasets from their lung, and blood tissues, followed by quantitative  ...  RNA-seq dataset.  ...  The data in this project regarding healthy individuals was obtained from the Genotype-Tissue Expression (GTEx) Project, extracted from the GTEx portal on 05.04.20.  ... 
doi:10.3389/fimmu.2020.590870 pmid:33163005 pmcid:PMC7581732 fatcat:lon5l4di5rbw3k6a462hngyhli

Capturing Natural Product Biosynthetic Pathways from Uncultivated Symbiotic Bacteria of Marine Sponges Through Metagenome Mining: A Mini-Review

Agustinus Robert Uria
2015 Squalen  
Subsequent expression of the pathways in easily culturable bacteria, such as Escherichia coli, could lead to the sustainable production of rare promising natural products.  ...  This includes detecting biosynthetic genes in sponge metagenome, creating large metagenomic library, rapid screening of metagenomic library, and clone sequencing.  ...  Sponge-derived natural products, in which their biosynthetic pathways have been cloned by metagenome mining.  ... 
doi:10.15578/squalen.v10i1.131 fatcat:aplgdsquhjcd5jg7jqh7x55qqy

Chimeric Peptides/Proteins Encoded by circRNA: An Update on Mechanisms and Functions in Human Cancers

Faiz Ali Khan, Bernard Nsengimana, Nazeer Hussain Khan, Zhenhua Song, Ebenezeri Erasto Ngowi, Yunyun Wang, Weijuan Zhang, Shaoping Ji
2022 Frontiers in Oncology  
The discovery of circular RNAs and exploration of their biological functions are increasingly attracting attention in cell bio-sciences.  ...  Owing to their unique characteristics of being highly conserved, having a relatively longer half-life, and involvement in RNA maturation, transportation, epigenetic regulation, and transcription of genes  ...  A database of circRNA, lncRNA, and mRNA derived from The integration and visualization of RNA expression profiles (126) exoRBase.org RNA-seq data analyses of human blood exosomes based on RNA-seq data  ... 
doi:10.3389/fonc.2022.781270 pmid:35223470 pmcid:PMC8874284 fatcat:7moehak67ze43hsgwqyrk3dyue

The lncRNA MALAT1 acts as a competing endogenous RNA to regulate KRAS expression by sponging miR-217 in pancreatic ductal adenocarcinoma

Pingping Liu, Haiyan Yang, Jing Zhang, Xiaozhong Peng, Zhaohui Lu, Weimin Tong, Jie Chen
2017 Scientific Reports  
MALAT1 is expressed at higher levels in pancreatic ductal adenocarcinoma (PDAC) tissues than in nontumour tissues and in metastatic PDAC than in localized tumours.  ...  Noncoding RNAs (ncRNAs) include microRNAs (miRNAs) and long noncoding RNAs (lncRNAs) 3, 4 .  ...  Kaplan-Meier analysis and the log-rank test were applied to evaluate the prognostic significance of gene expression levels with respect to patient survival.  ... 
doi:10.1038/s41598-017-05274-4 pmid:28701723 pmcid:PMC5507931 fatcat:nki5adlysngqpptpzcoi2okcau

Genomic Positional Dissection of RNA Editomes in Tumor and Normal Samples

Michael Chigaev, Hui Yu, David C. Samuels, Quanhu Sheng, Olufunmilola Oyebamiji, Scott Ness, Wei Yue, Ying-yong Zhao, Yan Guo
2019 Frontiers in Genetics  
RNA editing is phenomenon that occurs in both protein coding and non-coding RNAs.  ...  Using RNA editing datasets from two large consortiums: The Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression (GTEx) project, we quantitatively analyzed human genome-wide RNA editing events derived  ...  Frankly, the majority of the RNA editing source sequencing data were not designed for RNA editing detection initially but were data mined for RNA editing at a later time.  ... 
doi:10.3389/fgene.2019.00211 pmid:30949194 pmcid:PMC6435843 fatcat:gpmofromz5huxbckgjmtiveoly

Exon and intron sharing in opposite direction-an undocumented phenomenon in human genome-between Pou5f1 and Tcf19 genes

Majid Mehravar, Fatemeh Ghaemimanesh, Ensieh M Poursani
2021 BMC Genomics  
Expressed sequence tags (ESTs) analysis enabled us to uncover an overlapping gene pair in the human genome.  ...  By using in silico analysis of previous experimental documentations, we reveal a new form of overlapping genes in the human genome, in which two genes found on opposite strands (Pou5f1 and Tcf19), share  ...  We also mined transcriptome data (RNA-seq) from ENCODE/Caltech projects to figure out the expression of TCF19-D in different cell lines.  ... 
doi:10.1186/s12864-021-08039-6 pmid:34610795 pmcid:PMC8493703 fatcat:bwivtuacnbduvdigkwf5u5ufui

Mechanistic Insight Into the Regulation of Immune-Related Genes Expression in Autism Spectrum Disorder

Hani Sabaie, Hossein Dehghani, Shadi Shiva, Mohammad Reza Asadi, Omidvar Rezaei, Mohammad Taheri, Maryam Rezazadeh
2021 Frontiers in Molecular Biosciences  
In the current work, we used a bioinformatics approach to describe the role of long non-coding RNA (lncRNA)-associated competing endogenous RNAs (ceRNAs) in the peripheral blood (PB) samples to figure  ...  The Gene Expression Omnibus database was used to obtain the PB microarray dataset (GSE89594) from the subjects suffering from ASD and control subjects, containing the data related to both mRNAs and lncRNAs  ...  METHODS In the current research, we used a bioinformatics method for the aim of the data mining of the microarray dataset (GSE89594) containing the PB from patients with ASD and their matched controls.  ... 
doi:10.3389/fmolb.2021.754296 pmid:34746237 pmcid:PMC8568055 fatcat:62egvbdy5zhqfdkd6e74r3ei5q

Progress on the Regulation of Ruminant Milk Fat by Noncoding RNAs and ceRNAs

QinYue Lu, Zhi Chen, Dejun Ji, Yongjiang Mao, Qianming Jiang, Zhangping Yang, Juan J. Loor
2021 Frontiers in Genetics  
Despite the growing body of research on the role of functional noncoding RNA in the control of ruminant milk fat, most data are still not translatable for field applications.  ...  Although few data are available, merging evidence indicates that lncRNAs and circRNAs act on milk fat related genes through indirect action with microRNAs or RNAs in the ceRNA network to elicit positive  ...  Thus, comprehensive studies of ceRNA could help explain some biological phenomena.  ... 
doi:10.3389/fgene.2021.733925 pmid:34790222 pmcid:PMC8591074 fatcat:5pnx53qadjbrfgj5wmbbbl64ya

A-to-I RNA Editing in Cancer: From Evaluating the Editing Level to Exploring the Editing Effects

Heming Wang, Sinuo Chen, Jiayi Wei, Guangqi Song, Yicheng Zhao
2021 Frontiers in Oncology  
As an important regulatory mechanism at the posttranscriptional level in metazoans, adenosine deaminase acting on RNA (ADAR)-induced A-to-I RNA editing modification of double-stranded RNA has been widely  ...  Numerous RNA editing sites have been reported to be located in non-coding regions and can affect the biosynthesis of ncRNAs, including miRNAs and circular RNAs.  ...  As sponges of miRNAs, circular RNAs can inhibit the function of miRNAs.  ... 
doi:10.3389/fonc.2020.632187 pmid:33643923 pmcid:PMC7905090 fatcat:zbo2kufkeffrnop2ivoxxcp3ya

Genomics of Sponge-Associated Streptomyces spp. Closely Related to Streptomyces albus J1074: Insights into Marine Adaptation and Secondary Metabolite Biosynthesis Potential

Elena Ian, Dmitry B. Malko, Olga N. Sekurova, Harald Bredholt, Christian Rückert, Marina E. Borisova, Andreas Albersmeier, Jörn Kalinowski, Mikhail S. Gelfand, Sergey B. Zotchev, Paul Hoskisson
2014 PLoS ONE  
Genome mining targeted to secondary metabolite biosynthesis gene clusters identified several of those, which were not present in S. albus J1074, and likely to have been retained from a common ancestor,  ...  Certain genes and gene clusters were shown to be differentially acquired or lost, supporting the hypothesis of divergent evolution of the two Streptomyces species in different sponge hosts.  ...  Rapp for sponge identification. Author Contributions  ... 
doi:10.1371/journal.pone.0096719 pmid:24819608 pmcid:PMC4018334 fatcat:3fxtihrin5cwfp2vpnacu6mnvi

Comparison of molecular mechanisms mediating cell contact phenomena in model developmental systems: an exploration of universality

Vivienne M. Bowers-Morrow, Sinan O. Ali, Keith L. Williams
2004 Biological Reviews  
developmental processes involving cell contact phenomena, because cellular mobility and cellular interactions are important phenomena in all phases of the sponge life cycle.  ...  On some phenomena of coalescence and regeneration in sponges. Journal of Experimental Xoology V, 245-258. Winson, H. V. (1910). tissue cells.  ... 
doi:10.1017/s1464793103006389 pmid:15366765 fatcat:x4yr32l6ivfnnbs47afnnegiai

The emerging roles of microRNAs in CNS injuries

Oneil G. Bhalala, Maya Srikanth, John A. Kessler
2013 Nature Reviews Neurology  
MicroRNAs (miRNAs) are RNA molecules composed of 20-24 nucleotides that function to inhibit mRNA translation and have key roles in normal CNS development and function, as well as in disease.  ...  The consequences of injuries to the CNS are profound and persistent, resulting in substantial burden to both the individual patient and society.  ...  by cerebral oedema and neuronal death among other phenomena.  ... 
doi:10.1038/nrneurol.2013.67 pmid:23588363 pmcid:PMC3755895 fatcat:sosms6x3vnhwhkmg7zblgcuvga

A Signature of Five Long Non-Coding RNAs for Predicting the Prognosis of Alzheimer's Disease Based on Competing Endogenous RNA Networks

Cai Huaying, Jin Xing, Jin Luya, Ni Linhui, Sun Di, Ding Xianjun
2021 Frontiers in Aging Neuroscience  
A total of 255 AD-deficient messenger RNA (mRNA)-lncRNAs were identified by the expression correlation analysis.  ...  Genes in the dysregulated ceRNAs were found to be mainly enriched in transcription factors and micro RNAs (miRNAs).  ...  In this study, we obtained the expression profile data of 629 patients with AD and control samples from eight datasets in the gene expression omnibus (GEO) database.  ... 
doi:10.3389/fnagi.2020.598606 pmid:33584243 pmcid:PMC7876075 fatcat:ioqlpyiylfenlbwc7krim66eqy
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