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miRNA,long non-coding RNA,

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https://www.readbyqxmd.com/read/29141604/genome-wide-identification-of-mirnas-and-lncrnas-in-cajanus-cajan
#1
Chandran Nithin, Amal Thomas, Jolly Basak, Ranjit Prasad Bahadur
BACKGROUND: Non-coding RNAs (ncRNAs) are important players in the post transcriptional regulation of gene expression (PTGR). On one hand, microRNAs (miRNAs) are an abundant class of small ncRNAs (~22nt long) that negatively regulate gene expression at the levels of messenger RNAs stability and translation inhibition, on the other hand, long ncRNAs (lncRNAs) are a large and diverse class of transcribed non-protein coding RNA molecules (> 200nt) that play both up-regulatory as well as down-regulatory roles at the transcriptional level...
November 15, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29138229/genomic-structural-variations-lead-to-dysregulation-of-important-coding-and-non-coding-rna-species-in-dilated-cardiomyopathy
#2
Jan Haas, Stefan Mester, Alan Lai, Karen S Frese, Farbod Sedaghat-Hamedani, Elham Kayvanpour, Tobias Rausch, Rouven Nietsch, Jes-Niels Boeckel, Avisha Carstensen, Mirko Völkers, Carsten Dietrich, Dietmar Pils, Ali Amr, Daniel B Holzer, Diana Martins Bordalo, Daniel Oehler, Tanja Weis, Derliz Mereles, Sebastian Buss, Eva Riechert, Emil Wirsz, Maximilian Wuerstle, Jan O Korbel, Andreas Keller, Hugo A Katus, Andreas E Posch, Benjamin Meder
The transcriptome needs to be tightly regulated by mechanisms that include transcription factors, enhancers, and repressors as well as non-coding RNAs. Besides this dynamic regulation, a large part of phenotypic variability of eukaryotes is expressed through changes in gene transcription caused by genetic variation. In this study, we evaluate genome-wide structural genomic variants (SVs) and their association with gene expression in the human heart. We detected 3,898 individual SVs affecting all classes of gene transcripts (e...
November 14, 2017: EMBO Molecular Medicine
https://www.readbyqxmd.com/read/29119346/structure-target-specificity-and-expression-of-pn_lnc_n13-a-long-non-coding-rna-differentially-expressed-in-apomictic-and-sexual-paspalum-notatum
#3
Ana Ochogavía, Giulio Galla, José Guillermo Seijo, Ana María González, Michele Bellucci, Fulvio Pupilli, Gianni Barcaccia, Emidio Albertini, Silvina Pessino
KEY MESSAGE: ncRNA PN_LNC_N13 shows contrasting expression in reproductive organs of sexual and apomictic Paspalum notatum genotypes. Apomictic plants set genetically maternal seeds whose embryos derive by parthenogenesis from unreduced egg cells, giving rise to clonal offspring. Several Paspalum notatum apomixis related genes were identified in prior work by comparative transcriptome analyses. Here, one of these candidates (namely N13) was characterized. N13 belongs to a Paspalum gene family including 30-60 members, of which at least eight are expressed at moderate levels in florets...
November 8, 2017: Plant Molecular Biology
https://www.readbyqxmd.com/read/29113749/long-non-coding-rna-atb-promotes-emt-during-silica-induced-pulmonary-fibrosis-by-competitively-binding-mir-200c
#4
Yi Liu, Yan Li, Qi Xu, Wenxi Yao, Qiuyun Wu, Jiali Yuan, Weiwen Yan, Tiantian Xu, Xiaoming Ji, Chunhui Ni
Long non-coding RNAs (lncRNAs) are important signal transduction regulators that act by various patterns. However, little is known about the molecular mechanisms of lncRNA related pathways in occupational lung fibrosis. Our previous study found that epithelial-mesenchymal transition (EMT) was one of the key events in silica-induced pulmonary fibrosis. This study showed that the lncRNA-ATB promoted EMT by acting as a miR-200c sponge. miR-200c was identified by miRNA array as a potential target of lncRNA-ATB and verified by dual luciferase reporter gene together with RNA pull-down assays...
November 4, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/29109091/transcriptomic-profiling-of-mda-mb-231-cells-exposed-to-boswellia-serrata-and-3-o-acetyl-b-boswellic-acid-er-upr-mediated-programmed-cell-death
#5
REVIEW
Elizabeth A Mazzio, Charles A Lewis, Karam F A Soliman
BACKGROUND/AIM: Triple-negative breast cancer (TNBC) is characterized by the absence of hormone receptors (estrogen, progesterone and human epidermal growth factor receptor-2) and a relatively poor prognosis due to inefficacy of hormone receptor-based chemotherapies. It is imperative that we continue to explore natural products with potential to impede growth and metastasis of TNBC. In this study, we screened over 1,000 natural products for capacity to induce cell death in TNBC (MDA-MB -231) cells...
November 2017: Cancer Genomics & Proteomics
https://www.readbyqxmd.com/read/29107050/microrna-21-and-long-non-coding-rna-malat1-are-overexpressed-markers-in-medullary-thyroid-carcinoma
#6
Ying-Hsia Chu, Heather Hardin, David F Schneider, Herbert Chen, Ricardo V Lloyd
BACKGROUND: Non-coding RNAs, including microRNAs (miRNAs) and long non-coding RNAs (lncRNAs), are well-recognized post-transcriptional regulators of gene expression. This study examines the expression of microRNA-21 (miR-21) and lncRNA MALAT1 in medullary thyroid carcinomas (MTCs) and their effects on tumor behavior. METHODS: Tissue microarrays (TMAs) were constructed using normal thyroid (n=39), primary tumors (N=39) and metastatic MTCs (N=18) from a total of 42 MTC cases diagnosed between 1987 and 2016...
October 26, 2017: Experimental and Molecular Pathology
https://www.readbyqxmd.com/read/29106390/glycolysis-gatekeeper-pdk1-reprograms-breast-cancer-stem-cells-under-hypoxia
#7
F Peng, J-H Wang, W-J Fan, Y-T Meng, M-M Li, T-T Li, B Cui, H-F Wang, Y Zhao, F An, T Guo, X-F Liu, L Zhang, L Lv, D-K Lv, L-Z Xu, J-J Xie, W-X Lin, E W-F Lam, J Xu, Q Liu
Glycolysis is critical for cancer stem cell reprogramming; however, the underlying regulatory mechanisms remain elusive. Here, we show that pyruvate dehydrogenase kinase 1 (PDK1) is enriched in breast cancer stem cells (BCSCs), whereas depletion of PDK1 remarkably diminishes ALDH(+) subpopulations, decreases stemness-related transcriptional factor expression, and inhibits sphere-formation ability and tumor growth. Conversely, high levels of PDK1 enhance BCSC properties and are correlated with poor overall survival...
November 6, 2017: Oncogene
https://www.readbyqxmd.com/read/29106055/lnc-ntf3-5-promotes-osteogenic-differentiation-of-maxillary-sinus-membrane-stem-cells-via-sponging-mir-93-3p
#8
Wei Peng, Shuang-Xi Zhu, Jin Wang, Li-Li Chen, Jun-Quan Weng, Song-Ling Chen
BACKGROUND: The function and the mechanism of long non-coding RNAs (lncRNAs) on the osteogenic differentiation of maxillary sinus membrane stem cells (MSMSCs) remain largely unknown. MATERIALS AND METHODS: The expression of lnc-NTF3-5 and Runt-related transcription factor 2 (RUNX2), Osterix (OSX), and Alkaline Phosphatase (ALP) was examined by quantitative real-time PCR (qRT-PCR) in MSMSCs during the process osteogenic differentiation. Then the function of lnc-NTF3-5 was evaluated by loss- and gain-of-function techniques, as well as qRT-PCR, western blot, and Alizarin Red staining...
November 6, 2017: Clinical Implant Dentistry and related Research
https://www.readbyqxmd.com/read/29104512/identification-and-analysis-of-p53-mediated-competing-endogenous-rna-network-in-human-hepatocellular-carcinoma
#9
Yiming Zhang, Ran Kang, Wenrong Liu, Yalan Yang, Ruofan Ding, Qingqing Huang, Junhua Meng, Lili Xiong, Zhiyun Guo
Recent studies have indicated that long non-coding RNAs (lncRNAs) and mRNA function as competing endogenous RNAs (ceRNAs) that compete to bind to shared microRNA (miRNA) recognition elements (MREs) to perform specific biological functions during tumorigenesis. The tumor suppressor p53 is a master regulator of cancer-related biological processes by acting as a transcription factor to regulate target genes including miRNA and lncRNA. However, the mechanism in human hepatocellular carcinoma and whether p53-mediated RNA targets could form ceRNA network remain unclear...
2017: International Journal of Biological Sciences
https://www.readbyqxmd.com/read/29101304/functional-role-of-a-novel-long-noncoding-rna-ttn-as1-in-esophageal-squamous-cell-carcinoma-progression-and-metastasis
#10
Chenyu Lin, Nan Zhang, Ying Wang, Yuanshu Wang, Changying Guo, Edouard Nice, Erhao Zhang, Liting Yu, Mengwei Zhang, Chen Liu, Lirong Hu, Jingchao Hao, Weiyan Qi, Hanmei Xu
PURPOSE: Emerging studies demonstrate that long non-coding RNAs (lncRNAs)participate in the regulation of various cancers. In the current study, a novel lncRNA-TTN-AS1 has been identified and explored in esophageal squamous cell carcinoma (ESCC). EXPERIMENTAL DESIGN: To discover a new regulatory circuitry in which RNAs crosstalk with each other, the transcriptome of lncRNA-miRNA-mRNA from ESCC and adjacent non-malignant specimens were analyzed using multiple microarrays and diverse bioinformatics platforms...
November 3, 2017: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/29068471/long-non-coding-rna-ager-1-functionally-upregulates-the-innate-immunity-gene-ager-and-approximates-its-anti-tumor-effect-in-lung-cancer
#11
Zihua Pan, Li Liu, Wenjing Nie, Sinead Miggin, Fuman Qiu, Yi Cao, Jinbin Chen, Binyao Yang, Yifeng Zhou, Jiachun Lu, Lei Yang
BACKGROUND: Little is known about long non-coding RNA (lncRNA) related to innate immunity in lung cancer. The advanced glycosylation end-product specific receptor (AGER) belongs to the immunoglobulin superfamily, and currently, is the only innate immune pattern-recognition receptor whose abnormal expression has been detected in lung cancer. We aimed to explore the lncRNA that is related to AGER and test its effect on lung carcinogenesis. METHODS: We selected one lncRNA whose chromosome location is in close proximity to AGER namely lnc-AGER-1 (defined as lncAGER)...
October 25, 2017: Molecular Carcinogenesis
https://www.readbyqxmd.com/read/29061182/editing-inducer-elements-increases-a-to-i-editing-efficiency-in-the-mammalian-transcriptome
#12
Chammiran Daniel, Albin Widmark, Ditte Rigardt, Marie Öhman
BACKGROUND: Adenosine to inosine (A-to-I) RNA editing has been shown to be an essential event that plays a significant role in neuronal function, as well as innate immunity, in mammals. It requires a structure that is largely double-stranded for catalysis but little is known about what determines editing efficiency and specificity in vivo. We have previously shown that some editing sites require adjacent long stem loop structures acting as editing inducer elements (EIEs) for efficient editing...
October 23, 2017: Genome Biology
https://www.readbyqxmd.com/read/29052198/de-novo-identification-of-srna-loci-and-non-coding-rnas-by-high-throughput-sequencing
#13
Alice Lunardon, Cristian Forestan, Silvia Farinati, Serena Varotto
Non-coding RNA transcripts, such as long non-coding RNAs, miRNAs, siRNAs, and transposon-originating transcripts, are involved in the regulation of RNA stability, protein translation, and/or the modulation of chromatin states. RNA-Seq can be used to catalog this diversity of novel transcripts and a joint analysis of these transcriptomic data can provide useful insights into epigenetic regulation of dynamic responses such as the stress response, which may not be deciphered from individual analysis of single transcript categories...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29050002/urinary-erythrocyte-derived-mirnas-emerging-role-in-iga-nephropathy
#14
Zhi-Yu Duan, Guang-Yan Cai, Ji-Jun Li, Ru Bu, Xiang-Mei Chen
Hematuria is one of the basic clinical manifestations of IgA nephropathy (IgAN). Isolated microscopic hematuria or microscopic hematuria combined with proteinuria is risk factor for the long-term prognosis of IgAN. Current evidence of the consequences of glomerular hematuria rests on insights from basic research on the molecular mechanisms of hemoglobin and related reactive oxygen species-induced tubular injury as well as on the clinical evidence of macroscopic hematuria-associated acute kidney injury (AKI) in IgAN...
October 19, 2017: Kidney & Blood Pressure Research
https://www.readbyqxmd.com/read/29048648/long-non-coding-rna-xist-regulates-pdcd4-expression-by-interacting-with-mir-21-5p-and-inhibits-osteosarcoma-cell-growth-and-metastasis
#15
Rui Zhang, Tian Xia
lncRNA-X-inactive specific transcript (lncRNA XIST) has been demonstrated to be a tumor suppressor involved in the pathogenesis and development of various cancers. However, the function of XIST and its working mechanism in osteosarcoma (OS) remain enigmatic. Firstly, we determined the expression of XIST in OS tissues and cell lines by quantitative reverse transcription-PCR (qRT-PCR) and explored whether aberrant XIST expression was associated with recurrence and short overall survival. Furthermore, the effects of XIST on osteosarcoma cells were studied by lentivirus mediated overexpression approach in vitro and in vivo...
September 19, 2017: International Journal of Oncology
https://www.readbyqxmd.com/read/29040625/rise-a-database-of-rna-interactome-from-sequencing-experiments
#16
Jing Gong, Di Shao, Kui Xu, Zhipeng Lu, Zhi John Lu, Yucheng T Yang, Qiangfeng Cliff Zhang
We present RISE (http://rise.zhanglab.net), a database of RNA Interactome from Sequencing Experiments. RNA-RNA interactions (RRIs) are essential for RNA regulation and function. RISE provides a comprehensive collection of RRIs that mainly come from recent transcriptome-wide sequencing-based experiments like PARIS, SPLASH, LIGR-seq, and MARIO, as well as targeted studies like RIA-seq, RAP-RNA and CLASH. It also includes interactions aggregated from other primary databases and publications. The RISE database currently contains 328,811 RNA-RNA interactions mainly in human, mouse and yeast...
October 4, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29039552/prospective-lncrna-mirna-mrna-regulatory-network-of-long-non-coding-rna-linc00968-in-non-small-cell-lung-cancer-a549-cells-a-mirna-microarray-and-bioinformatics-investigation
#17
Dong-Yao Li, Wen-Jie Chen, Lei Luo, Yong-Kun Wang, Jun Shang, Yu Zhang, Gang Chen, Shi-Kang Li
Accumulating evidence suggests that the dysregulation of long non-coding RNAs (lncRNAs) serves vital roles in the incidence and progression of lung cancer. However, the molecular mechanisms of LINC00968, a recently identified lncRNA, remain unknown. The objective of present study was to investigate the role of a prospective lncRNA-miRNA‑mRNA network regulated by LINC00968 in non-small cell lung cancer cells. Following the transfection of lentiviruses carrying LINC00968 into A549 cells, the microRNA (miRNA) expression profile of the cells in response to the overexpression of LINC00968 was detected using an miRNA microarray...
October 12, 2017: International Journal of Molecular Medicine
https://www.readbyqxmd.com/read/29038661/assembly-and-annotation-of-transcriptome-provided-evidence-of-mirna-mobility-between-wheat-and-wheat-stem-sawfly
#18
Halise B Cagirici, Sezgi Biyiklioglu, Hikmet Budak
Wheat Stem Sawfly (WSS), Cephus Cinctus Norton (Hymenoptera: Cephidae), is one of the most important pests, causing yield and economic losses in wheat and barley. The lack of information about molecular mechanisms of WSS for defeating plant's resistance prevents application of effective pest control strategies therefore, it is essential to identify the genes and their regulators behind WSS infestations. Long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) are recognized with their regulatory functions on gene expression, tuning protein production by controlling transcriptional and post-transcriptional activities...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29036429/genome-re-annotation-of-the-wild-strawberry-fragaria-vesca-using-extensive-illumina-and-smrt-based-rna-seq-datasets
#19
Yongping Li, Wei Wei, Jia Feng, Huifeng Luo, Mengting Pi, Zhongchi Liu, Chunying Kang
The genome of the wild diploid strawberry species Fragaria vesca, an ideal model system of cultivated strawberry (Fragaria × ananassa, octoploid) and other Rosaceae family crops, was first published in 2011 and followed by a new assembly (Fvb). However, the annotation for Fvb mainly relied on ab initio predictions and included only predicted coding sequences, therefore an improved annotation is highly desirable. Here, a new annotation version named v2.0.a2 was created for the Fvb genome by a pipeline utilizing one PacBio library, 90 Illumina RNA-seq libraries, and 9 small RNA-seq libraries...
September 23, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/29029488/integrated-analysis-of-competing-endogenous-rna-network-revealing-lncrnas-as-potential-prognostic-biomarkers-in-human-lung-squamous-cell-carcinoma
#20
Jing Sui, Si-Yi Xu, Jiali Han, Song-Ru Yang, Cheng-Yun Li, Li-Hong Yin, Yue-Pu Pu, Ge-Yu Liang
Accumulating evidence shows the important role of long non-coding RNAs (lncRNAs) in competing endogenous RNA (ceRNA) networks for predicting survival in tumor patients. However, prognostic biomarkers for lung squamous cell carcinoma (LUSC) are still lacking. The objective of this study is to identify a lncRNA signature for evaluation of overall survival (OS) in 474 LUSC patients from The Cancer Genome Atlas (TCGA) database. A total of 474 RNA sequencing profiles in LUSC patients with clinical data were obtained, providing a large sample of RNA sequencing data, and 83 LUSC-specific lncRNAs, 26 miRNAs, and 85 mRNAs were identified to construct the ceRNA network (fold change>2, P<0...
September 12, 2017: Oncotarget
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