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https://www.readbyqxmd.com/read/29434199/single-cell-full-length-total-rna-sequencing-uncovers-dynamics-of-recursive-splicing-and-enhancer-rnas
#1
Tetsutaro Hayashi, Haruka Ozaki, Yohei Sasagawa, Mana Umeda, Hiroki Danno, Itoshi Nikaido
Total RNA sequencing has been used to reveal poly(A) and non-poly(A) RNA expression, RNA processing and enhancer activity. To date, no method for full-length total RNA sequencing of single cells has been developed despite the potential of this technology for single-cell biology. Here we describe random displacement amplification sequencing (RamDA-seq), the first full-length total RNA-sequencing method for single cells. Compared with other methods, RamDA-seq shows high sensitivity to non-poly(A) RNA and near-complete full-length transcript coverage...
February 12, 2018: Nature Communications
https://www.readbyqxmd.com/read/29433989/downregulation-of-long-non-coding-rna-ensg00000241684-is-associated-with-poor-prognosis-in-advanced-clear-cell-renal-cell-carcinoma
#2
Hengchuan Su, Hongkai Wang, Guohai Shi, Hailiang Zhang, Fukang Sun, Dingwei Ye
OBJECTIVE: In order to identify potential novel biomarkers of advanced clear cell renal cell carcinoma (ccRCC), we re-evaluated published long non-coding RNA (lncRNA) expression profiling data. MATERIALS AND METHODS: The lncRNA expression profiles in ccRCC microarray dataset GSE47352 were analyzed and an independent cohort of 61 clinical samples including 21 advanced and 40 localized ccRCC patients was used to confirm the most statistically significant lncRNAs by real time PCR...
January 13, 2018: European Journal of Surgical Oncology
https://www.readbyqxmd.com/read/29416922/long-noncoding-rna-neat1-promotes-the-metastasis-of-osteosarcoma-via-interaction-with-the-g9a-dnmt1-snail-complex
#3
Yong Li, Cai Cheng
Osteosarcoma (OS) is the most common histological form of primary bone cancer. Long noncoding RNA nuclear enriched abundant transcript 1 (NEAT1) functions as an oncogene in some cancers. However, the functional role of NEAT1 in OS metastasis remains elusive. In the present study, we found that NEAT1 expression was significantly increased in OS tissues and cell lines. Overexpression of NEAT1 in OS tissues was correlated with higher clinical stage, distant metastasis and poorer prognosis. Loss- and gain-of-function assays showed that NEAT1 positively regulated metastasis in vitro and in vivo...
2018: American Journal of Cancer Research
https://www.readbyqxmd.com/read/29416780/lncrna-neat1-enhances-the-radio-resistance-of-cervical-cancer-via-mir-193b-3p-ccnd1-axis
#4
Dongmei Han, Jianfeng Wang, Guanghui Cheng
LncRNAs have become a hot topic in various cancer-related researches. Radio-resistance is a great threat for cancer therapy. However, how lncRNAs affect the radio-resistance in cervical cancer is masked. As for our paper, it was discovered that NEAT1 was highly expressed in cervical cancer tissues and non-sensitive tissues as well as radio-resistant cell lines. And the overexpression of NEAT1 accelerated proliferation, while the knockdown of NEAT1 had the opposite result. The effect of NEAT1 on cell proliferation was dependent on the dose of ionizing radiation...
January 5, 2018: Oncotarget
https://www.readbyqxmd.com/read/29396444/differential-long-non-coding-rna-expression-profiles-in-human-oocytes-and-cumulus-cells
#5
Julien Bouckenheimer, Patricia Fauque, Charles-Henri Lecellier, Céline Bruno, Thérèse Commes, Jean-Marc Lemaître, John De Vos, Said Assou
Progress in assisted reproductive technologies strongly relies on understanding the regulation of the dialogue between oocyte and cumulus cells (CCs). Little is known about the role of long non-coding RNAs (lncRNAs) in the human cumulus-oocyte complex (COC). To this aim, publicly available RNA-sequencing data were analyzed to identify lncRNAs that were abundant in metaphase II (MII) oocytes (BCAR4, C3orf56, TUNAR, OOEP-AS1, CASC18, and LINC01118) and CCs (NEAT1, MALAT1, ANXA2P2, MEG3, IL6STP1, and VIM-AS1)...
February 2, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29394378/structural-analyses-of-neat1-lncrnas-suggest-long-range-rna-interactions-that-may-contribute-to-paraspeckle-architecture
#6
Yizhu Lin, Brigitte F Schmidt, Marcel P Bruchez, C Joel McManus
Paraspeckles are nuclear bodies that regulate multiple aspects of gene expression. The long non-coding RNA (lncRNA) NEAT1 is essential for paraspeckle formation. NEAT1 has a highly ordered spatial organization within the paraspeckle, such that its 5' and 3' ends localize on the periphery of paraspeckle, while central sequences of NEAT1 are found within the paraspeckle core. As such, the structure of NEAT1 RNA may be important as a scaffold for the paraspeckle. In this study, we used SHAPE probing and computational analyses to investigate the secondary structure of human and mouse NEAT1...
January 31, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29388017/systematical-analysis-of-lncrna-mrna-competing-endogenous-rna-network-in-breast-cancer-subtypes
#7
Shunheng Zhou, Lihong Wang, Qian Yang, Haizhou Liu, Qianqian Meng, Leiming Jiang, Shuyuan Wang, Wei Jiang
BACKGROUND: Breast cancer is one of the most common solid tumors in women involving multiple subtypes. However, the mechanism for subtypes of breast cancer is still complicated and unclear. Recently, several studies indicated that long non-coding RNAs (lncRNAs) could act as sponges to compete miRNAs with mRNAs, participating in various biological processes. METHODS: We concentrated on the competing interactions between lncRNAs and mRNAs in four subtypes of breast cancer (basal-like, HER2+, luminal A and luminal B), and analyzed the impacts of competing endogenous RNAs (ceRNAs) on each subtype systematically...
February 1, 2018: Breast Cancer Research and Treatment
https://www.readbyqxmd.com/read/29363783/long-noncoding-rna-neat1-modualted-mir-506-regulates-gastric-cancer-development-through-targeting-stat3
#8
Hai-Yang Tan, Changcheng Wang, Gao Liu, Xiang Zhou
Accumulating evidence has indicated that lncRNA NEAT1 exerts critical roles in cancers. So far, the detailed biological role and mechanisms of NEAT1 which are responsible for human gastric cancer (GC) is still largely unknown. Here, we observed that NEAT1 and STAT3 expression were significantly upregulated in human gastric cancer cells including BGC823, SGC-7901, AGS, MGC803 and MKN28 cells compared to normal gastric epithelial cells GES-1 while miR-506 was downregulated. We inhibited NEAT1 and observed that NEAT1 inhibition was able to repress the growth, migration and invasion of gastric cancer cells...
January 24, 2018: Journal of Cellular Biochemistry
https://www.readbyqxmd.com/read/29323713/neat1-contributes-to-breast-cancer-progression-through-modulating-mir-448-and-zeb1
#9
Xing Jiang, Yong Zhou, Ai-Jun Sun, Jun-Li Xue
Breast cancer is a kind of common female cancers. Increasing evidence has exhibited that lncRNAs exert a crucial role in breast cancer. So far, the mechanism of lncRNAs in breast cancer is still not well established. In our current study, we focused on the biological role of lncRNA Nuclear Enriched Abundant Transcript 1 (NEAT1) in breast cancer. We observed that NEAT1 levels were significantly increased in human breast cancer cells including MCF-7, MDA-MB-453, MDA-MB-231and SKBR3 cells compared to normal mammary epithelial cells MCF-10A while miR-448 was decreased...
January 11, 2018: Journal of Cellular Physiology
https://www.readbyqxmd.com/read/29319165/long-noncoding-rna-neat1-regulate-papillary-thyroid-cancer-progression-by-modulating-mir-129-5p-klk7-expression
#10
Hong Zhang, Yuechang Cai, Li Zheng, Zhanlei Zhang, Xiaofeng Lin, Ningyi Jiang
PURPOSE: Considering the dilemma in papillary thyroid cancer treatment, this study intended to find solution in molecular respect. By probing into lncRNA-NEAT1/miR-129-5p/ KLK7 interaction, this study would provide new targets for future treatment. METHODS: Microarray analysis and R language package were applied to select possible lncRNA and miRNA. Luciferase reporter assay and RNA pull-down test were employed in the detection of target relationship between lncRNA and miRNA...
January 10, 2018: Journal of Cellular Physiology
https://www.readbyqxmd.com/read/29312630/neat1-in-hematopoietic-stem-cells
#11
Noam Fallik, Yael Bar-Lavan, Yariv Greenshpan, Oron Goldstein, Markus Grosch, Micha Drukker, Roi Gazit
Hematopoietic Stem Cells (HSCs) generate blood and immune cells through a hierarchical process of differentiation. Genes that regulate this process are of great interest for understanding normal and also malignant hematopoiesis. Surprisingly, however, very little is known about long-non-coding RNAs (lncRNA) in HSCs. Neat1 is a lncRNA that plays a major role in the formation of sub-nuclear structures called paraspeckles, and was reported to regulate proliferation and differentiation in other cells types. We detected Neat1 expression using RNA-seq data and RT-qPCR in HSCs, progenitors and effector immune cells, by specific detection of its isoforms...
December 12, 2017: Oncotarget
https://www.readbyqxmd.com/read/29287722/lncrna-neat1-promotes-autophagy-in-mptp-induced-parkinson-s-disease-through-stabilizing-pink1-protein
#12
Wang Yan, Zhao-Ying Chen, Jia-Qi Chen, Hui-Min Chen
BACKGROUND: Long non-coding RNA nuclear paraspeckle assembly transcript 1 (lncRNA NEAT1) was found to be closely related to the pathological changes in brain and nervous system. However, the role of NEAT1 and its potential mechanism in Parkinson's disease (PD) largely remain uncharacterized. METHODS: In this study, PD mouse model was established by intraperitoneal injection of MPTP. The numbers of TH + neurons, NEAT1 expression and the level of PINK1, LC3-II, LC3-I protein were assessed in PD mice...
December 26, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/29242407/central-role-of-the-p53-pathway-in-the-noncoding-rna-response-to-oxidative-stress
#13
Paola Fuschi, Matteo Carrara, Christine Voellenkle, Jose Manuel Garcia-Manteiga, Paolo Righini, Biagina Maimone, Elena Sangalli, Francesco Villa, Claudia Specchia, Mario Picozza, Giovanni Nano, Carlo Gaetano, Gaia Spinetti, Annibale A Puca, Alessandra Magenta, Fabio Martelli
Oxidative stress plays a fundamental role in many conditions. Specifically, redox imbalance inhibits endothelial cell (EC) growth, inducing cell death and senescence. We used global transcriptome profiling to investigate the involvement of noncoding-RNAs in these phenotypes. By RNA-sequencing, transcriptome changes were analyzed in human ECs exposed to H2O2, highlighting a pivotal role of p53-signaling. Bioinformatic analysis and validation in p53-silenced ECs, identified several p53-targets among both mRNAs and long noncoding-RNAs (lncRNAs), including MALAT1 and NEAT1...
December 12, 2017: Aging
https://www.readbyqxmd.com/read/29225160/oncogenic-non-coding-rna-neat1-promotes-the-prostate-cancer-cell-growth-through-the-src3-igf1r-akt-pathway
#14
Wei Xiong, Changkun Huang, Huanghao Deng, Chengzhu Jian, Cong Zen, Kun Ye, Zhaohui Zhong, Xiaokun Zhao, Liang Zhu
Steroid receptor co-activator3 (SRC3) has been known to severe as an androgen receptor (AR) coactivator and is involved in the prostate cancer progression. Non-coding RNA (ncRNA) plays an important role in the cancer progression. However, the mechanism underlying the relationship between ncRNA and AR coactivators is still unclear. Here, we found a ncRNA, Nuclear Enriched Abundant Transcript 1 (NEAT1), was able to interact with SRC3 in the prostate cancer cell lines. NEAT1 can upregulate the AKT phosphorylation via a SRC3/IGF1R pathway...
December 7, 2017: International Journal of Biochemistry & Cell Biology
https://www.readbyqxmd.com/read/29222807/long-non-coding-rna-expression-in-bladder-cancer
#15
REVIEW
Mohammad Taheri, Mir Davood Omrani, Soudeh Ghafouri-Fard
The advent of novel high-throughput sequencing methods has facilitated identification of non-coding RNAs with fundamental roles in cellular biological and pathological conditions. A group of these consisting of at least 200 nucleotides are called long non-coding RNAs (lncRNAs). Their participation in the pathogenesis of cancer has been highlighted in recent years. Bladder cancer, one of the most prevalent cancers worldwide, exhibits altered expression levels of several lncRNAs. Several in vitro and in vivo studies have assessed the effects of silencing RNAs on cancer cell phenotypes and in vivo tumor growth...
December 8, 2017: Biophysical Reviews
https://www.readbyqxmd.com/read/29219178/the-long-noncoding-rna-neat1-contributes-to-hepatocellular-carcinoma-development-by-sponging-mir-485-and-enhancing-the-expression-of-the-stat3
#16
Xu-Nan Zhang, Chang-Cheng Wang, Jun Zhou
Accumulating evidence has supported the significance of lncRNAs in tumorigenesis. Recently, some studies indicate the oncogenic role of lncRNA Nuclear Enriched Abundant Transcript 1 (NEAT1) in hepatocellular carcinoma (HCC). In our present study, we focused on the biological mechanisms through which NEAT1 can regulate HCC development. We found that NEAT1 was greatly upregulated in human HCC cell lines including Huh7, Hep3B, HepG2, Bel-7404 and SK-Hep1 cells compared to the normal human liver cell line LO2. In addition, we observed that miR-485 was significantly downregulated in HCC cells...
December 8, 2017: Journal of Cellular Physiology
https://www.readbyqxmd.com/read/29207151/long-non%C3%A2-coding-nuclear-paraspeckle-assembly-transcript-1-acts-as-prognosis-biomarker-and-increases-cell-growth-and-invasion-in-cervical-cancer-by-sequestering-microrna%C3%A2-101
#17
Li Wang, Hongying Zhu
Emerging studies have focused on the essential role of long non‑coding RNAs (lncRNAs) in cervical carcinogenesis. A recent study has indicated that nuclear paraspeckle assembly transcript 1 (NEAT1) is highly expressed in the human cervical tissue. However, whether NEAT1 is involved in cervical cancer remains to be elucidated. Reverse transcription‑quantitative polymerase chain reaction results demonstrated that the expression of NEAT1 was higher in cervical cancer cells/tissues compared with that in normal human keratinocytes/tissues...
November 29, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/29205703/lncrna-neat1-promotes-dexamethasone-resistance-in-multiple-myeloma-by-targeting-mir-193a-mcl1-pathway
#18
Yilan Wu, Han Wang
Although dexamethasone (DEX) remains a first-line agent for multiple myeloma (MM) therapy, the development of DEX resistance has become an indicator of poor prognosis in MM patients. It is thus urgent to develop strategies to restore the vulnerability of MM to DEX. This study demonstrated long non-coding RNA (lncRNA) nuclear paraspeckle assembly transcript 1 (NEAT1) was highly expressed in DEX-resistant myeloma cell lines, and upregulation of NEAT1 was tightly linked to poor prognosis. The in-depth study revealed that during the development of DEX resistance in these cells, the miR-193a levels were decreased, which resulted in the increased expression of the target gene myeloid cell leukemia-1 (MCL1)...
December 4, 2017: Journal of Biochemical and Molecular Toxicology
https://www.readbyqxmd.com/read/29180871/lncrna-neat1-contributes-to-paclitaxel-resistance-of-ovarian-cancer-cells-by-regulating-zeb1-expression-via-mir-194
#19
Jihong An, Weiling Lv, Yongzhou Zhang
Background: Chemoresistance is one of the major obstacles for cancer therapy in the clinic. Nuclear paraspeckle assembly transcript 1 (NEAT1) has been reported as an oncogene in most malignancies such as lung cancer, esophageal cancer, and gastric cancer. This study is designed to investigate the function of NEAT1 in paclitaxel (PTX) resistance of ovarian cancer and its potential molecular mechanism. Patients and methods: The expressions of NEAT1 and miR-194 in ovarian cancer tissues and cells were estimated by quantitative real-time polymerase chain reaction (qRT-PCR)...
2017: OncoTargets and Therapy
https://www.readbyqxmd.com/read/29176322/differential-expression-profiles-of-the-transcriptome-in-breast-cancer-cell-lines-revealed-by-next-generation-sequencing
#20
Yu Shi, Peng Ye, Xinghua Long
BACKGROUND/AIMS: As MCF-7 and MDA-MB-231 cells are the typical cell lines of two clinical breast tumour subtypes, the aim of the present study was to elucidate the transcriptome differences between MCF-7 and MDA-MB-231 breast cancer cell lines. METHODS: The mRNA, miRNA (MicroRNA) and lncRNA (Long non-coding RNA) expression profiles were examined using NGS (next generation sequencing) instrument Illumina HiSeq-2500. GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway analyses were performed to identify the biological functions of differentially expressed coding RNAs...
November 24, 2017: Cellular Physiology and Biochemistry
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