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long noncoding Rnas

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https://www.readbyqxmd.com/read/27935117/long-noncoding-rna-malat1-affects-the-efficacy-of-radiotherapy-for-esophageal-squamous-cell-carcinoma-by-regulating-cks1-expression
#1
Zhijun Li, Yang Zhou, Bo Tu, Yu Bu, Aqiu Liu, Conghua Xie
OBJECTIVE: Long noncoding RNA MALAT1 has been well-studied in the progression of many malignancies. However, its association with the radioresistance of tumors has not been well-understood yet. This study tried to explore the role of MALAT1 in regulating the radiosensitivity of esophageal cancer (EC), especially esophageal squamous cell carcinoma (ESCC), involving its regulation on Cks1 expression. METHODS: KYSE150 cells were subcutaneously inoculated into nude mice to establish ESCC xenografts...
December 9, 2016: Journal of Oral Pathology & Medicine
https://www.readbyqxmd.com/read/27933111/aberrant-dna-hypermethylation-silenced-sox21-as1-gene-expression-and-its-clinical-importance-in-oral-cancer
#2
Cheng-Mei Yang, Tsung-Han Wang, Hung-Chih Chen, Sung-Chou Li, Ming-Chien Lee, Huei-Han Liou, Pei-Feng Liu, Yu-Kai Tseng, Yow-Ling Shiue, Luo-Ping Ger, Kuo-Wang Tsai
BACKGROUND: Long noncoding RNAs (lncRNAs) are more than 200 nucleotides in length and lack transcriptional ability. The biological function of lncRNAs in oral squamous cell carcinoma (OSCC) remains unclear. The aim of this study was to identify the dysfunction of lncRNA in OSCC. RESULTS: We analyzed the transcriptome profiles of human OSCC tissues and paired adjacent normal tissues from two patients through a next-generation sequencing approach. A total of 14 lncRNAs were upregulated (fold change ≥3) and 13 were downregulated (fold change ≤-3) in OSCC tissues compared with the adjacent normal tissues...
2016: Clinical Epigenetics
https://www.readbyqxmd.com/read/27932875/screening-of-long-non-coding-rna-and-tug1-inhibits-proliferation-with-tgf-%C3%AE-induction-in-patients-with-copd
#3
Wenxiang Tang, Zhenyu Shen, Jiang Guo, Shenghua Sun
OBJECTIVE: To evaluate differentially expressed long noncoding RNAs (lncRNAs) and the potential role of lncRNA TUG1 in patients with chronic obstructive pulmonary disease (COPD). METHODS: Total RNA was extracted from both COPD and non-COPD lung tissues, and microarray analysis was performed with 25,628 lncRNA probes and 20,106 mRNA probes. In addition, five up-regulated and five down-regulated lncRNAs were selected for identification using quantitative real-time polymerase chain reaction...
2016: International Journal of Chronic Obstructive Pulmonary Disease
https://www.readbyqxmd.com/read/27931286/knockdown-of-long-noncoding-rna-ghet1-inhibits-cell-proliferation-and-invasion-of-colorectal-cancer
#4
Jianyu Zhou, Xiaorong Li, Meirong Wu, Changwei Lin, Yihang Guo, Buning Tian
Emerging evidence has identified the vital role of long noncoding RNAs (lncRNAs) in the development of colorectal cancer. In this study, we aimed to investigate the role of lncRNA gastric carcinoma highly expressed transcript 1 (GHET1) in colorectal cancer. We analyzed the expression of GHET1 in colorectal cancer (CRC) tissues by using ISH. We found that GHET1 expression was significantly increased in the CRC samples compared with adjacent tissues. Furthermore, the cancer tissues had higher GHET1 mRNA levels than their matched adjacent tissues...
May 2016: Oncology Research
https://www.readbyqxmd.com/read/27929737/long-noncoding-rna-hit000218960-promotes-papillary-thyroid-cancer-oncogenesis-and-tumor-progression-by-upregulating-the-expression-of-high-mobility-group-at-hook-2-hmga2-gene
#5
Tao Li, Xiao-Dong Yang, Chun-Xiang Ye, Zhan-Long Shen, Yang Yang, Bo Wang, Peng Guo, Zhi-Dong Gao, Ying-Jiang Ye, Ke-Wei Jiang, Shan Wang
Accumulating evidence suggests that long noncoding RNAs (lncRNAs) play an important role in oncogenesis and tumor progression. However, our knowledge of lncRNAs in thyroid cancer is still limited. To explore the crucial lncRNAs involved in oncogenesis of papillary thyroid cancer (PTC), we acquired data of differentially expressed lncRNAs between PTC tissues and paired adjacent noncancerous thyroid tissues through lncRNA microarray. In the microarray data, we observed that a newly identified lncRNA, HIT000218960, was significantly upregulated in PTC tissues and associated with a well-known oncogene, high mobility group AT-hook 2 (HMGA2) gene...
December 8, 2016: Cell Cycle
https://www.readbyqxmd.com/read/27928018/expression-of-the-antisense-to-latency-transcript-long-noncoding-rna-in-kaposi-s-sarcoma-associated-herpesvirus
#6
Jason M Schifano, Kathleen Corcoran, Hemant Kelkar, Dirk P Dittmer
: The regulation of latency is central to herpesvirus biology. Recent transcriptome-wide surveys have uncovered evidence for promiscuous transcription across the entirety of the Kaposi sarcoma-associated herpesvirus genome and postulated the existence of multiple viral long noncoding RNAs (lncRNAs). NextGen sequencing studies are highly dependent on the specific experimental approach and particular algorithms of analysis, and therefore benefit from independent confirmation of the results...
December 7, 2016: Journal of Virology
https://www.readbyqxmd.com/read/27927715/chromatin-environment-transcriptional-regulation-and-splicing-distinguish-lincrnas-and-mrnas
#7
Marta Melé, Kaia Mattioli, William Mallard, David M Shechner, Chiara Gerhardinger, John L Rinn
While long intergenic noncoding RNAs (lincRNAs) and mRNAs share similar biogenesis pathways, these transcript classes differ in many regards. LincRNAs are less evolutionarily conserved, less abundant, and more tissue-specific, suggesting that their pre- and post-transcriptional regulation is different from that of mRNAs. Here, we perform an in-depth characterization of the features that contribute to lincRNA regulation in multiple human cell lines. We find that lincRNA promoters are depleted of transcription factor (TF) binding sites, yet enriched for some specific factors such as GATA and FOS relative to mRNA promoters...
December 7, 2016: Genome Research
https://www.readbyqxmd.com/read/27927271/long-noncoding-rna-expression-signatures-of-abdominal-aortic-aneurysm-revealed-by-microarray
#8
Yao Guo Yang, Mei Xia Li, Lei Kou, You Zhou, Yan Wen Qin, Xiao Jun Liu, Zhong Chen
OBJECTIVE: This study is aimed at observing the role of long noncoding RNAs (lncRNAs) in the pathogenesis of abdominal aortic aneurysm (AAA). METHODS: LncRNA and mRNA expression signatures of AAA tissues and normal abdominal aortic tissues (NT) were analyzed by microarray and further verified by Real-time quantitative reverse-transcription PCR (qRT-PCR). The lncRNAs-mRNAs targeting relationships were identified using computational analysis. The effect of lnc-ARG on 5-lipoxygenase (ALOX5) expression was tested in HeLa cells...
October 2016: Biomedical and Environmental Sciences: BES
https://www.readbyqxmd.com/read/27924044/plamom-a-comprehensive-database-compiles-plant-mobile-macromolecules
#9
Daogang Guan, Bin Yan, Christoph Thieme, Jingmin Hua, Hailong Zhu, Kenneth R Boheler, Zhongying Zhao, Friedrich Kragler, Yiji Xia, Shoudong Zhang
In plants, various phloem-mobile macromolecules including noncoding RNAs, mRNAs and proteins are suggested to act as important long-distance signals in regulating crucial physiological and morphological transition processes such as flowering, plant growth and stress responses. Given recent advances in high-throughput sequencing technologies, numerous mobile macromolecules have been identified in diverse plant species from different plant families. However, most of the identified mobile macromolecules are not annotated in current versions of species-specific databases and are only available as non-searchable datasheets...
October 24, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27923049/expression-of-lncrnas-in-low-grade-gliomas-and-glioblastoma-multiforme-an-in-silico-analysis
#10
Brian J Reon, Jordan Anaya, Ying Zhang, James Mandell, Benjamin Purow, Roger Abounader, Anindya Dutta
BACKGROUND: Each year, over 16,000 patients die from malignant brain cancer in the US. Long noncoding RNAs (lncRNAs) have recently been shown to play critical roles in regulating neurogenesis and brain tumor progression. To better understand the role of lncRNAs in brain cancer, we performed a global analysis to identify and characterize all annotated and novel lncRNAs in both grade II and III gliomas as well as grade IV glioblastomas (glioblastoma multiforme [GBM]). METHODS AND FINDINGS: We determined the expression of all lncRNAs in over 650 brain cancer and 70 normal brain tissue RNA sequencing datasets from The Cancer Genome Atlas (TCGA) and other publicly available datasets...
December 2016: PLoS Medicine
https://www.readbyqxmd.com/read/27922056/identification-and-functional-analysis-of-long-intergenic-noncoding-rna-genes-in-porcine-pre-implantation-embryonic-development
#11
Jingyu Li, Zhengling Gao, Xingyu Wang, Hongbo Liu, Yan Zhang, Zhonghua Liu
Genome-wide transcriptome studies have identified thousands of long intergenic noncoding RNAs (lincRNAs), some of which play important roles in pre-implantation embryonic development (PED). Pig is an ideal model for reproduction, however, porcine lincRNAs are still poorly characterized and it is unknown if they are associated with porcine PED. Here we reconstructed 195,531 transcripts in 122,007 loci, and identified 7,618 novel lincRNAs from 4,776 loci based on published RNA-seq data. These lincRNAs show low exon number, short length, low expression level, tissue-specific expression and cis-acting, which is consistent with previous reports in other species...
December 6, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27920576/hmmr-antisense-rna-1-a-novel-long-noncoding-rna-regulates-the-progression-of-basal-like-breast-cancer-cells
#12
Wei Liu, Jun Ma, Yong Cheng, Hongbo Zhang, Wengguang Luo, Hongyan Zhang
Recently, accumulating evidence has suggested that long noncoding RNAs (lncRNAs) play crucial roles in carcinogenesis and cancer progression. Hyaluronan-mediated motility receptor (HMMR) is an essential cancer-related gene in basal-like breast cancer (BLBC). In our study, HMMR antisense RNA 1 (HMMR-AS1) was analyzed in BLBC patients through polymerase chain reaction analysis. Here, we found that the expression of HMMR was positively correlated with HMMR-AS1 (RP11-80G.1). When HMMR-AS1 (RP11-80G.1) was knocked down, the expression of HMMR markedly reduced...
2016: Breast Cancer: Targets and Therapy
https://www.readbyqxmd.com/read/27919747/h19-mediates-methotrexate-resistance-in-colorectal-cancer-through-activating-wnt-%C3%AE-catenin-pathway
#13
Ke-Feng Wu, Wei-Cheng Liang, Lu Feng, Jian-Xin Pang, Mary Miu-Yee Waye, Jin-Fang Zhang, Wei-Ming Fu
Colorectal cancer (CRC) is a common malignancy, most of which remain unresponsive to chemotherapy. As one of the earliest cytotoxic drugs, methotrexate (MTX) serves as an anti-metabolite and anti-folate chemotherapy for various cancers. Unfortunately, MTX resistance prevents its clinical application in cancer therapy. Thereby, overcoming the drug resistance is an alternative strategy to maximize the therapeutic efficacy of MTX in clinics. Long noncoding RNAs (lncRNAs) have gained widespread attention in recent years...
December 2, 2016: Experimental Cell Research
https://www.readbyqxmd.com/read/27919571/long-noncoding-rnas-in-osteoarthritis
#14
Shi-de Jiang, Jian Lu, Zhen-Han Deng, Yu-Sheng Li, Guang-Hua Lei
Osteoarthritis (OA) is the most common form of arthritis that may affect all joint tissues. Unfortunately, the pathogenesis of OA is not fully understood yet and it cannot be cured totally. Long noncoding RNA (lncRNA) is a type of RNA molecule greater than 200 nucleotides, and deregulated expression of lncRNAs plays an important role in many types of inflammation-related diseases. In this review, we have focused on the association of lncRNAs in the development and progression of OA and the possibility of lncRNAs as a therapeutic agent for the treatment of OA...
December 2, 2016: Joint, Bone, Spine: Revue du Rhumatisme
https://www.readbyqxmd.com/read/27919067/genome-wide-changes-in-lncrna-splicing-and-regional-gene-expression-patterns-in-autism
#15
Neelroop N Parikshak, Vivek Swarup, T Grant Belgard, Manuel Irimia, Gokul Ramaswami, Michael J Gandal, Christopher Hartl, Virpi Leppa, Luis de la Torre Ubieta, Jerry Huang, Jennifer K Lowe, Benjamin J Blencowe, Steve Horvath, Daniel H Geschwind
Autism spectrum disorder (ASD) involves substantial genetic contributions. These contributions are profoundly heterogeneous but may converge on common pathways that are not yet well understood. Here, through post-mortem genome-wide transcriptome analysis of the largest cohort of samples analysed so far, to our knowledge, we interrogate the noncoding transcriptome, alternative splicing, and upstream molecular regulators to broaden our understanding of molecular convergence in ASD. Our analysis reveals ASD-associated dysregulation of primate-specific long noncoding RNAs (lncRNAs), downregulation of the alternative splicing of activity-dependent neuron-specific exons, and attenuation of normal differences in gene expression between the frontal and temporal lobes...
December 5, 2016: Nature
https://www.readbyqxmd.com/read/27917920/transcriptome-and-long-noncoding-rna-sequencing-of-three-extracellular-vesicle-subtypes-released-from-the-human-colon-cancer-lim1863-cell-line
#16
Maoshan Chen, Rong Xu, Hong Ji, David W Greening, Alin Rai, Keiichi Izumikawa, Hideaki Ishikawa, Nobuhiro Takahashi, Richard J Simpson
Previously we reported that LIM1863 colorectal cancer (CRC) cells secrete three distinct extracellular vesicle subtypes - two subpopulations of exosomes (apical EpCAM-Exos and basolateral A33-Exos) and shed microvesicles (sMVs) - with distinct protein and miRNA signatures. Here, we extend our omics approach to understand the fundamental role of LIM1863-derived EVs by performing a comprehensive analysis of their mRNAs and long non-coding RNAs (lncRNAs) using RNA-Seq. We show that 2,389 mRNAs, 317 pseudogene transcripts, 1,028 lncRNAs and 206 short non-coding RNAs selectively distributed to (i...
December 5, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27913643/biogenesis-and-transcriptional-regulation-of-long-noncoding-rnas-in-the-human-immune-system
#17
REVIEW
Charles F Spurlock, Philip S Crooke, Thomas M Aune
The central dogma of molecular biology states that DNA makes RNA makes protein. Discoveries over the last quarter of a century found that the process of DNA transcription into RNA gives rise to a diverse array of functional RNA species, including genes that code for protein and noncoding RNAs. For decades, the focus has been on understanding how protein-coding genes are regulated to influence protein expression. However, with the completion of the Human Genome Project and follow-up ENCODE data, it is now appreciated that only 2-3% of the genome codes for protein-coding gene exons and that the bulk of the transcribed genome, apart from ribosomal RNAs, is at the level of noncoding RNA genes...
December 15, 2016: Journal of Immunology: Official Journal of the American Association of Immunologists
https://www.readbyqxmd.com/read/27913295/dissection-of-functional-lncrnas-in-alzheimer-s-disease-by-construction-and-analysis-of-lncrna-mrna-networks-based-on-competitive-endogenous-rnas
#18
Lian-Kun Wang, Xiao-Feng Chen, Dan-Dan He, You Li, Jin Fu
Alzheimer's disease (AD) is a neurodegenerative disorder that is the most common cause of dementia in the elderly, and intracellular neurofibrillary tangles (NFTs) are one of the pathological features of AD. Recent studies have suggested long noncoding RNAs (lncRNAs) play important roles in AD. Competing endogenous RNAs (ceRNAs) is a mechanism that has recently been proposed, in which lncRNAs compete for common miRNA-binding sites with mRNAs. However, the roles of lncRNAs and ceRNA in AD NFTs is limited. In this study, we constructed a global triple network based on ceRNA theory, then an AD NFT lncRNA-mRNA network (NFTLMN) was generated...
November 29, 2016: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/27913185/mir-346-promotes-the-biological-function-of-breast-cancer-cells-by-targeting-srcin1-and-reduces-chemosensitivity-to-docetaxel
#19
Fan Yang, Long-Ji Luo, Lei Zhang, Dan-Dan Wang, Su-Jin Yang, Li Ding, Jian Li, Dan Chen, Rong Ma, Jian-Zhong Wu, Jin-Hai Tang
MicroRNAs (miRNAs) are a class of highly conserved small noncoding RNAs that play pivotal roles at the post-transcriptional level in the biological function of various cancers, including breast cancer. In our study, miR-346 mimic, inhibitor, negative control or si-SRCIN1 were transfected into MCF-7 and MCF-7/Doc cells, respectively. Quantitative real time PCR (qRT-PCR) was used to measure miR-346 and SRCIN1 mRNA expressions and western blot was used to detect the expression of SRCIN1 in protein level. CCK-8 and colony formation were employed to verify cell viability and proliferation...
November 29, 2016: Gene
https://www.readbyqxmd.com/read/27906963/lncrna-rmrp-acts-as-an-oncogene-in-lung-cancer
#20
Qingjun Meng, Mingming Ren, Yanguang Li, Xiang Song
Accumulating studies have demonstrated that long noncoding RNAs (lncRNAs) act a crucial role in the development of tumors. However, the role of lncRNAs in lung cancer remains largely unknown. In this study, we demonstrated that theexpression of RMRP was upregulated in lung adenocarcinoma tissues compared to the matched adjacent normal tissues. Moreover, of 35 lung adenocarcinoma samples, RMRP expression was upregulated in 25 cases (25/35; 71.4%) compared to the adjacent normal tissues. We also showed that RMRP expression was upregulated in lung adenocarcinoma cell lines (A549, SPC-A1, H1299 and H23) compared to the bronchial epithelial cell line (16HBE)...
2016: PloS One
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