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https://www.readbyqxmd.com/read/27922056/identification-and-functional-analysis-of-long-intergenic-noncoding-rna-genes-in-porcine-pre-implantation-embryonic-development
#1
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/27900030/oleanolic-acid-suppresses-vascular-smooth-muscle-cell-proliferation-by-increasing-lincrna-p21-expression
#2
Di Han, Xuejuan Zhang, Jietao Zhang, Xiaozi Guo, Yu Zheng, Shihua Sui, Jiaping Zheng
Arteriosclerosis poses a significant risk to human health and involves the thickening and hardening of the walls of arteries. Accumulated evidence demonstrates that aberrant proliferation of vascular smooth muscle cells (VSMCs) accounts for the onset and progression of arteriosclerosis. Suppression of their proliferation has been demonstrated to be an effective anti-arteriosclerosis strategy. Long non-coding RNAs (lncRNAs) have recently been observed to be implicated in the proliferation of VSMCs and arteriosclerosis...
November 2016: Oncology Letters
https://www.readbyqxmd.com/read/27897201/long-intergenic-non-coding-rna-expression-signature-in-human-breast-cancer
#3
Yanfeng Zhang, Erin K Wagner, Xingyi Guo, Isaac May, Qiuyin Cai, Wei Zheng, Chunyan He, Jirong Long
Breast cancer is a complex disease, characterized by gene deregulation. There is less systematic investigation of the capacity of long intergenic non-coding RNAs (lincRNAs) as biomarkers associated with breast cancer pathogenesis or several clinicopathological variables including receptor status and patient survival. We designed a two-stage study, including 1,000 breast tumor RNA-seq data from The Cancer Genome Atlas (TCGA) as the discovery stage, and RNA-seq data of matched tumor and adjacent normal tissue from 50 breast cancer patients as well as 23 normal breast tissue from healthy women as the replication stage...
November 29, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27878653/single-cell-rna-seq-reveals-lincrna-expression-differences-in-hela-s3-cells
#4
Jie Wang, Bhaskar Roy
OBJECTIVE: To characterize transcriptome-wide lincRNAs of Hela-S3 cell line by analyzing RNA sequencing data to provide a foundation for further functional verification and clinical application of cervical carcinoma development. RESULTS: Single-cell RNA sequencing data of 37 Hela-S3 cells were analysed. On average, 511 lincRNAs were expressed in each cell. Comparing the expression difference of the lincRNAs and protein-coding genes, we found that lincRNAs expression displayed more cell specificity than that of protein-coding genes (t-test, P<2...
November 23, 2016: Biotechnology Letters
https://www.readbyqxmd.com/read/27872710/linc-ror-and-its-spliced-variants-2-and-4-are-significantly-up-regulated-in-esophageal-squamous-cell-carcinoma
#5
Reza Sahebi, Mahshid Malakootian, Baharak Balalaee, Alireza Shahryari, Masoud Khoshnia, Mohammad Reza Abbaszadegan, Abdolvahab Moradi, Seyed Javad Mowla
OBJECTIVES: Similar characteristics of molecular pathways between cellular reprogramming events and tumorigenesis have been accentuated in recent years. Reprogramming-related transcription factors, also known as Yamanaka factors (OCT4, SOX2, KLF4, and c-MYC), are also well-known oncogenes promoting cancer initiation, progression, and cellular transformation into cancer stem cells. Long non-coding RNAs (lncRNAs) are a major class of RNA molecules with emerging roles in stem cell pluripotency, cellular reprogramming, cellular transformation, and tumorigenesis...
October 2016: Iranian Journal of Basic Medical Sciences
https://www.readbyqxmd.com/read/27872161/identification-of-urinary-exosomal-non-coding-rnas-as-novel-biomarkers-in-chronic-kidney-disease
#6
Rimpi Khurana, Glory Ranches, Simon Schafferer, Melanie Lukasser, Michael Rudnicki, Gert Mayer, Alexander Hüttenhofer
In chronic kidney disease (CKD), the decline in glomerular filtration rate is associated with increased morbidity and mortality and thus poses a major challenge for healthcare systems. While the contribution of tissue-derived miRNAs and mRNAs to CKD progression has extensively been studied, little is known about the role of urinary exosomes and their association with CKD. Exosomes are small, membrane-derived endocytic vesicles that contribute to cell-to-cell communication and are present in various body fluids, such as blood or urine...
November 21, 2016: RNA
https://www.readbyqxmd.com/read/27855392/the-emerging-roles-of-long-noncoding-rna-ror-lincrna-ror-and-its-possible-mechanisms-in-human-cancers
#7
Yan Pan, Chen Li, Jing Chen, Kai Zhang, Xiaoyuan Chu, Rui Wang, Longbang Chen
To date, there is only up to 2% of protein-coding genes that are stably transcribed, whereas the vast majority are non-coding RNAs (ncRNAs). These ncRNAs, also known as non-messenger RNAs (nmRNAs) or functional RNAs (fRNAs), include transfer RNAs, ribosomal RNAs, microRNAs and long non-coding RNAs (lncRNAs). With the advance of high-resolution microarrays and massively parallel sequencing technology, lncRNAs have gained extended attentions nowadays and are found to play important roles in tumorigenesis and progression of human cancers...
2016: Cellular Physiology and Biochemistry
https://www.readbyqxmd.com/read/27855366/hox-antisense-lincrna-hoxa-as2-promotes-tumorigenesis-of-hepatocellular-carcinoma
#8
Fuqiang Wang, Huili Yang, Zhigang Deng, Yongjie Su, QinLiang Fang, Zhenyu Yin
BACKGROUND: Recent studies reveal that long non-coding RNAs (LncRNAs) play critical roles in the proliferation and migration of human cancer. Previous report has shown that LncRNA HOXA-AS2 was involved in carcinoma processes. However, the expression and biological function of HOXA-AS2 in hepatocellular carcinoma (HCC) are poorly understood. METHODS: Quantitative real-time PCR (qRT-PCR) was performed to detect the expression of HOXA-AS2 in HCC tissues and cell lines...
2016: Cellular Physiology and Biochemistry
https://www.readbyqxmd.com/read/27824113/a-comprehensive-characterization-of-the-function-of-lincrnas-in-transcriptional-regulation-through-long-range-chromatin-interactions
#9
Liuyang Cai, Huidan Chang, Yaping Fang, Guoliang Li
LincRNAs are emerging as important regulators with various cellular functions. However, the mechanisms behind their role in transcriptional regulation have not yet been fully explored. In this report, we proposed to characterize the diverse functions of lincRNAs in transcription regulation through an examination of their long-range chromatin interactions. We found that the promoter regions of lincRNAs displayed two distinct patterns of chromatin states, promoter-like and enhancer-like, indicating different regulatory functions for lincRNAs...
November 8, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27803687/emerging-putative-associations-between-non-coding-rnas-and-protein-coding-genes-in-neuropathic-pain-added-value-from-reusing-microarray-data
#10
Hemalatha B Raju, Nicholas F Tsinoremas, Enrico Capobianco
Regeneration of injured nerves is likely occurring in the peripheral nervous system, but not in the central nervous system. Although protein-coding gene expression has been assessed during nerve regeneration, little is currently known about the role of non-coding RNAs (ncRNAs). This leaves open questions about the potential effects of ncRNAs at transcriptome level. Due to the limited availability of human neuropathic pain (NP) data, we have identified the most comprehensive time-course gene expression profile referred to sciatic nerve (SN) injury and studied in a rat model using two neuronal tissues, namely dorsal root ganglion (DRG) and SN...
2016: Frontiers in Neurology
https://www.readbyqxmd.com/read/27791479/two-distinct-extracellular-rna-signatures-released-by-a-single-cell-type-identified-by-microarray-and-next-generation-sequencing
#11
Cecilia Lässer, Ganesh Vilas Shelke, Ashish Yeri, Dae-Kyum Kim, Rossella Crescitelli, Stefania Raimondo, Margareta Sjöstrand, Yong Song Gho, Kendall Van Keuren Jensen, Jan Lötvall
Cells secrete extracellular RNA (exRNA) to their surrounding environment and exRNA has been found in many body fluids such as blood, breast milk and cerebrospinal fluid. However, there are conflicting results regarding the nature of exRNA. Here, we have separated two distinct exRNA profiles released by mast cells, here termed high-density (HD) and low-density (LD) exRNA. The exRNA in both fractions was characterized by microarray and next-generation sequencing. Both exRNA fractions contained mRNA and miRNA, and the mRNAs in the LD exRNA correlated closely with the cellular mRNA, whereas the HD mRNA did not...
October 28, 2016: RNA Biology
https://www.readbyqxmd.com/read/27777857/long-noncoding-rna-malat1-can-serve-as-a-valuable-biomarker-for-prognosis-and-lymph-node-metastasis-in-various-cancers-a-meta-analysis
#12
Ping Shuai, Yu Zhou, Bo Gong, Zhilin Jiang, Chong Yang, Hongji Yang, Dingding Zhang, Shikai Zhu
BACKGROUND: Metastasis-associated lung adenocarcinoma transcript 1 (MALAT1), a newly discovered long intergenic noncoding RNA (lincRNA), has been reported to be aberrantly expressed in various cancers, and may serve as a novel potential biomarker for cancer prognosis. This meta-analysis was conducted to investigate the effects of MALAT1 on cancer prognosis and lymph node metastasis. METHODS: A quantitative meta-analysis was performed using a systematic search of PubMed, Medline and Web of Science databases to identify eligible papers on prognostic value of MALAT1 in cancers...
2016: SpringerPlus
https://www.readbyqxmd.com/read/27760142/identification-of-aedes-aegypti-long-intergenic-non-coding-rnas-and-their-association-with-wolbachia-and-dengue-virus-infection
#13
Kayvan Etebari, Sultan Asad, Guangmei Zhang, Sassan Asgari
Long intergenic non-coding RNAs (lincRNAs) are appearing as an important class of regulatory RNAs with a variety of biological functions. The aim of this study was to identify the lincRNA profile in the dengue vector Aedes aegypti and evaluate their potential role in host-pathogen interaction. The majority of previous RNA-Seq transcriptome studies in Ae. aegypti have focused on the expression pattern of annotated protein coding genes under different biological conditions. Here, we used 35 publically available RNA-Seq datasets with relatively high depth to screen the Ae...
October 2016: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/27738133/global-and-cell-type-specific-properties-of-lincrnas-with-ribosome-occupancy
#14
Hongwei Wang, Yan Wang, Shangqian Xie, Yizhi Liu, Zhi Xie
Advances in transcriptomics have led to the discovery of a large number of long intergenic non-coding RNAs (lincRNAs), which are now recognized as important regulators of diverse cellular processes. Although originally thought to be non-coding, recent studies have revealed that many lincRNAs are bound by ribosomes, with a few lincRNAs even having ability to generate micropeptides. The question arises: how widespread the translation of lincRNAs may be and whether such translation is likely to be functional. To better understand biological relevance of lincRNA translation, we systematically characterized lincRNAs with ribosome occupancy by the expression, structural, sequence, evolutionary and functional features for eight human cell lines, revealed that lincRNAs with ribosome occupancy have remarkably distinctive properties compared with those without ribosome occupancy, indicating that translation has important biological implication in categorizing and annotating lincRNAs...
October 13, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27713513/computational-identification-of-putative-lincrnas-in-mouse-embryonic-stem-cell
#15
Hui Liu, Jie Lyu, Hongbo Liu, Yang Gao, Jing Guo, Hongjuan He, Zhengbin Han, Yan Zhang, Qiong Wu
As the regulatory factors, lncRNAs play critical roles in embryonic stem cells. And lincRNAs are most widely studied lncRNAs, however, there might still might exist a large member of uncovered lncRNAs. In this study, we constructed the de novo assembly of transcriptome to detect 6,701 putative long intergenic non-coding transcripts (lincRNAs) expressed in mouse embryonic stem cells (ESCs), which might be incomplete with the lack coverage of 5' ends assessed by CAGE peaks. Comparing the TSS proximal regions between the known lincRNAs and their closet protein coding transcripts, our results revealed that the lincRNA TSS proximal regions are associated with the characteristic genomic and epigenetic features...
October 7, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27696511/the-long-non-coding-rna-ror-promotes-the-resistance-of-radiotherapy-for-human-colorectal-cancer-cells-by-targeting-the-p53-mir-145-pathway
#16
Pengxiang Yang, Yue Yang, Weiwei An, Jianyu Xu, Gan Zhang, Jing Jie, Qingyuan Zhang
BACKGROUND AND AIM: LincRNAs have critical roles in elevating efficacy of anticancer therapy and tumor progression. Recent studies show that long intergenic noncoding RNA-ROR (lincRNA-ROR) is aberrantly expressed in several types of cancer, including colorectal cancer (CRC). Radiotherapy is considered as a standard preoperative treatment. However, a considerable number of CRCs are resistant to radiotherapy. In this study, we evaluated the role of lincRNA-ROR in radiotherapy for CRC and detected the underlying molecular mechanism...
October 3, 2016: Journal of Gastroenterology and Hepatology
https://www.readbyqxmd.com/read/27681237/long-noncoding-rna-lincrna-a-new-paradigm-in-gene-expression-control
#17
Emre Deniz, Batu Erman
Long intergenic non-coding RNAs (lincRNAs) are defined as RNA transcripts that are longer than 200 nucleotides. By definition, these RNAs must not have open reading frames that encode proteins. Many of these transcripts are encoded by RNA polymerase II, are spliced, and are poly-adenylated. This final fact indicates that there is a trove of information about lincRNAs in databases such as the Gene Expression Omnibus (GEO), which is a repository for RNAseq and microarray data. Recent experiments indicate that there are upwards of 15,000 lincRNAs encoded by the human genome...
September 28, 2016: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/27661005/systematically-characterizing-dysfunctional-long-intergenic-non-coding-rnas-in-multiple-brain-regions-of-major-psychosis
#18
Jing Hu, Jinyuan Xu, Lin Pang, Hongying Zhao, Feng Li, Yulan Deng, Ling Liu, Yujia Lan, Xinxin Zhang, Tingting Zhao, Chaohan Xu, Chun Xu, Yun Xiao, Xia Li
Schizophrenia (SZ) and bipolar disorder (BD) are severe neuropsychiatric disorders with serious impact on patients, together termed "major psychosis". Recently, long intergenic non-coding RNAs (lincRNAs) were reported to play important roles in mental diseases. However, little was known about their molecular mechanism in pathogenesis of SZ and BD. Here, we performed RNA sequencing on 82 post-mortem brain tissues from three brain regions (orbitofrontal cortex (BA11), anterior cingulate cortex (BA24) and dorsolateral prefrontal cortex (BA9)) of patients with SZ and BD and control subjects, generating over one billion reads...
September 19, 2016: Oncotarget
https://www.readbyqxmd.com/read/27660052/c14orf132-gene-is-possibly-related-to-extremely-low-birth-weight
#19
Airi Tiirats, Triin Viltrop, Margit Nõukas, Ene Reimann, Andres Salumets, Sulev Kõks
BACKGROUND: Despite extensive research the genetic component of extremely low birth weight (ELBW) in newborns has remained obscure. RESULTS: The aim of the case study was to identify candidate gene(s) causing ELBW in newborns and hypotrophy in infants. A family of four was studied: mother, father and two ELBW-phenotype children. Studies were made of the medical conditions of the second child at birth and post-partum - peculiar phenotype, micro-anomalies, recurrent infections, suspicion of autoimmune hepatitis, multifactorial encephalopathy and suspected metabolic and chromosomal abnormalities...
2016: BMC Genetics
https://www.readbyqxmd.com/read/27628568/genome-wide-analysis-of-long-intergenic-non-coding-rnas-in-chickpea-and-their-potential-role-in-flower-development
#20
Niraj Khemka, Vikash Kumar Singh, Rohini Garg, Mukesh Jain
Non-coding RNAs constitute a major portion of the transcriptome in most of eukaryotes. Long non-coding transcripts originating from the DNA segment present between the protein coding genes are termed as long intergenic non-coding RNAs (lincRNAs). Several evidences suggest the role of lincRNAs in regulation of various biological processes. In this study, we identified a total of 2248 lincRNAs in chickpea using RNA-seq data from eight successive stages of flower development and three vegetative tissues via an optimized pipeline...
2016: Scientific Reports
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