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https://www.readbyqxmd.com/read/28107589/serum-lincrna-p21-as-a-potential-biomarker-of-liver-fibrosis-in-chronic-hepatitis-b-patients
#1
Fujun Yu, Guangyao Zhou, Kate Huang, XuFei Fan, Guojun Li, Bicheng Chen, Peihong Dong, Jianjian Zheng
Serum long non-coding RNAs (lncRNAs) are emerging as promising biomarkers for various human diseases. The aim of this study was to investigate the feasibility of using serum long intergenic non-coding RNA-p21 (lincRNA-p21) as a biomarker for chronic hepatitis B patients. Serum lincRNA-p21 levels were quantified using real-time PCR in 417 CHB patients and 363 healthy controls. The promoter methylation level of lincRNA-p21 was detected using bisulfite-sequencing analysis in primary hepatic stellate cells (HSCs)...
January 20, 2017: Journal of Viral Hepatitis
https://www.readbyqxmd.com/read/28106309/transposable-elements-tes-contribute-to-stress-related-long-intergenic-noncoding-rnas-in-plants
#2
Dong Wang, Zhipeng Qu, Lan Yang, Qingzhu Zhang, Zhi-Hong Liu, Trung Do, David L Adelson, Zhen-Yu Wang, Iain Searle, Jian-Kang Zhu
Noncoding RNAs have been extensively described in plant and animal transcriptomes by using high-throughput sequencing technology. Of these non-coding RNAs, a growing number of long intergenic noncoding RNAs (lincRNAs) have been described in multicellular organisms, however the origins and functions of many lincRNAs remain to be explored. In many eukaryotic genomes, transposable elements (TEs) are widely distributed and often account for large fractions of plant and animal genomes yet the contribution of TEs to lincRNAs is largely unknown...
January 20, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28040802/dysregulated-long-intergenic-non-coding-rna-modules-contribute-to-heart-failure
#3
Lin Pang, Jing Hu, Guanxiong Zhang, Xiang Li, Xinxin Zhang, Fulong Yu, Yujia Lan, Jinyuan Xu, Bo Pang, Dong Han, Yun Xiao, Xia Li
Long intergenic non-coding RNAs (lincRNAs) are emerging as important regulatory molecules involved in diseases including heart failure. However, little is known about how the lincRNAs work together with protein-coding genes (PCGs) contributing to the pathogenesis of heart failure. In this study, we constructed a comprehensive transcriptome profile of lincRNAs, PCGs and miRNAs using RNA-seq and miRNA-seq data of 16 heart failure patients (HFs) and 8 non-failing individuals (NFs). Through integrating lincRNA and PCG expression profiles, we identified HF-associated lincRNA modules...
September 13, 2016: Oncotarget
https://www.readbyqxmd.com/read/28033318/a-point-mutation-in-a-lincrna-upstream-of-gdnf-is-associated-to-a-canine-insensitivity-to-pain-a-spontaneous-model-for-human-sensory-neuropathies
#4
Jocelyn Plassais, Laetitia Lagoutte, Solenne Correard, Manon Paradis, Eric Guaguère, Benoit Hédan, Alix Pommier, Nadine Botherel, Marie-Christine Cadiergues, Philippe Pilorge, David Silversides, Maud Bizot, Mark Samuels, Carme Arnan, Rory Johnson, Christophe Hitte, Gilles Salbert, Agnès Méreau, Pascale Quignon, Thomas Derrien, Catherine André
Human Hereditary Sensory Autonomic Neuropathies (HSANs) are characterized by insensitivity to pain, sometimes combined with self-mutilation. Strikingly, several sporting dog breeds are particularly affected by such neuropathies. Clinical signs appear in young puppies and consist of acral analgesia, with or without sudden intense licking, biting and severe self-mutilation of the feet, whereas proprioception, motor abilities and spinal reflexes remain intact. Through a Genome Wide Association Study (GWAS) with 24 affected and 30 unaffected sporting dogs using the Canine HD 170K SNP array (Illumina), we identified a 1...
December 2016: PLoS Genetics
https://www.readbyqxmd.com/read/28017589/distinctive-patterns-of-transcription-and-rna-processing-for-human-lincrnas
#5
Margarita Schlackow, Takayuki Nojima, Tomas Gomes, Ashish Dhir, Maria Carmo-Fonseca, Nick J Proudfoot
Numerous long intervening noncoding RNAs (lincRNAs) are generated from the mammalian genome by RNA polymerase II (Pol II) transcription. Although multiple functions have been ascribed to lincRNAs, their synthesis and turnover remain poorly characterized. Here, we define systematic differences in transcription and RNA processing between protein-coding and lincRNA genes in human HeLa cells. This is based on a range of nascent transcriptomic approaches applied to different nuclear fractions, including mammalian native elongating transcript sequencing (mNET-seq)...
January 5, 2017: Molecular Cell
https://www.readbyqxmd.com/read/27999969/functions-of-long-intergenic-non-coding-linc-rnas-in-plants
#6
Masashi Yamada
Whole transcriptome analyses in many organisms have revealed that most transcribed RNAs do not encode proteins. These non-coding RNAs likely contribute to the regulation of gene expression during the development of multicellular organisms. In eukaryotes, the roles of small RNAs, one class of non-coding RNAs, in transcriptional and post-transcriptional regulation have been well characterized. However, the functions of a second class of non-coding RNAs, long intergenic noncoding (linc) RNAs, are relatively unknown, especially in plants...
January 2017: Journal of Plant Research
https://www.readbyqxmd.com/read/27988178/a-novel-protein-coding-potential-of-long-intergenic-non-coding-rnas-lincrnas-in-the-kinetoplastid-protozoan-parasite-leishmania-major
#7
Harsh Pawar, Kalpana Pai, Milind S Patole
Cutaneous leishmaniasis (CL) is caused by a kinetoplastid protozoan parasite Leishmania major, as a skin ulcer at the site of the sandfly bite. CL is curable and in most cases ulcers heal spontaneously within three to six months leaving a scar and disfiguration. Complete genome of L. major was reported in 2005 at the very initial phase of kinetoplastid parasite genome sequencing project. Presently, L. major genome is most studied and comprehensively annotated genome and therefore, it is being used as a reference genome for annotating recently sequenced Leishmanial genomes...
December 14, 2016: Acta Tropica
https://www.readbyqxmd.com/read/27979905/a-long-noncoding-rna-lincrna-tnfaip3-acts-as-a-coregulator-of-nf-%C3%AE%C2%BAb-to-modulate-inflammatory-gene-transcription-in-mouse-macrophages
#8
Shibin Ma, Zhenping Ming, Ai-Yu Gong, Yang Wang, Xiqiang Chen, Guoku Hu, Rui Zhou, Annemarie Shibata, Patrick C Swanson, Xian-Ming Chen
Long intergenic noncoding RNAs (lincRNAs) are long noncoding transcripts (>200 nt) from the intergenic regions of annotated protein-coding genes. We report here that the lincRNA gene lincRNA-Tnfaip3, located at mouse chromosome 10 proximal to the tumor necrosis factor α-induced protein 3 (Tnfaip3) gene, is an early-primary response gene controlled by nuclear factor-κB (NF-κB) signaling in murine macrophages. Functionally, lincRNA- Tnfaip3 appears to mediate both the activation and repression of distinct classes of inflammatory genes in macrophages...
December 15, 2016: FASEB Journal: Official Publication of the Federation of American Societies for Experimental Biology
https://www.readbyqxmd.com/read/27976428/long-intragenic-non-coding-rna-lincrna-p21-suppresses-development-of-human-prostate-cancer
#9
Xiaohai Wang, Yuan Ruan, Xingjie Wang, Wei Zhao, Qi Jiang, Chenyi Jiang, Yuyang Zhao, Yongzhi Xu, Feng Sun, Yiping Zhu, Shujie Xia, Dongliang Xu
OBJECTIVES: Prostate cancer is one of the most frequent malignancies in men, worldwide, although its underlying mechanisms are not fully understood. Long non-coding RNAs participate in development of human cancers. In this invetsigation, we aimed to study the roles of lincRNA-p21 in development of human prostate cancer. MATERIALS AND METHODS: Expression of lincRNA-p21 was assessed by real-time PCR in cell lines and in human tissues. Lentivirus carrying sh-lincRNA-p21, lincRNA-p21 or control constructs were used to determine their effects on cell proliferation and apoptosis...
December 14, 2016: Cell Proliferation
https://www.readbyqxmd.com/read/27927715/chromatin-environment-transcriptional-regulation-and-splicing-distinguish-lincrnas-and-mrnas
#10
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...
January 2017: Genome Research
https://www.readbyqxmd.com/read/27927215/functional-characterisation-of-long-intergenic-non-coding-rnas-through-genetic-interaction-profiling-in-saccharomyces-cerevisiae
#11
Dimitris Kyriakou, Emmanouil Stavrou, Panayiota Demosthenous, Georgia Angelidou, Bryan-Joseph San Luis, Charles Boone, Vasilis J Promponas, Antonis Kirmizis
BACKGROUND: Transcriptome studies have revealed that many eukaryotic genomes are pervasively transcribed producing numerous long non-coding RNAs (lncRNAs). However, only a few lncRNAs have been ascribed a cellular role thus far, with most regulating the expression of adjacent genes. Even less lncRNAs have been annotated as essential hence implying that the majority may be functionally redundant. Therefore, the function of lncRNAs could be illuminated through systematic analysis of their synthetic genetic interactions (GIs)...
December 7, 2016: BMC Biology
https://www.readbyqxmd.com/read/27922056/identification-and-functional-analysis-of-long-intergenic-noncoding-rna-genes-in-porcine-pre-implantation-embryonic-development
#12
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
#13
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
#14
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
#15
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
#16
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-noncoding-rnas-as-novel-biomarkers-in-chronic-kidney-disease
#17
Rimpi Khurana, Glory Ranches, Simon Schafferer, Melanie Lukasser, Michael Rudnicki, Gert Mayer, Alexander Hüttenhofer
In chronic kidney disease (CKD), the decline in the 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 been extensively 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...
February 2017: RNA
https://www.readbyqxmd.com/read/27855392/the-emerging-roles-of-long-noncoding-rna-ror-lincrna-ror-and-its-possible-mechanisms-in-human-cancers
#18
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
#19
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
#20
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
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