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https://www.readbyqxmd.com/read/28820723/a-lncrna-fine-tunes-the-dynamics-of-a-cell-state-transition-involving-lin28-let-7-and-de-novo-dna-methylation
#1
Meng Amy Li, Paulo P Amaral, Priscilla Cheung, Jan H Bergmann, Masaki Kinoshita, Tüzer Kalkan, Meryem Ralser, Sam Robson, Ferdinand von Meyenn, Maike Paramor, Fengtang Yang, Caifu Chen, Jennifer Nichols, David L Spector, Tony Kouzarides, Lin He, Austin Smith
Execution of pluripotency requires progression from the naïve status represented by mouse embryonic stem cells (ESCs) to a state capacitated for lineage specification. This transition is coordinated at multiple levels. Non-coding RNAs may contribute to this regulatory orchestra. We identified a rodent-specific long non-coding RNA (lncRNA) linc1281, hereafter Ephemeron (Eprn), that modulates the dynamics of exit from naïve pluripotency. Eprn deletion delays the extinction of ESC identity, an effect associated with perduring Nanog expression...
August 18, 2017: ELife
https://www.readbyqxmd.com/read/28819376/part1-expression-is-associated-with-poor-prognosis-and-tumor-recurrence-in-stage-i-iii-non-small-cell-lung-cancer
#2
Ming Li, Weiwei Zhang, Shenjun Zhang, Changhui Wang, Yinping Lin
Purpose: Long noncoding RNAs (lncRNAs) have been demonstrated as effective markers for cancer detection and prognosis prediction. The aim of this study was to determine whether tissue PART1 could be used as a biomarker for prognosis prediction of non-small cell lung cancer (NSCLC). Methods: PART1 expression was detected in 208 cases of stage I-III NSCLC specimens and adjacent normal tissues. The Cox proportional-hazards regression model was used to analyze the association between PART1 expression and overall survival (OS) and disease-free survival (DFS) of the patients...
2017: Journal of Cancer
https://www.readbyqxmd.com/read/28819235/expression-of-long-non-coding-rna-mfi2-as1-is-a-strong-predictor-of-recurrence-in-sporadic-localized-clear-cell-renal-cell-carcinoma
#3
Ronan Flippot, Roger Mouawad, Jean-Philippe Spano, Morgan Rouprêt, Eva Compérat, Marc-Olivier Bitker, Jérôme Parra, Christophe Vaessen, Frederick Allanic, Quentin Manach, Nizar M Tannir, David Khayat, Xiaoping Su, Gabriel G Malouf
Prediction of recurrence is a challenge for the development of adjuvant treatments in clear-cell renal cell carcinoma (ccRCC). In these tumors, expression of long non-coding RNAs (lncRNAs) are deregulated and closely associated with prognosis. Thus, we aimed to predict ccRCC recurrence risk using lncRNA expression. We identified prognostic lncRNAs in a training set of 351 localized ccRCCs from The Cancer Genome Atlas and validated lncRNA-based recurrence classification in an independent cohort of 167 localized ccRCCs...
August 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28819115/genome-wide-identification-and-expression-profiling-of-long-non-coding-rnas-in-auditory-and-vestibular-systems
#4
Kathy Ushakov, Tal Koffler-Brill, Aviv Rom, Kobi Perl, Igor Ulitsky, Karen B Avraham
Mammalian genomes encode multiple layers of regulation, including a class of RNA molecules known as long non-coding RNAs (lncRNAs). These are >200 nucleotides in length and similar to mRNAs, they are capped, polyadenylated, and spliced. In contrast to mRNAs, lncRNAs are less abundant and have higher tissue specificity, and have been linked to development, epigenetic processes, and disease. However, little is known about lncRNA function in the auditory and vestibular systems, or how they play a role in deafness and vestibular dysfunction...
August 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28819095/non-coding-rnas-participate-in-the-regulatory-network-of-cldn4-via-cerna-mediated-mirna-evasion
#5
Yong-Xi Song, Jing-Xu Sun, Jun-Hua Zhao, Yu-Chong Yang, Jin-Xin Shi, Zhong-Hua Wu, Xiao-Wan Chen, Peng Gao, Zhi-Feng Miao, Zhen-Ning Wang
Thousands of genes have been well demonstrated to play important roles in cancer progression. As genes do not function in isolation, they can be grouped into "networks" based on their interactions. In this study, we discover a network regulating Claudin-4 in gastric cancer. We observe that Claudin-4 is up-regulated in gastric cancer and is associated with poor prognosis. Claudin-4 reinforce proliferation, invasion, and EMT in AGS, HGC-27, and SGC-7901 cells, which could be reversed by miR-596 and miR-3620-3p...
August 18, 2017: Nature Communications
https://www.readbyqxmd.com/read/28818073/role-of-the-lncrna-abhd11-as1-in-the-tumorigenesis-and-progression-of-epithelial-ovarian-cancer-through-targeted-regulation-of-rhoc
#6
Dan-Dan Wu, Xi Chen, Kai-Xuan Sun, Li-Li Wang, Shuo Chen, Yang Zhao
BACKGROUND: There is increasing evidence in support of the role of lncRNAs in tumor cell proliferation, differentiation and apoptosis. METHODS: We examined the expression of the lncRNA ABHD11-AS1 in epithelial ovarian cancer (EOC) tissues and normal ovarian tissues by real-time quantitative PCR (qRT-PCR). After inducing ABHD11-AS1 downregulation by small interfering RNA (siRNA) or ABHD11-AS1 overexpression by plasmid transfection, we examined the EOC cell phenotypes and expression of related molecules...
August 17, 2017: Molecular Cancer
https://www.readbyqxmd.com/read/28818070/rs1859168-a%C3%A2-%C3%A2-c-polymorphism-regulates-hottip-expression-and-reduces-risk-of-pancreatic-cancer-in-a-chinese-population
#7
Pinghai Hu, Ou Qiao, Jun Wang, Jiao Li, Hao Jin, Zhaolian Li, Yan Jin
BACKGROUND: Long non-coding RNAs (lncRNAs) are aberrantly expressed in many types of human cancer including pancreatic cancer (PC) and correlated with tumorigenesis and cancer prognosis, whereas knowledge about regulatory mechanism of lncRNA expression is few known. This study aimed to explore whether polymorphisms in lncRNAs genes are associated with PC susceptibility by affecting its expression. METHODS: We first genotyped three common single-nucleotide polymorphisms (SNPs) of lncRNA genes (HOTTIP rs1859168, HOTAIR rs4759314, and H19 rs217727) in 416 paired PC patients and controls, and then validated the results in another 505 paired PC patients and controls...
August 17, 2017: World Journal of Surgical Oncology
https://www.readbyqxmd.com/read/28817151/comprehensive-analysis-of-long-noncoding-rna-mrna-co-expression-patterns-in-thyroid-cancer
#8
Yaying Du, Wenfei Xia, Jinjun Zhang, Dongyi Wan, Zhifang Yang, Xingrui Li
Novel molecular-targeted treatments show great prospects for radioiodine-refractory and surgically inoperable thyroid carcinomas. While aberrations in protein-coding genes are a focus in molecular thyroid cancer medicine, the impact of oncogenes on the expression of long noncoding RNAs (lncRNAs) has been largely uncharacterized. We aimed to identify the expression patterns of lncRNAs and mRNAs in high-throughput molecular profiles of 18 papillary thyroid cancer (PTC) patients. We identified 452 mRNAs and 240 unannotated lncRNAs that were differentially expressed in PTC...
August 17, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28815544/technological-developments-in-lncrna-biology
#9
Sonali Jathar, Vikram Kumar, Juhi Srivastava, Vidisha Tripathi
It is estimated that more than 90% of the mammalian genome is transcribed as non-coding RNAs. Recent evidences have established that these non-coding transcripts are not junk or just transcriptional noise, but they do serve important biological purpose. One of the rapidly expanding fields of this class of transcripts is the regulatory lncRNAs, which had been a major challenge in terms of their molecular functions and mechanisms of action. The emergence of high-throughput technologies and the development in various conventional approaches have led to the expansion of the lncRNA world...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/28815543/understanding-the-role-of-lncrnas-in-nervous-system-development
#10
Brian S Clark, Seth Blackshaw
The diversity of lncRNAs has expanded within mammals in tandem with the evolution of increased brain complexity, suggesting that lncRNAs play an integral role in this process. In this chapter, we will highlight the identification and characterization of lncRNAs in nervous system development. We discuss the potential role of lncRNAs in nervous system and brain evolution, along with efforts to create comprehensive catalogues that analyze spatial and temporal changes in lncRNA expression during nervous system development...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/28815542/long-noncoding-rnas-in-pluripotency-of-stem-cells-and-cell-fate-specification
#11
Debosree Pal, M R S Rao
Since the annotation of the mouse genome (FANTOM project) [Kawai J et al (2001) Functional annotation of a full-length mouse cDNA collection. Nature 409(6821):685-690] or the human genome [An integrated encyclopedia of DNA elements in the human genome. (2012) Nature 489(7414):57-74; Harrow J et al (2012) GENCODE: the reference human genome annotation for the ENCODE project. Genome Res 22(9):1760-1774], the roles of long noncoding RNAs in coordinating specific signaling pathways have been established in a wide variety of model systems...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/28815541/long-noncoding-rnas-in-cancer-and-therapeutic-potential
#12
Arun Renganathan, Emanuela Felley-Bosco
Long noncoding RNAs (lncRNAs) are the major elements of the mammalian transcriptome that is emerging as a central player controlling diverse cellular mechanisms. Most of the well-studied lncRNAs so far are found to be crucial in regulating cellular processes such as cell cycle, growth, and apoptosis that ensure homeostasis. Owing to their location and distribution in the genome, lncRNAs influence the transcription of a wide range of proteins directly or indirectly by transcriptional and posttranscriptional alterations, which opens up the "LncRNA-cancer paradigm" in a context-dependent manner, i...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/28815539/long-noncoding-rnas-in-plants
#13
Hsiao-Lin V Wang, Julia A Chekanova
The eukaryotic genomes are pervasively transcribed. In addition to protein-coding RNAs, thousands of long noncoding RNAs (lncRNAs) modulate key molecular and biological processes. Most lncRNAs are found in the nucleus and associate with chromatin, but lncRNAs can function in both nuclear and cytoplasmic compartments. Emerging work has found that many lncRNAs regulate gene expression and can affect genome stability and nuclear domain organization both in plant and in the animal kingdom. Here, we describe the major plant lncRNAs and how they act, with a focus on research in Arabidopsis thaliana and our emerging understanding of lncRNA functions in serving as molecular sponges and decoys, functioning in regulation of transcription and silencing, particularly in RNA-directed DNA methylation, and in epigenetic regulation of flowering time...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/28815538/long-noncoding-rnas-in-the-yeast-s-%C3%A2-cerevisiae
#14
Rachel O Niederer, Evan P Hass, David C Zappulla
Long noncoding RNAs have recently been discovered to comprise a sizeable fraction of the RNA World. The scope of their functions, physical organization, and disease relevance remain in the early stages of characterization. Although many thousands of lncRNA transcripts recently have been found to emanate from the expansive DNA between protein-coding genes in animals, there are also hundreds that have been found in simple eukaryotes. Furthermore, lncRNAs have been found in the bacterial and archaeal branches of the tree of life, suggesting they are ubiquitous...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/28815537/from-heterochromatin-to-long-noncoding-rnas-in-drosophila-expanding-the-arena-of-gene-function-and-regulation
#15
Subhash C Lakhotia
Recent years have witnessed a remarkable interest in exploring the significance of pervasive noncoding transcripts in diverse eukaryotes. Classical cytogenetic studies using the Drosophila model system unraveled the perplexing attributes and "functions" of the "gene"-poor heterochromatin. Recent molecular studies in the fly model are likewise revealing the very diverse and significant roles played by long noncoding RNAs (lncRNAs) in development, gene regulation, chromatin organization, cell and nuclear architecture, etc...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/28815536/long-noncoding-rna-genome-organization-and-mechanism-of-action
#16
Vijay Suresh Akhade, Debosree Pal, Chandrasekhar Kanduri
For the last four decades, we have known that noncoding RNAs maintain critical housekeeping functions such as transcription, RNA processing, and translation. However, in the late 1990s and early 2000s, the advent of high-throughput sequencing technologies and computational tools to analyze these large sequencing datasets facilitated the discovery of thousands of small and long noncoding RNAs (lncRNAs) and their functional role in diverse biological functions. For example, lncRNAs have been shown to regulate dosage compensation, genomic imprinting, pluripotency, cell differentiation and development, immune response, etc...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/28815535/history-discovery-and-classification-of-lncrnas
#17
Julien Jarroux, Antonin Morillon, Marina Pinskaya
The RNA World Hypothesis suggests that prebiotic life revolved around RNA instead of DNA and proteins. Although modern cells have changed significantly in 4 billion years, RNA has maintained its central role in cell biology. Since the discovery of DNA at the end of the nineteenth century, RNA has been extensively studied. Many discoveries such as housekeeping RNAs (rRNA, tRNA, etc.) supported the messenger RNA model that is the pillar of the central dogma of molecular biology, which was first devised in the late 1950s...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/28814798/genetic-polymorphisms-of-lncrna-p53-regulatory-network-genes-are-associated-with-concurrent-chemoradiotherapy-toxicities-and-efficacy-in-nasopharyngeal-carcinoma-patients
#18
Youhong Wang, Zhen Guo, Yu Zhao, Yi Jin, Liang An, Bin Wu, Zhaoqian Liu, Xiaoping Chen, Xiang Chen, Honghao Zhou, Hui Wang, Wei Zhang
The relevance of the transcription factor p53 in cancer is inarguable, and numerous lncRNAs are involved in the p53 regulatory network as either regulators or effectors, triggering a transcriptional response that causes either cell arrest or apoptosis following DNA damage in a p53-dependent manner. Despite the fact that the therapeutic response is improved in NPC, heterogeneity among people remains with regard to the susceptibility of adverse effects and the efficacy of treatments. Therefore, we analysed eight potentially functional SNPs of five genes in the lncRNA-p53 regulatory network in a discovery cohort of 505 NPC patients...
August 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28814771/rna-sequencing-of-db-db-mice-liver-identifies-lncrna-h19-as-a-key-regulator-of-gluconeogenesis-and-hepatic-glucose-output
#19
Neha Goyal, Ambily Sivadas, K V Shamsudheen, Rijith Jayarajan, Ankit Verma, Sridhar Sivasubbu, Vinod Scaria, Malabika Datta
Liver plays a key role in maintaining glucose homeostasis and impaired hepatic glucose metabolism is associated with type 2 diabetes. In the present study, we used RNA sequencing to profile the transcriptome of the livers of diabetic db/db mice as compared to the normal db/+ mice and identified 218 differentially expressed genes. Amongst these, there were 3 lncRNAs that were significantly downregulated and H19 was the most altered lncRNA in the livers of db/db mice. H19 expression significantly correlated with the expression of genes of the glycolysis and gluconeogenesis pathways, which suggest that altered hepatic H19 levels can directly or indirectly modulate their expression...
August 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28811863/long-noncoding-rnas-and-rna-binding-proteins-in-oxidative-stress-cellular-senescence-and-age-related-diseases
#20
REVIEW
Chongtae Kim, Donghee Kang, Eun Kyung Lee, Jae-Seon Lee
Cellular senescence is a complex biological process that leads to irreversible cell-cycle arrest. Various extrinsic and intrinsic insults are associated with the onset of cellular senescence and frequently accompany genomic or epigenomic alterations. Cellular senescence is believed to contribute to tumor suppression, immune response, and tissue repair as well as aging and age-related diseases. Long noncoding RNAs (lncRNAs) are >200 nucleotides long, poorly conserved, and transcribed in a manner similar to that of mRNAs...
2017: Oxidative Medicine and Cellular Longevity
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