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https://www.readbyqxmd.com/read/29138516/the-functions-and-unique-features-of-long-intergenic-non-coding-rna
#1
REVIEW
Julia D Ransohoff, Yuning Wei, Paul A Khavari
Long intergenic non-coding RNA (lincRNA) genes have diverse features that distinguish them from mRNA-encoding genes and exercise functions such as remodelling chromatin and genome architecture, RNA stabilization and transcription regulation, including enhancer-associated activity. Some genes currently annotated as encoding lincRNAs include small open reading frames (smORFs) and encode functional peptides and thus may be more properly classified as coding RNAs. lincRNAs may broadly serve to fine-tune the expression of neighbouring genes with remarkable tissue specificity through a diversity of mechanisms, highlighting our rapidly evolving understanding of the non-coding genome...
November 15, 2017: Nature Reviews. Molecular Cell Biology
https://www.readbyqxmd.com/read/29137272/immunological-cytokine-profiling-identifies-tnf-%C3%AE-as-a-key-molecule-dysregulated-in-autistic-children
#2
Jiang Xie, Li Huang, Xiaohong Li, Hua Li, Yongmei Zhou, Hua Zhu, Tianying Pan, Keith M Kendrick, Wenming Xu
Recent studies have suggested that the etiology of autism spectrum disorder (ASD) may be caused by immunological factors, particularly abnormalities in the innate immune system. However, it is still unclear which specific cytokines may be of most importance. The current study therefore investigated which cytokines showed altered concentrations in blood in ASD compared with healthy control children and which were also correlated with symptom severity. Our study sample included 32 children diagnosed with ASD and 28 age and sex-matched typically developing children...
October 10, 2017: Oncotarget
https://www.readbyqxmd.com/read/29137177/comprehensive-profiling-of-lincrnas-in-lung-adenocarcinoma-of-never-smokers-reveals-their-roles-in-cancer-development-and-prognosis
#3
Ying Li, Zheng Wang, Asha Nair, Wei Song, Ping Yang, Xiaoju Zhang, Zhifu Sun
Long intergenic non-coding RNA (lincRNA) is a family of gene transcripts, the functions of which are largely unknown. Although cigarette smoking is the main cause for lung cancer, lung cancer in non-smokers is a separate entity and its underlying cause is little known. Growing evidence suggests lincRNAs play a significant role in cancer development and progression; however, such data is lacking for lung cancer in non-smokers, or those who have never smoked. This study conducted comprehensive profiling of lincRNAs from RNA sequencing (RNA-seq) data of non-smoker patients with lung adenocarcinoma...
November 13, 2017: Genes
https://www.readbyqxmd.com/read/29133519/deep-rna-sequencing-uncovers-a-repertoire-of-human-macrophage-long-intergenic-noncoding-rnas-modulated-by-macrophage-activation-and-associated-with-cardiometabolic-diseases
#4
Hanrui Zhang, Chenyi Xue, Ying Wang, Jianting Shi, Xuan Zhang, Wenjun Li, Sara Nunez, Andrea S Foulkes, Jennie Lin, Christine C Hinkle, Wenli Yang, Edward E Morrisey, Daniel J Rader, Mingyao Li, Muredach P Reilly
BACKGROUND: Sustained and dysfunctional macrophage activation promotes inflammatory cardiometabolic disorders, but the role of long intergenic noncoding RNA (lincRNA) in human macrophage activation and cardiometabolic disorders is poorly defined. Through transcriptomics, bioinformatics, and selective functional studies, we sought to elucidate the lincRNA landscape of human macrophages. METHODS AND RESULTS: We used deep RNA sequencing to assemble the lincRNA transcriptome of human monocyte-derived macrophages at rest and following stimulation with lipopolysaccharide and IFN-γ (interferon γ) for M1 activation and IL-4 (interleukin 4) for M2 activation...
November 13, 2017: Journal of the American Heart Association
https://www.readbyqxmd.com/read/29109091/transcriptomic-profiling-of-mda-mb-231-cells-exposed-to-boswellia-serrata-and-3-o-acetyl-b-boswellic-acid-er-upr-mediated-programmed-cell-death
#5
REVIEW
Elizabeth A Mazzio, Charles A Lewis, Karam F A Soliman
BACKGROUND/AIM: Triple-negative breast cancer (TNBC) is characterized by the absence of hormone receptors (estrogen, progesterone and human epidermal growth factor receptor-2) and a relatively poor prognosis due to inefficacy of hormone receptor-based chemotherapies. It is imperative that we continue to explore natural products with potential to impede growth and metastasis of TNBC. In this study, we screened over 1,000 natural products for capacity to induce cell death in TNBC (MDA-MB -231) cells...
November 2017: Cancer Genomics & Proteomics
https://www.readbyqxmd.com/read/29100395/long-noncoding-rna-malat-1-is-a-novel-inflammatory-regulator-in-human-systemic-lupus-erythematosus
#6
Huaxia Yang, Naixin Liang, Min Wang, Yunyun Fei, Jian Sun, Zhiyuan Li, Yuan Xu, Chao Guo, Zhili Cao, Shanqing Li, Yuchen Jiao
Despite growing evidence that Long noncoding RNAs (lncRNAs) can regulate gene expression and widely take part in autoimmune and inflammatory diseases, our knowledge of systemic lupus erythematosus (SLE)-related lincRNAs remains limited. In this study, we aimed to explore the contribution of the lncRNA metastasis associated lung adenocarcinoma transcript 1 (MALAT1) to the pathogenesis of SLE. PBMCs were obtained from SLE patients and healthy donors. The expression levels of MALAT-1 were measured by quantitative PCR...
September 29, 2017: Oncotarget
https://www.readbyqxmd.com/read/29093522/genome-wide-discovery-of-long-intergenic-noncoding-rnas-and-their-epigenetic-signatures-in-the-rat
#7
Aimin Li, Zhong-Yin Zhou, Xinhong Hei, Newton O Otecko, Junying Zhang, Yajun Liu, Hongfang Zhou, Zhiqiang Zhao, Lei Wang
Long intergenic noncoding RNAs (lincRNAs) play a crucial role in many biological processes. The rat is an important model organism in biomedical research. Recent studies have detected rat lincRNA genes from several samples. However, identification of rat lincRNAs using large-scale RNA-seq datasets remains unreported. Herein, using more than 100 billion RNA-seq reads from 59 publications together with RefSeq and UniGene annotated RNAs, we report 39,154 lincRNA transcripts encoded by 19,162 lincRNA genes in the rat...
November 1, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29090518/detection-and-analysis-of-circulating-large-intergenic-non-coding-rna-regulator-of-reprogramming-in-plasma-for-breast-cancer
#8
Kaijiong Zhang, Zhenglian Luo, Yi Zhang, Yuzhi Wang, Meng Cui, Lian Liu, Li Zhang, Jinbo Liu
BACKGROUND: Previous studies have indicated that large intergenic non-coding RNA regulator of reprogramming (lincRNA-ROR) plays an important role in regulating tumor carcinogenesis and metastasis; however, whether circulating lincRNA-ROR could function as a potential biomarker for breast cancer (BC) diagnosis and monitoring is unknown. This study was conducted to investigate circulating lincRNA-ROR in plasma as a potential biomarker for BC diagnosis and monitoring. METHODS: We performed reverse transcription-quantitative-PCR to examine lincRNA-ROR expression levels in cell lines, 24 pairs of BC tissue samples, and 94 plasma samples from BC patients...
November 1, 2017: Thoracic Cancer
https://www.readbyqxmd.com/read/29089527/cross-platform-analysis-of-transcriptomic-data-identifies-ageing-has-distinct-and-opposite-effects-on-tendon-in-males-and-females
#9
Louise I Pease, Peter D Clegg, Carole J Proctor, Daryl J Shanley, Simon J Cockell, Mandy J Peffers
The development of tendinopathy is influenced by a variety of factors including age, gender, sex hormones and diabetes status. Cross platform comparative analysis of transcriptomic data elucidated the connections between these entities in the context of ageing. Tissue-engineered tendons differentiated from bone marrow derived mesenchymal stem cells from young (20-24 years) and old (54-70 years) donors were assayed using ribonucleic acid sequencing (RNA-seq). Extension of the experiment to microarray and RNA-seq data from tendon identified gender specific gene expression changes highlighting disparity with existing literature and published pathways...
October 31, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29075020/the-rbm14-coaa-interacting-long-intergenic-non-coding-rna-paral1-regulates-adipogenesis-and-coactivates-the-nuclear-receptor-ppar%C3%AE
#10
François F Firmin, Frederik Oger, Céline Gheeraert, Julie Dubois-Chevalier, Anne-Sophie Vercoutter-Edouart, Fawaz Alzaid, Claire Mazuy, Hélène Dehondt, Jeremy Alexandre, Bruno Derudas, Quentin Dhalluin, Maheul Ploton, Alexandre Berthier, Eloise Woitrain, Tony Lefebvre, Nicolas Venteclef, François Pattou, Bart Staels, Jérôme Eeckhoute, Philippe Lefebvre
Adipocyte differentiation and function relies on a network of transcription factors, which is disrupted in obesity-associated low grade, chronic inflammation leading to adipose tissue dysfunction. In this context, there is a need for a thorough understanding of the transcriptional regulatory network involved in adipose tissue pathophysiology. Recent advances in the functional annotation of the genome has highlighted the role of non-coding RNAs in cellular differentiation processes in coordination with transcription factors...
October 26, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29051223/crispr-cas9-based-screening-of-long-noncoding-rnas-lncrnas-in-macrophages-with-an-nf-kappa-b-reporter
#11
Sergio Covarrubias, Elektra K Robinson, Barbara Shapleigh, Apple Vollmers, Solomon Katzman, Nicole Hanley, Nicholas Fong, Michael T McManus, Susan Carpenter
The innate immune system protects against infections by initiating an inducible inflammatory response. NF-kappa B (NF-KB) is one of the critical transcription factors controlling this complex response, but some aspects of its regulation remain unclear. For example, although long noncoding RNAs (lncRNAs) have been shown to critically regulate gene expression, only a fraction of these have been functionally characterized, and the extent to which lncRNAs control NF-KB expression is unknown. Here, we describe the generation of a GFP-based NF-KB reporter system in immortalized murine bone marrow-derived macrophages (iBMDMs)...
October 19, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29050779/transcriptome-landscape-of-long-intergenic-non-coding-rnas-in-endometrial-cancer
#12
Bei Jun Chen, Frances L Byrne, Konii Takenaka, Susan C Modesitt, Ellen M Olzomer, James D Mills, Rhonda Farrell, Kyle L Hoehn, Michael Janitz
Endometrial cancer is the most common gynecological malignancy in the developed world. It is the fifth most common cancer and accounts for 4.8% of all cancers in women. Long intergenic non-coding RNAs (lincRNAs), a subclass of long non-coding RNAs, are pervasively transcribed throughout the human genome. OBJECTIVE: LincRNA expression patterns in endometrial cancer compared to normal healthy tissue are poorly characterised. In this study, the lincRNA transcriptome of endometrial cancers and adjacent normal endometrium from the same patients was sequenced and compared with transcriptomes of other gynaecologic malignancies including ovarian and cervical cancers...
October 16, 2017: Gynecologic Oncology
https://www.readbyqxmd.com/read/29039457/high-throughput-sequencing-reveals-novel-lincrna-in-age-related-cataract
#13
Na Zhang, Chunmei Zhang, Xu Wang, Yanhua Qi
Age-related cataract (ARC) is a major cause of blindness. Long non-coding RNAs (lncRNAs) are a heterogeneous class of RNAs that are non-protein-coding transcripts >200 nucleotides in length. LncRNAs are involved in various critical biological processes, such as chromatin remodeling, gene transcription, and protein transport and trafficking. Furthermore, the dysregulation of lncRNAs causes a number of complex human diseases, including coronary artery diseases, autoimmune diseases, neurological disorders and various cancers...
October 11, 2017: International Journal of Molecular Medicine
https://www.readbyqxmd.com/read/29037146/comparative-genomic-analyses-highlight-the-contribution-of-pseudogenized-protein-coding-genes-to-human-lincrnas
#14
Wan-Hsin Liu, Zing Tsung-Yeh Tsai, Huai-Kuang Tsai
BACKGROUND: The regulatory roles of long intergenic noncoding RNAs (lincRNAs) in humans have been revealed through the use of advanced sequencing technology. Recently, three possible scenarios of lincRNA origins have been proposed: de novo origination from intergenic regions, duplication from other long noncoding RNAs, and pseudogenization from protein-coding genes. The first two scenarios are largely studied and supported, yet few studies focused on the evolution from pseudogenized protein-coding sequence to lincRNA...
October 16, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29030469/single-cell-gene-expression-analysis-reveals-regulators-of-distinct-cell-subpopulations-among-developing-human-neurons
#15
Jiaxu Wang, Piroon Jenjaroenpun, Akshay Bhinge, Vladimir Espinosa Angarica, Antonio Del Sol, Intawat Nookaew, Vladimir A Kuznetsov, Lawrence W Stanton
The stochastic dynamics and regulatory mechanisms that govern differentiation of individual human neural precursor cells (NPC) into mature neurons are currently not fully understood. Here, we used single-cell RNA-sequencing (scRNA-seq) of developing neurons to dissect/identify NPC subtypes and critical developmental stages of alternative lineage specifications. This study comprises an unsupervised, high-resolution strategy for identifying cell developmental bifurcations, tracking the stochastic transcript kinetics of the subpopulations, elucidating regulatory networks, and finding key regulators...
November 2017: Genome Research
https://www.readbyqxmd.com/read/29024969/preconception-urinary-phthalate-concentrations-and-sperm-dna-methylation-profiles-among-men-undergoing-ivf-treatment-a-cross-sectional-study
#16
Haotian Wu, Molly S Estill, Alexander Shershebnev, Alexander Suvorov, Stephen A Krawetz, Brian W Whitcomb, Holly Dinnie, Tayyab Rahil, Cynthia K Sites, J Richard Pilsner
STUDY QUESTION: Are preconception phthalate and phthalate replacements associated with sperm differentially methylated regions (DMRs) among men undergoing IVF? SUMMARY ANSWER: Ten phthalate metabolites were associated with 131 sperm DMRs that were enriched in genes related to growth and development, cell movement and cytoskeleton structure. WHAT IS KNOWN ALREADY: Several phthalate compounds and their metabolites are known endocrine disrupting compounds and are pervasive environmental contaminants...
November 1, 2017: Human Reproduction
https://www.readbyqxmd.com/read/28994148/lincrna-p21-suppresses-development-of-human-prostate-cancer-through-inhibition-of-pkm2
#17
Xiaohai Wang, Yongzhi Xu, Xingjie Wang, Chenyi Jiang, Sha Han, Kai Dong, Mengjun Shen, Shujie Xia, Dongliang Xu
OBJECTIVES: Previously, we found that long intergenic non-coding RNA-p21 (lincRNA-p21) inhibited the development of human prostate cancer. However, the underlying molecular mechanisms are poorly understood. Here, we attempted to investigate the downstream targets of lincRNA-p21 in prostate cancer. MATERIALS AND METHODS: Expression of lincRNA-p21 and PKM2 was determined by qRT-PCR and Western blot. Lentivirus expressing shPKM2 or shCtrl was used to explore the role of PKM2 on the enhanced cell proliferation and glycolysis of lincRNA-p21-silenced prostate cancer cells...
October 9, 2017: Cell Proliferation
https://www.readbyqxmd.com/read/28992244/lincrna-1614-coordinates-sox2-prc2-mediated-repression-of-developmental-genes-in-pluripotency-maintenance
#18
Xudong Guo, Zikang Wang, Chenqi Lu, Wujun Hong, Guiying Wang, Yanxin Xu, Zhongmin Liu, Jiuhong Kang
Large-intergenic noncoding RNAs (lincRNAs) cooperate with core transcription factors to coordinate the pluripotency network of embryonic stem cells. The mechanisms by which lincRNAs affect chromatin structure and gene transcription remain mostly unknown. Here, we identified that a lincRNA (linc1614), occupied by pluripotency factors at its promoter, was indispensable for both maintenance and acquisition of pluripotency. Linc1614 served as a specific partner of core factor Sox2 in maintaining pluripotency, primarily by mediating the function of Sox2 in the repression of developmental genes...
September 14, 2017: Journal of Molecular Cell Biology
https://www.readbyqxmd.com/read/28984028/linc00511-acts-as-a-competing-endogenous-rna-to-regulate-vegfa-expression-through-sponging-hsa-mir-29b-3p-in-pancreatic-ductal-adenocarcinoma
#19
Xiaohui Zhao, Yimin Liu, Zhihua Li, Shangyou Zheng, Zairui Wang, Wenzhu Li, Zhuofei Bi, Liting Li, Yanhui Jiang, Yuming Luo, Qing Lin, Zhiqiang Fu, Chen Rufu
Pancreatic ductal adenocarcinoma (PDAC) is a lethal malignancy. Long non-coding RNAs (lncRNAs) are important regulators in pathological processes, yet their potential roles in PDAC are poorly understood. Here, we identify a fundamental role for a novel lincRNA, linc00511, in the progression of PDAC. Linc00511 levels in PDAC tissue specimens and cell lines were examined by quantitative real-time PCR. Corresponding adjacent non-neoplastic tissues were used as controls. The function of linc00511 in PDAC cell lines was determined by RNA interference approach in vitro and in vivo...
October 5, 2017: Journal of Cellular and Molecular Medicine
https://www.readbyqxmd.com/read/28983628/long-intergenic-noncoding-rna-p21-mediates-oxidized-ldl%C3%A2-induced-apoptosis-and-expression-of-lox%C3%A2-1-in-human-coronary-artery-endothelial-cells
#20
Tao Zhou, Xiaofang Chen
Atherosclerosis is the most common pathological cause of cardiovascular diseases, and endothelial dysfunction has a vital role. It has been suggested that inhibiting endothelial cell apoptosis induced by oxidized low‑density lipoprotein (ox‑LDL), an essential atherosclerotic factor, is a potential novel therapeutic strategy against atherosclerosis. Previous studies have revealed that endothelial lectin‑like ox‑LDL receptor‑1 (LOX‑1) and long intergenic noncoding RNA p21 (lincRNA‑p21) may serve as therapeutic targets for atherosclerosis and associated cardiovascular disorders...
December 2017: Molecular Medicine Reports
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