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https://www.readbyqxmd.com/read/28810830/annotating-long-intergenic-non-coding-rnas-under-artificial-selection-during-chicken-domestication
#1
Yun-Mei Wang, Hai-Bo Xu, Ming-Shan Wang, Newton Otieno Otecko, Ling-Qun Ye, Dong-Dong Wu, Ya-Ping Zhang
BACKGROUND: Numerous biological functions of long intergenic non-coding RNAs (lincRNAs) have been identified. However, the contribution of lincRNAs to the domestication process has remained elusive. Following domestication from their wild ancestors, animals display substantial changes in many phenotypic traits. Therefore, it is possible that diverse molecular drivers play important roles in this process. RESULTS: We analyzed 821 transcriptomes in this study and annotated 4754 lincRNA genes in the chicken genome...
August 15, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28790305/single-cardiomyocyte-nuclear-transcriptomes-reveal-a-lincrna-regulated-de-differentiation-and-cell-cycle-stress-response-in-vivo
#2
Kelvin See, Wilson L W Tan, Eng How Lim, Zenia Tiang, Li Ting Lee, Peter Y Q Li, Tuan D A Luu, Matthew Ackers-Johnson, Roger S Foo
Cardiac regeneration may revolutionize treatment for heart failure but endogenous progenitor-derived cardiomyocytes in the adult mammalian heart are few and pre-existing adult cardiomyocytes divide only at very low rates. Although candidate genes that control cardiomyocyte cell cycle re-entry have been implicated, expression heterogeneity in the cardiomyocyte stress-response has never been explored. Here, we show by single nuclear RNA-sequencing of cardiomyocytes from both mouse and human failing, and non-failing adult hearts that sub-populations of cardiomyocytes upregulate cell cycle activators and inhibitors consequent to the stress-response in vivo...
August 9, 2017: Nature Communications
https://www.readbyqxmd.com/read/28777303/novel-biomarkers-in-the-diagnosis-of-chronic-kidney-disease-and-the-prediction-of-its-outcome
#3
REVIEW
Jacek Rysz, Anna Gluba-Brzózka, Beata Franczyk, Zbigniew Jabłonowski, Aleksandra Ciałkowska-Rysz
In its early stages, symptoms of chronic kidney disease (CKD) are usually not apparent. Significant reduction of the kidney function is the first obvious sign of disease. If diagnosed early (stages 1 to 3), the progression of CKD can be altered and complications reduced. In stages 4 and 5 extensive kidney damage is observed, which usually results in end-stage renal failure. Currently, the diagnosis of CKD is made usually on the levels of blood urea and serum creatinine (sCr), however, sCr has been shown to be lacking high predictive value...
August 4, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28767393/immunological-cytokine-profiling-identifies-tnf-%C3%AE-as-a-key-molecule-dysregulated-in-autistic-children
#4
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...
July 18, 2017: Oncotarget
https://www.readbyqxmd.com/read/28767188/linc01101-and-linc00277-expression-levels-as-novel-factors-in-hpv-induced-cervical-neoplasia
#5
Iulia Virginia Iancu, Gabriela Anton, Anca Botezatu, Irina Huica, Anca Nastase, Demetra Gabriela Socolov, Anca Daniela Stanescu, Simona Olimpia Dima, Nicolae Bacalbasa, Adriana Plesa
Recently long non-coding RNAs were identified as new factors involved in gene expression regulation. To gain insight into expression pattern of these factors related to E7 HPV18 oncogene, this study uses HeLa cell culture transfected with E7-siRNA. Gene expression profile was investigated using microarray analysis. After analysing the microarray results, we identified 15,387 RNA species differentially expressed in E7-siRNA-transfected cells compared with controls (fold change >2). The expression profiles of lncRNA species highlighted 731 lncRNAs and 203 lincRNAs...
August 2, 2017: Journal of Cellular and Molecular Medicine
https://www.readbyqxmd.com/read/28754963/transcriptome-profiling-of-monocytes-from-xla-patients-revealed-the-innate-immune-function-dysregulation-due-to-the-btk-gene-expression-deficiency
#6
Hoda Mirsafian, Adiratna Mat Ripen, Wai-Mun Leong, Chai Teng Chear, Saharuddin Bin Mohamad, Amir Feisal Merican
X-linked agammaglobulinemia (XLA) is a rare genetic disorder, caused by mutations in BTK (Bruton's Tyrosine Kinase) gene. Deep high-throughput RNA sequencing (RNA-Seq) approach was utilized to explore the possible differences in transcriptome profiles of primary monocytes in XLA patients compared with healthy subjects. Our analysis revealed the differences in expression of 1,827 protein-coding genes, 95 annotated long non-coding RNAs (lncRNAs) and 20 novel lincRNAs between XLA patients and healthy subjects...
July 28, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28733557/down-regulation-of-lincrna-p21-contributes-to-gastric-cancer-development-through-hippo-independent-activation-of-yap
#7
Ying Chen, Guoqing Wei, Hongwei Xia, Huangfei Yu, Qiuling Tang, Feng Bi
Long intergenic non-coding RNA p21 (lincRNA-p21), known as the direct transcriptional target of p53, was found down-regulated in several human solid tumors. However, little is known about the role of lincRNA-p21 in gastric cancer. The expression levels of lincRNA-p21 in tissue samples and cell lines were detected by qRT-PCR. MGC-803 and MKN-45 cells were transfected with siRNAs targeting lincRNA-p21 or control siRNAs to determine the effect of reduced lincRNA-p21 expression on tumorigenesis. We also overexpressed lincRNA-p21 in MGC-803 cells...
July 10, 2017: Oncotarget
https://www.readbyqxmd.com/read/28732076/eincr1-is-an-egf-inducible-lincrna-overexpressed-in-lung-adenocarcinomas
#8
Karol Nowicki-Osuch, Yaoyong Li, Mairi Challinor, David T Gerrard, Neil A Hanley, Andrew D Sharrocks
Long non-coding RNAs are being increasingly recognised as important molecules involved in regulating a diverse array of biological functions. For example, many long non-coding RNAs have been associated with tumourigenesis and in this context their molecular functions often involves impacting on chromatin and transcriptional control processes. One important cellular control system that is often deregulated in cancer cells is the ERK MAP kinase pathway. Here we have investigated whether ERK pathway signaling in response to EGF stimulation, leads to changes in the production of long non-coding RNAs...
2017: PloS One
https://www.readbyqxmd.com/read/28724410/identification-and-characterization-of-long-non-coding-rnas-in-subcutaneous-adipose-tissue-from-castrated-and-intact-full-sib-pair-huainan-male-pigs
#9
Jing Wang, Liushuai Hua, Junfeng Chen, Jiaqing Zhang, Xianxiao Bai, Binwen Gao, Congjun Li, Zhihai Shi, Weidong Sheng, Yuan Gao, Baosong Xing
BACKGROUND: Long non-coding RNAs (lncRNAs) regulate adipose tissue metabolism, however, their function on testosterone deficiency related obesity in humans is less understood. For this research, intact and castrated male pigs are the best model animal because of their similar proportional organ sizes, cardiovascular systems and metabolic features. RESULTS: We identified lncRNAs in subcutaneous adipose tissue by deep RNA-sequencing using the intact and castrated Huainan male pigs...
July 19, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28721075/lincrna-p21-inhibits-invasion-and-metastasis-of-hepatocellular-carcinoma-through-mir-9-e-cadherin-cascade-signaling-pathway-molecular-mechanism
#10
Gangqiang Ding, Zhen Peng, Jia Shang, Yi Kang, Huibin Ning, Chongshan Mao
In the previous study, it was found that long intergenic noncoding RNA-p21 (lincRNA-p21) was downregulated in hepatocellular carcinoma (HCC) and lincRNA-p21 overexpression inhibited tumor invasion through inducing epithelial-mesenchymal transition. However, the underlying mechanism was not fully elaborated. In this study, lincRNA-p21 expression was measured in 12 paired HCC and nontumor adjacent normal tissues by quantitative real-time polymerase chain reaction. The effects of lincRNA-p21 on HCC cells were studied using lentivirus expressing lincRNA-p21 vector in vitro...
2017: OncoTargets and Therapy
https://www.readbyqxmd.com/read/28720099/association-between-genome-wide-copy-number-variation-and-arsenic-induced-skin-lesions-a-prospective-study
#11
Muhammad G Kibriya, Farzana Jasmine, Faruque Parvez, Maria Argos, Shantanu Roy, Rachelle Paul-Brutus, Tariqul Islam, Alauddin Ahmed, Muhammad Rakibuz-Zaman, Justin Shinkle, Vesna Slavkovich, Joseph H Graziano, Habibul Ahsan
BACKGROUND: Exposure to arsenic in drinking water is a global health problem and arsenic-induced skin lesions are hallmark of chronic arsenic toxicity. We and others have reported germline genetic variations as risk factors for such skin lesions. The role of copy number variation (CNV) in the germline DNA in this regard is unknown. METHODS: From a large prospectively followed-up cohort, exposed to arsenic, we randomly selected 2171 subjects without arsenic-induced skin lesions at enrollment and genotyped their whole blood DNA samples on Illumina Cyto12v2...
July 18, 2017: Environmental Health: a Global Access Science Source
https://www.readbyqxmd.com/read/28701691/spatiotemporal-expression-profiling-of-long-intervening-noncoding-rnas-in-caenorhabditis-elegans
#12
Weihong Liu, Enchao Yu, Siyu Chen, Xiaopeng Ma, Yiwen Lu, Xiao Liu
To better understand the biological function of long noncoding RNAs, it is critical to determine their spatiotemporal expression patterns. We generated transgenic reporter strains for 149 out of the 170 annotated C. elegans long intervening noncoding RNAs (lincRNAs) and profiled their temporal activity. For the 68 lincRNAs with integrated reporter lines, we profiled their expression at the resolution of single cells in L1 larvae, and revealed that the expression of lincRNAs is more specific, heterogeneous and at lower level than transcription factors (TFs)...
July 12, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28698299/neat1-is-a-p53-inducible-lincrna-essential-for-transformation-suppression
#13
Stephano S Mello, Carolyn Sinow, Nitin Raj, Pawel K Mazur, Kathryn Bieging-Rolett, Daniela Kenzelmann Broz, Jamie F Conklin Imam, Hannes Vogel, Laura D Wood, Julien Sage, Tetsuro Hirose, Shinichi Nakagawa, John Rinn, Laura D Attardi
The p53 gene is mutated in over half of all cancers, reflecting its critical role as a tumor suppressor. Although p53 is a transcriptional activator that induces myriad target genes, those p53-inducible genes most critical for tumor suppression remain elusive. Here, we leveraged p53 ChIP-seq (chromatin immunoprecipitation [ChIP] combined with high-throughput sequencing) and RNA-seq (RNA sequencing) data sets to identify new p53 target genes, focusing on the noncoding genome. We identify Neat1, a noncoding RNA (ncRNA) constituent of paraspeckles, as a p53 target gene broadly induced by mouse and human p53 in different cell types and by diverse stress signals...
June 1, 2017: Genes & Development
https://www.readbyqxmd.com/read/28689810/lincrna-p21-knockdown-enhances-radiosensitivity-of-hypoxic-tumor-cells-by-reducing-autophagy-through-hif-1-akt-mtor-p70s6k-pathway
#14
Yueming Shen, Yingying Liu, Ting Sun, Wei Yang
Hypoxic conditions are common in solid tumors and have a significant effect on tumor progression, therapeutic and prognosis. Long noncoding RNAs (lncRNAs) are longer than 200 nucleotides and cannot be translated into proteins, which play important roles in some diseases including cancer. Although previous analysis have showed that long intergenic non-coding RNA (lincRNA)-p21 is hypoxia-responsive and functions as a new regulator of cell cycle, apoptosis and warburg effect in cervical cancer, its biological roles in hypoxic hepatoma and glioma are unknown...
July 6, 2017: Experimental Cell Research
https://www.readbyqxmd.com/read/28680141/the-lincrna-ror-mir-145-axis-promotes-invasion-and-metastasis-in-hepatocellular-carcinoma-via-induction-of-epithelial-mesenchymal-transition-by-targeting-zeb2
#15
Chen Li, Lu Lu, Bing Feng, Kai Zhang, Siqi Han, Daorong Hou, Longbang Chen, Xiaoyuan Chu, Rui Wang
Emerging evidence show that long noncoding RNAs (lncRNAs) play critical roles in tumor development. LincRNA-ROR (linc-ROR) is known to promote tumor progress in several human cancers, including hepatocellular carcinoma (HCC). Nevertheless, the roles of linc-ROR in HCC metastasis and its underlying mechanisms remain fully unclear. In the present study, we showed that linc-ROR was upregulated in HCC tissues and high linc-ROR expression level predicted poor prognosis. Functionally, linc-ROR significantly induced epithelial-mesenchymal transition (EMT), and increased in vitro invasion and in vivo metastasis of HCC cells...
July 5, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28674423/a-four-gene-lincrna-expression-signature-predicts-risk-in-multiple-cohorts-of-acute-myeloid-leukemia-patients
#16
D Beck, J A I Thoms, C Palu, T Herold, A Shah, J Olivier, L Boelen, Y Huang, D Chacon, A Brown, M Babic, C Hahn, M Perugini, X Zhou, B J Huntly, A Schwarzer, J-H Klusmann, W E Berdel, B Wörmann, T Büchner, W Hiddemann, S K Bohlander, L B To, H S Scott, I D Lewis, R J D'Andrea, J W H Wong, J E Pimanda
Prognostic gene expression signatures have been proposed as clinical tools to clarify therapeutic options in Acute Myeloid Leukemia (AML). However, these signatures rely on measuring large numbers of genes and often perform poorly when applied to independent cohorts or those with older patients. Long intergenic noncoding RNAs (lincRNAs) are emerging as important regulators of cell identity and oncogenesis, but knowledge of their utility as prognostic markers in AML is limited. Here we analyse transcriptomic data from multiple cohorts of clinically annotated AML patients and report that (i) microarrays designed for coding gene expression can be repurposed to yield robust lincRNA expression data, (ii) some lincRNA-genes are located in close proximity to hematopoietic coding-genes and show strong expression correlations in AML, (iii) lincRNA-gene expression patterns distinguish cytogenetic and molecular subtypes of AML, (iv) lincRNA-signatures composed of three or four genes are independent predictors of clinical outcome and further dichotomise survival in ELN risk groups, and (v) an analytical tool based on logistic regression analysis of quantitative PCR measurement of four lincRNA genes (LINC4) can be used to determine risk in AML...
July 4, 2017: Leukemia: Official Journal of the Leukemia Society of America, Leukemia Research Fund, U.K
https://www.readbyqxmd.com/read/28673235/comparative-analysis-of-lincrna-in-insect-species
#17
Alberto Lopez-Ezquerra, Mark C Harrison, Erich Bornberg-Bauer
BACKGROUND: The ever increasing availability of genomes makes it possible to investigate and compare not only the genomic complements of genes and proteins, but also of RNAs. One class of RNAs, the long noncoding RNAs (lncRNAs) and, in particular, their subclass of long intergenic noncoding RNAs (lincRNAs) have recently gained much attention because of their roles in regulation of important biological processes such as immune response or cell differentiation and as possible evolutionary precursors for protein coding genes...
July 3, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28668092/dissecting-the-role-of-non-coding-rnas-in-the-accumulation-of-amyloid-and-tau-neuropathologies-in-alzheimer-s-disease
#18
Ellis Patrick, Sathyapriya Rajagopal, Hon-Kit Andus Wong, Cristin McCabe, Jishu Xu, Anna Tang, Selina H Imboywa, Julie A Schneider, Nathalie Pochet, Anna M Krichevsky, Lori B Chibnik, David A Bennett, Philip L De Jager
BACKGROUND: Given multiple studies of brain microRNA (miRNA) in relation to Alzheimer's disease (AD) with few consistent results and the heterogeneity of this disease, the objective of this study was to explore their mechanism by evaluating their relation to different elements of Alzheimer's disease pathology, confounding factors and mRNA expression data from the same subjects in the same brain region. METHODS: We report analyses of expression profiling of miRNA (n = 700 subjects) and lincRNA (n = 540 subjects) from the dorsolateral prefrontal cortex of individuals participating in two longitudinal cohort studies of aging...
July 1, 2017: Molecular Neurodegeneration
https://www.readbyqxmd.com/read/28662497/identification-and-characterization-of-long-non-coding-rnas-in-osteogenic-differentiation-of-human-adipose-derived-stem-cells
#19
Guangxin Huang, Yan Kang, Zhiyu Huang, Zhiqi Zhang, Fangang Meng, Weishen Chen, Ming Fu, Weiming Liao, Ziji Zhang
BACKGROUND/AIMS: Long noncoding RNAs (lncRNAs) play important roles in stem cell differentiation. However, their role in osteogenesis of human adipose-derived stem cells (ASCs), a promising cell source for bone regeneration, remains unknown. Here, we investigated the expression profile and potential roles of lncRNAs in osteogenic differentiation of human ASCs. METHODS: Human ASCs were induced to differentiate into osteoblasts in vitro, and the expression profiles of lncRNAs and mRNAs in undifferentiated and osteogenic differentiated ASCs were obtained by microarray...
June 28, 2017: Cellular Physiology and Biochemistry
https://www.readbyqxmd.com/read/28653111/seed-weight-differences-between-wild-and-domesticated-soybeans-are-associated-with-specific-changes-in-gene-expression
#20
Chao Yu, Zhipeng Qu, Yueting Zhang, Xifeng Zhang, Tingting Lan, David L Adelson, Dong Wang, Youlin Zhu
Our study systematically explored potential genes and molecular pathways as candidates for differences in seed weight resulting from soybean domestication. In addition, potential contributions of lncRNAs to seed weight were also investigated. Soybeans have a long history of domestication in China, and there are several significant phenotypic differences between cultivated and wild soybeans, for example, seeds of cultivars are generally larger and heavier than those from wild accessions. We analyzed seed transcriptomes from thirteen soybean samples, including six landraces and seven wild accessions using strand-specific RNA sequencing...
June 26, 2017: Plant Cell Reports
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