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Chromatin-associated LncRNA

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https://www.readbyqxmd.com/read/27900563/lncrna-hotair-promotes-cisplatin-resistance-in-gastric-cancer-by-targeting-mir-126-to-activate-the-pi3k-akt-mrp1-genes
#1
Jin Yan, Yini Dang, Shiyu Liu, Yifeng Zhang, Guoxin Zhang
Altered expression of long noncoding RNAs (lncRNAs) has shown to associate with human cancer development and progression and drug resistance. LncRNA HOX antisense intergenic RNA (HOTAIR) regulates chromatin state and highly expressed in various human cancers. This study analyzed HOTAIR expression in gastric cancer cells and tissues and then assessed the effects of HOTAIR on modulation of gastric cancer cell sensitivity to cisplatin and the underlying molecular events. The data showed that HOTAIR was significantly upregulated in cisplatin-resistant gastric cancer cells and tissues compared with control cells and noncancerous gastric tissues...
November 30, 2016: Tumour Biology: the Journal of the International Society for Oncodevelopmental Biology and Medicine
https://www.readbyqxmd.com/read/27852821/meg3-long-noncoding-rna-contributes-to-the-epigenetic-regulation-of-epithelial-mesenchymal-transition-in-lung-cancer-cell-lines
#2
Minoru Terashima, Shoichiro Tange, Akihiko Ishimura, Takeshi Suzuki
Histone methylation is implicated in a number of biological and pathological processes including cancer development. In this study, we investigated the molecular mechanism for the recruitment of Polycomb repressive complex-2 (PRC2) and its accessory component, JARID2, to chromatin, which regulates methylation of lysine 27 of histone H3 (H3K27), during epithelial-mesenchymal transition (EMT) of cancer cells. The expression of MEG3 long noncoding RNA (lncRNA), which could interact with JARID2, was clearly increased during Transforming Growth Factor-beta (TGF-β)-induced EMT of human lung cancer cell lines...
November 16, 2016: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/27789700/reciprocal-regulation-of-chromatin-state-and-architecture-by-hotairm1-contributes-to-temporal-collinear-hoxa-gene-activation
#3
Xue Q D Wang, Josée Dostie
Thousands of long non-coding RNAs (lncRNAs) have been identified in mammals, many of which represent important regulators of gene expression. However, the mechanisms used by lncRNAs to control transcription remain largely uncharacterized. Here, we report on HOTAIRM1, a promising lncRNA biomarker in leukemia and solid tumors. We find that HOTAIRM1 contributes to three-dimensional chromatin organization changes required for the temporal collinear activation of HOXA genes. We show that distinct HOTAIRM1 variants preferentially associate with either UTX/MLL or PRC2 complexes to modulate the levels of activating and silencing marks at the bivalent domain...
October 26, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27779094/long-non-coding-rna-produced-by-rna-polymerase-v-determines-boundaries-of-heterochromatin
#4
Gudrun Böhmdorfer, Shriya Sethuraman, M Jordan Rowley, Michal Krzyszton, M Hafiz Rothi, Lilia Bouzit, Andrzej T Wierzbicki
RNA-mediated transcriptional gene silencing is a conserved process where small RNAs target transposons and other sequences for repression by establishing chromatin modifications. A central element of this process are long non-coding RNAs (lncRNA), which in Arabidopsis thaliana are produced by a specialized RNA polymerase known as Pol V. Here we show that non-coding transcription by Pol V is controlled by preexisting chromatin modifications located within the transcribed regions. Most Pol V transcripts are associated with AGO4 but are not sliced by AGO4...
October 25, 2016: ELife
https://www.readbyqxmd.com/read/27777512/long-non-coding-rna-dbccr1-003-regulate-the-expression-of-dbccr1-via-dnmt1-in-bladder-cancer
#5
Defeng Qi, Jinhui Li, Biao Que, Jialin Su, Mengxi Li, Chaofeng Zhang, Mei Yang, Guoren Zhou, Weidong Ji
BACKGROUND: Many long non coding RNAs have been identified as key modulators in cancer development. A lncRNA, DBCCR1-003, derived from the locus of tumor suppressor gene DBCCR1 (deleted in bladder cancer chromosome region 1), has unknown function. In the present study, we explored function and molecular mechanism of DBCCR1-003 in bladder cancer (BC) development. METHODS: We evaluated the expression levels of DBCCR1-003 in tissues and cells with western blot and quantitative real-time polymerase chain reaction...
2016: Cancer Cell International
https://www.readbyqxmd.com/read/27753829/sy-03-2-pathophysiologic-significance-of-non-coding-rna-in-hypertension
#6
Stephen Harrap
Genetic discovery in blood pressure is generally referenced in relation to protein-coding genes, despite the fact that genes less than 2% of the genome. Recent exploration of the DNA sequences between genes, once called "junk" DNA, has revealed a wealth of transcripts for RNA species that do not encode protein. These non-coding RNAs (ncRNAs) have emerged as dynamic managers of the business of the genome, able to coordinate the expression of genes in time and space to achieve the complexities of normal development and growth...
September 2016: Journal of Hypertension
https://www.readbyqxmd.com/read/27729869/hypoxia-promotes-gastric-cancer-malignancy-partly-through-the-hif-1%C3%AE-dependent-transcriptional-activation-of-the-long-non-coding-rna-gaplinc
#7
Lei Liu, Xihe Zhao, Huawei Zou, Rubing Bai, Keyu Yang, Zhong Tian
Hypoxia-inducible factor (HIF) activates the transcription of genes involved in cancer progression. Recently, HIF was reported to regulate the transcription of non-coding RNAs. Here, we show that the transcription of a long non-coding RNA (lncRNA), Gastric Adenocarcinoma Associated, Positive CD44 Regulator, Long Intergenic Non-Coding RNA (GAPLINC), is directly activated by HIF-1α in gastric cancer (GC). GAPLINC was overexpressed in GC tissues and promoted tumor migration and invasive behavior. GAPLINC overexpression was associated with poor prognosis in GC patients...
2016: Frontiers in Physiology
https://www.readbyqxmd.com/read/27690106/impact-of-the-autism-associated-long-noncoding-rna-msnp1as-on-neuronal-architecture-and-gene-expression-in-human-neural-progenitor-cells
#8
Jessica J DeWitt, Nicole Grepo, Brent Wilkinson, Oleg V Evgrafov, James A Knowles, Daniel B Campbell
We previously identified the long noncoding RNA (lncRNA) MSNP1AS (moesin pseudogene 1, antisense) as a functional element revealed by genome wide significant association with autism spectrum disorder (ASD). MSNP1AS expression was increased in the postmortem cerebral cortex of individuals with ASD and particularly in individuals with the ASD-associated genetic markers on chromosome 5p14.1. Here, we mimicked the overexpression of MSNP1AS observed in postmortem ASD cerebral cortex in human neural progenitor cell lines to determine the impact on neurite complexity and gene expression...
September 28, 2016: Genes
https://www.readbyqxmd.com/read/27669232/long-noncoding-rna-lnccamta1-promotes-proliferation-and-cancer-stem-cell-like-properties-of-liver-cancer-by-inhibiting-camta1
#9
Li-Juan Ding, Yan Li, Shu-Dong Wang, Xin-Sen Wang, Fang Fang, Wei-Yao Wang, Peng Lv, Dong-Hai Zhao, Feng Wei, Ling Qi
Hepatocellular carcinoma (HCC) is the most common subtype of liver malignancy, and it is characterized by poor prognosis because of cancer stem cell (CSC)-mediated high postsurgical recurrence rates. Thus, targeting CSCs, or HCC cells with CSC-like properties, is an effective strategy for HCC therapy. Here, using long noncoding RNA (lncRNA) microarray analysis, we identified a novel lncRNA termed lncCAMTA1 that is increased in both liver CSCs and HCC. High lncCAMTA1 expression in HCC indicates poor clinical outcome...
2016: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/27659977/capture-hybridization-analysis-of-dna-targets
#10
Alec N Sexton, Martin Machyna, Matthew D Simon
There are numerous recent cases where chromatin modifying complexes associate with long noncoding RNA (lncRNA), stoking interest in lncRNA genomic localization and associated proteins. Capture Hybridization Analysis of RNA Targets (CHART) uses complementary oligonucleotides to purify an RNA with its associated genomic DNA or proteins from formaldehyde cross-linked chromatin. Deep sequencing of the purified DNA fragments gives a comprehensive profile of the potential lncRNA biological targets in vivo. The combined identification of the genomic localization of RNA and its protein partners can directly inform hypotheses about RNA function, including recruitment of chromatin modifying complexes...
2016: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27651312/lncrna-hoxa11-as-promotes-proliferation-and-invasion-of-gastric-cancer-by-scaffolding-the-chromatin-modification-factors-prc2-lsd1-and-dnmt1
#11
Ming Sun, Fengqi Nie, Yunfei Wang, Zhihong Zhang, Jiakai Hou, Dandan He, Min Xie, Wei De, Zhaoxia Wang, Jun Wang
Long noncoding RNAs (lncRNA) have been implicated in human cancer but their mechanisms of action are mainly undocumented. In this study, we investigated lncRNA alterations that contribute to gastric cancer (GC) through an analysis of TCGA RNA sequencing data and other publicly available microarray data. Here we report the GC-associated lncRNA HOXA11-AS as a key regulator of GC development and progression. Patients with high HOXA11-AS expression had a shorter survival and poorer prognosis. In vitro and in vivo assays of HOXA11-AS alterations revealed a complex integrated phenotype affecting cell growth, migration, invasion and apoptosis...
September 20, 2016: Cancer Research
https://www.readbyqxmd.com/read/27642882/sy-03-2-pathophysiologic-significance-of-non-coding-rna-in-hypertension
#12
Stephen Harrap
Genetic discovery in blood pressure is generally referenced in relation to protein-coding genes, despite the fact that genes less than 2% of the genome. Recent exploration of the DNA sequences between genes, once called "junk" DNA, has revealed a wealth of transcripts for RNA species that do not encode protein. These non-coding RNAs (ncRNAs) have emerged as dynamic managers of the business of the genome, able to coordinate the expression of genes in time and space to achieve the complexities of normal development and growth...
September 2016: Journal of Hypertension
https://www.readbyqxmd.com/read/27613421/transcription-coupled-changes-to-chromatin-underpin-gene-silencing-by-transcriptional-interference
#13
Ryan Ard, Robin C Allshire
Long non-coding RNA (lncRNA) transcription into a downstream promoter frequently results in transcriptional interference. However, the mechanism of this repression is not fully understood. We recently showed that drug tolerance in fission yeast Schizosaccharomyces pombe is controlled by lncRNA transcription upstream of the tgp1(+) permease gene. Here we demonstrate that transcriptional interference of tgp1(+) involves several transcription-coupled chromatin changes mediated by conserved elongation factors Set2, Clr6CII, Spt6 and FACT...
September 8, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27507049/the-pseudogene-derived-long-noncoding-rna-duxap8-promotes-gastric-cancer-cell-proliferation-and-migration-via-epigenetically-silencing-plekho1-expression
#14
Hong-Wei Ma, Min Xie, Ming Sun, Tian-Yu Chen, Rong-Rong Jin, Tian-Shi Ma, Qin-Nan Chen, Er-Bao Zhang, Xue-Zhi He, Wei De, Zhi-Hong Zhang
Gastric cancer (GC) is the third leading cause of cancer death due to its poor prognosis and limited treatment options. Evidence indicates that pseudogene-derived long noncoding RNAs (lncRNAs) may be important players in human cancer progression, including GC. In this paper, we report that a newly discovered pseudogene-derived lncRNA named DUXAP8, a 2107-bp RNA, was remarkably upregulated in GC. Additionally, a higher level of DUXAP8 expression in GC was significantly associated with greater tumor size, advanced clinical stage, and lymphatic metastasis...
August 5, 2016: Oncotarget
https://www.readbyqxmd.com/read/27434588/long-non-coding-rna-bgas-regulates-the-cystic-fibrosis-transmembrane-conductance-regulator
#15
Sheena M Saayman, Amanda Ackley, Jon Burdach, Matthew Clemson, Dieter C Gruenert, Kiyoshi Tachikawa, Pad Chivukula, Marc S Weinberg, Kevin V Morris
Cystic fibrosis (CF) is a life-shortening genetic disease. The root cause of CF is heritable recessive mutations that affect the cystic fibrosis transmembrance conductance regulator (CFTR) gene and the subsequent expression and activity of encoded ion channels at the cell surface. We show that CFTR is regulated transcriptionally by the actions of a novel long noncoding RNA (lncRNA), designated as BGas, that emanates from intron 11 of the CFTR gene and is expressed in the antisense orientation relative to the protein coding sense strand...
August 2016: Molecular Therapy: the Journal of the American Society of Gene Therapy
https://www.readbyqxmd.com/read/27417130/challenges-in-the-analysis-of-long-noncoding-rna-functionality
#16
REVIEW
Sergio Leone, Raffaella Santoro
Long noncoding RNA (lncRNA) are emerging as important regulators of diverse biological functions. Although mechanistic models are starting to emerge, it is also clear that the lncRNA field needs appropriate model systems in order to better elucidate the functions of lncRNA and their roles in both physiological and pathological conditions. The field of lncRNA is new, and the biochemical and genetic methods used to address function and mechanisms of lncRNA have only recently been developed or adapted from techniques used to investigate protein-coding genes...
August 2016: FEBS Letters
https://www.readbyqxmd.com/read/27329359/high-tug1-expression-is-associated-with-chemotherapy-resistance-and-poor-prognosis-in-esophageal-squamous-cell-carcinoma
#17
Lin Jiang, Wenchao Wang, Guoli Li, Canlin Sun, Zhenqin Ren, Haihui Sheng, Hengjun Gao, Chaofu Wang, Hong Yu
PURPOSE: Long noncoding RNAs (lncRNAs) play critical roles in diverse biological processes such as tumorigenesis and metastasis. Taurine upregulated gene 1 (TUG1) is a cancer-related lncRNA that is associated with chromatin-modifying complexes and plays an important role in gene regulation. In this study, we determined the expression patterns of TUG1 in esophageal squamous cell carcinoma (ESCC) and evaluated its clinical significance. METHODS: The expression level of TUG1 was examined in 218 pairs of ESCC and adjacent non-cancerous tissues by using quantitative real-time polymerase chain reaction...
August 2016: Cancer Chemotherapy and Pharmacology
https://www.readbyqxmd.com/read/27308347/long-noncoding-rnas-in-prostate-cancer-mechanisms-and-applications
#18
REVIEW
Chunlai Li, Liuqing Yang, Chunru Lin
A large proportion of the control of gene expression in humans is mediated by noncoding elements in the genome. Long noncoding RNAs (lncRNAs) have emerged as a new class of pivotal regulatory components, orchestrating extensive cellular processes and connections. LncRNAs play various roles from chromatin modification to alternative splicing and post-transcriptional processing and are involved in almost all aspects of eukaryotic regulation. LncRNA-based mechanisms modulate cell fates during development, and their dysregulation underscores many human disorders, especially cancer, through chromosomal translocation, deletion, and nucleotide expansions...
July 2014: Molecular & Cellular Oncology
https://www.readbyqxmd.com/read/27267320/lncrna-up-regulated-in-nonmuscle-invasive-bladder-cancer-facilitates-tumor-growth-and-acts-as-a-negative-prognostic-factor-of-recurrence
#19
Simin Zhang, Guangzheng Zhong, Wang He, Hao Yu, Jian Huang, Tianxin Lin
PURPOSE: While lncRNAs (long noncoding RNAs) have been shown to have critical regulatory roles in cancer biology, the biological functions and prognostic values in nonmuscle invasive bladder cancer remain largely unknown. We identified a lncRNA termed lncRNA-UNMIBC (up-regulated in nonmuscle invasive bladder cancer) and evaluated its prognostic value in patients with primary nonmuscle invasive bladder cancer. MATERIALS AND METHODS: We analyzed the expression of lncRNA-UNMIBC in the tissues of 75 cases of primary nonmuscle invasive bladder cancer and adjacent normal mucosa by quantitative real-time polymerase chain reaction...
October 2016: Journal of Urology
https://www.readbyqxmd.com/read/27215978/a-genomic-screen-for-long-noncoding-rna-genes-epigenetically-silenced-by-aberrant-dna-methylation-in-colorectal-cancer
#20
Kohei Kumegawa, Reo Maruyama, Eiichiro Yamamoto, Masami Ashida, Hiroshi Kitajima, Akihiro Tsuyada, Takeshi Niinuma, Masahiro Kai, Hiro-O Yamano, Tamotsu Sugai, Takashi Tokino, Yasuhisa Shinomura, Kohzoh Imai, Hiromu Suzuki
Long noncoding RNAs (lncRNAs) have emerged as key components in multiple cellular processes, although their physiological and pathological functions are not fully understood. To identify cancer-related lncRNAs, we screened for those that are epigenetically silenced in colorectal cancer (CRC). Through a genome-wide analysis of histone modifications in CRC cells, we found that the transcription start sites (TSSs) of 1,027 lncRNA genes acquired trimethylation of histone H3 lysine 4 (H3K4me3) after DNA demethylation...
2016: Scientific Reports
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