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Chromatin-associated LncRNA

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https://www.readbyqxmd.com/read/28615992/overexpression-of-lncrna-hoxa11-as-promotes-cell-epithelial-mesenchymal-transition-by-repressing-mir-200b-in-non-small-cell-lung-cancer
#1
Jian-Hui Chen, Li-Yang Zhou, Suo Xu, Yu-Long Zheng, Yu-Feng Wan, Cheng-Ping Hu
BACKGROUND: Recent studies have verified that long noncoding RNAs (lncRNAs) involved in many biological functions and play crucial roles in human cancers progression, the study aimed to detect the association between long non-coding RNA HOXA11-AS and epithelial-mesenchymal transition (EMT) process in non-small cell lung cancer (NSCLC). METHODS: The lncRNA HOXA11-AS expression levels were determined by quantitative real-time polymerase chain reaction (qRT-PCR) assays in 78 paired of tumor tissue and adjacent normal tissue samples in NSCLC patients...
2017: Cancer Cell International
https://www.readbyqxmd.com/read/28615056/oct4-transcriptionally-regulates-the-expression-of-long-non-coding-rnas-neat1-and-malat1-to-promote-lung-cancer-progression
#2
Jayu Jen, Yen-An Tang, Ying-Hung Lu, Che-Chung Lin, Wu-Wei Lai, Yi-Ching Wang
BACKGROUND: Oct4, a key stemness transcription factor, is overexpressed in lung cancer. Here, we reveal a novel transcription regulation of long non-coding RNAs (lncRNAs) by Oct4. LncRNAs have emerged as important players in cancer progression. METHODS: Oct4 chromatin-immunoprecipitation (ChIP)-sequencing and several lncRNA databases with literature annotation were integrated to identify Oct4-regulated lncRNAs. Luciferase activity, qRT-PCR and ChIP-PCR assays were conducted to examine transcription regulation of lncRNAs by Oct4...
June 14, 2017: Molecular Cancer
https://www.readbyqxmd.com/read/28558830/lincin-a-novel-nf90-binding-long-non-coding-rna-is-overexpressed-in-advanced-breast-tumors-and-involved-in-metastasis
#3
Zhengyu Jiang, Carolyn M Slater, Yan Zhou, Karthik Devarajan, Karen J Ruth, Yueran Li, Kathy Q Cai, Mary Daly, Xiaowei Chen
BACKGROUND: Recent genome-wide profiling by sequencing and distinctive chromatin signatures has identified thousands of long non-coding RNA (lncRNA) species (>200 nt). LncRNAs have emerged as important regulators of gene expression, involving in both developmental and pathological processes. While altered expression of lncRNAs has been observed in breast cancer development, their roles in breast cancer progression and metastasis are still poorly understood. METHODS: To identify novel breast cancer-associated lncRNA candidates, we employed a high-density SNP array-based approach to uncover intergenic lncRNA genes that are aberrantly expressed in breast cancer...
May 30, 2017: Breast Cancer Research: BCR
https://www.readbyqxmd.com/read/28548932/lncrna-tincr-attenuates-cardiac-hypertrophy-by-epigenetic-silencing-of-camkii
#4
Mingjing Shao, Guangdong Chen, Fengli Lv, Yanyan Liu, Hongjun Tian, Ran Tao, Ronghuan Jiang, Wei Zhang, Chuanjun Zhuo
In the previous study, we established a mouse model of cardiac hypertrophy using transverse aortic constriction (TAC) and found that the expression of long non-coding RNAs TINCR was downregulated in myocardial tissue. The present study was designed to determine the potential role of TINCR in the pathogenesis of cardiac hypertrophy. Our results showed that enforced expression of TINCR could attenuate cardiac hypertrophy in TAC mice. Angiotensin II (Ang-II) was found to be associated with reduced TINCR expression and increased hypertrophy in cultured neonatal cardiomyocytes...
May 10, 2017: Oncotarget
https://www.readbyqxmd.com/read/28500258/transposon-driven-transcription-is-a-conserved-feature-of-vertebrate-spermatogenesis-and-transcript-evolution
#5
Matthew P Davis, Claudia Carrieri, Harpreet K Saini, Stijn van Dongen, Tommaso Leonardi, Giovanni Bussotti, Jack M Monahan, Tania Auchynnikava, Angelo Bitetti, Juri Rappsilber, Robin C Allshire, Alena Shkumatava, Dónal O'Carroll, Anton J Enright
Spermatogenesis is associated with major and unique changes to chromosomes and chromatin. Here, we sought to understand the impact of these changes on spermatogenic transcriptomes. We show that long terminal repeats (LTRs) of specific mouse endogenous retroviruses (ERVs) drive the expression of many long non-coding transcripts (lncRNA). This process occurs post-mitotically predominantly in spermatocytes and round spermatids. We demonstrate that this transposon-driven lncRNA expression is a conserved feature of vertebrate spermatogenesis...
May 12, 2017: EMBO Reports
https://www.readbyqxmd.com/read/28496150/long-non-coding-rna-particle-bridges-histone-and-dna-methylation
#6
Valerie Bríd O'Leary, Sarah Hain, Doris Maugg, Jan Smida, Omid Azimzadeh, Soile Tapio, Saak Victor Ovsepian, Michael John Atkinson
PARTICLE (Gene PARTICL- 'Promoter of MAT2A-Antisense RadiaTion Induced Circulating LncRNA) expression is transiently elevated following low dose irradiation typically encountered in the workplace and from natural sources. This long non-coding RNA recruits epigenetic silencers for cis-acting repression of its neighbouring Methionine adenosyltransferase 2A gene. It now emerges that PARTICLE operates as a trans-acting mediator of DNA and histone lysine methylation. Chromatin immunoprecipitation sequencing (ChIP-seq) and immunological evidence established elevated PARTICLE expression linked to increased histone 3 lysine 27 trimethylation...
May 11, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28468635/prc2-represses-transcribed-genes-on-the-imprinted-inactive-x-chromosome-in-mice
#7
Emily Maclary, Michael Hinten, Clair Harris, Shriya Sethuraman, Srimonta Gayen, Sundeep Kalantry
BACKGROUND: Polycomb repressive complex 2 (PRC2) catalyzes histone H3K27me3, which marks many transcriptionally silent genes throughout the mammalian genome. Although H3K27me3 is associated with silenced gene expression broadly, it remains unclear why some but not other PRC2 target genes require PRC2 and H3K27me3 for silencing. RESULTS: Here we define the transcriptional and chromatin features that predict which PRC2 target genes require PRC2/H3K27me3 for silencing by interrogating imprinted mouse X-chromosome inactivation...
May 3, 2017: Genome Biology
https://www.readbyqxmd.com/read/28441948/over-expressed-long-noncoding-rna-hoxa11-as-promotes-cell-cycle-progression-and-metastasis-in-gastric-cancer
#8
Zhili Liu, Zhenyao Chen, Ruihua Fan, Bin Jiang, Xin Chen, Qinnan Chen, Fengqi Nie, Kaihua Lu, Ming Sun
BACKGROUND: Long noncoding RNAs (lncRNAs) have emerged as critical regulators in a variety of human cancers, including gastric cancer (GC). However, the function and mechanisms responsible for these molecules in GC are not fully understood. In our previous study, we found that GC associated lncRNA HOXA11-AS is significantly upregulated in GC tissues. Over-expressed HOXA11-AS promotes GC cells proliferation and invasion through scaffolding the chromatin modification factors PRC2, LSD1 and DNMT1...
April 26, 2017: Molecular Cancer
https://www.readbyqxmd.com/read/28405676/ulinastatin-protects-against-lipopolysaccharide-induced-cardiac-microvascular-endothelial-cell-dysfunction-via-downregulation-of-lncrna-malat1-and-ezh2-in-sepsis
#9
Zhaoxia Yu, Aisa Rayile, Xiangyang Zhang, Ying Li, Qiang Zhao
The present study aimed to evaluate the effects of ulinastatin on the permeability and apoptosis of lipopolysaccharide (LPS)-induced cardiac microvascular endothelial cells (CMVECs), and investigate its molecular mechanisms in sepsis. The sepsis rat model was induced by cecal ligation and puncture (CLP), and rat CMVECs were isolated and treated with LPS or/and ulinastatin. Then, cell permeability was evaluated by transendothelial electrical resistance, reactive oxygen species (ROS) levels were assessed by 2,7-dichlorofluorescein diacetate, cell apoptosis was detected using Annexin V-FITC apoptosis detection kit, and the expression levels of Bcl-2, Bax, caspase-3, metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) and EZH2 were detected by RT-qPCR and/or western blotting...
May 2017: International Journal of Molecular Medicine
https://www.readbyqxmd.com/read/28247536/melatonin-regulates-parp1-to-control-the-senescence-associated-secretory-phenotype-sasp-in-human-fetal-lung-fibroblast-cells
#10
Songtao Yu, Xiaojiao Wang, Peiliang Geng, Xudong Tang, Lisha Xiang, Xin Lu, Jianjun Li, Zhihua Ruan, Jianfang Chen, Ganfeng Xie, Zhe Wang, Juanjuan Ou, Yuan Peng, Xi Luo, Xuan Zhang, Yan Dong, Hongshan Chen, Houjie Liang
Cellular senescence is an important tumor-suppressive mechanism. However, acquisition of a senescence-associated secretory phenotype (SASP) in senescent cells has deleterious effects on the tissue microenvironment and, paradoxically, promotes tumor progression. In a drug screen, we identified melatonin as a novel SASP suppressor in human cells. Strikingly, melatonin blunts global SASP gene expression upon oncogene-induced senescence (OIS). Moreover, poly(ADP-ribose) polymerase-1 (PARP-1), a sensor of DNA damage, was identified as a new melatonin-dependent regulator of SASP gene induction upon OIS...
March 1, 2017: Journal of Pineal Research
https://www.readbyqxmd.com/read/28209301/iswi-atp-dependent-remodeling-of-nucleoplasmic-%C3%AF-speckles-in-the-brain-of-drosophila-melanogaster
#11
Luca Lo Piccolo, Andrea Attardi, Rosa Bonaccorso, Lorenzo Li Greci, Giorgio Giurato, Antonia Maria Rita Ingrassia, Maria Cristina Onorati
Heterogeneous nuclear ribonucleoproteins (hnRNPs) belong to the RNA-binding proteins family. They are involved in processing heterogeneous nuclear RNAs (hnRNAs) into mature mRNAs. These proteins participate in every step of mRNA cycle, such as mRNA export, localization, translation, stability and alternative splicing. At least 14 major hnRNPs, which have structural and functional homologues in mammals, are expressed in Drosophila melanogaster. Until now, six of these hnRNPs are known to be nucleus-localized and associated with the long non-coding RNA (lncRNA) heat shock responsive ω (hsrω) in the omega speckle compartments (ω-speckles)...
February 20, 2017: Journal of Genetics and Genomics, Yi Chuan Xue Bao
https://www.readbyqxmd.com/read/28193769/long-noncoding-rnas-at-the-intersection-of-cancer-and-chromatin-biology
#12
Adam M Schmitt, Howard Y Chang
Although only 2% of the genome encodes protein, RNA is transcribed from the majority of the genetic sequence, suggesting a massive degree of cellular functionality is programmed in the noncoding genome. The mammalian genome contains tens of thousands of long noncoding RNAs (lncRNAs), many of which occur at disease-associated loci or are specifically expressed in cancer. Although the vast majority of lncRNAs have no known function, recurring molecular mechanisms for lncRNAs are now being observed in chromatin regulation and cancer pathways and emerging technologies are now providing tools to interrogate lncRNA molecular interactions and determine function of these abundant cellular macromolecules...
February 13, 2017: Cold Spring Harbor Perspectives in Medicine
https://www.readbyqxmd.com/read/28132848/vernalization-triggered-intragenic-chromatin-loop-formation-by-long-noncoding-rnas
#13
Dong-Hwan Kim, Sibum Sung
Long noncoding RNAs (lncRNAs) affect gene regulation through structural and regulatory interactions with associated proteins. The Polycomb complex often binds to lncRNAs in eukaryotes, and an lncRNA, COLDAIR, associates with Polycomb to mediate silencing of the floral repressor FLOWERING LOCUS C (FLC) during the process of vernalization in Arabidopsis. Here, we identified an additional Polycomb-binding lncRNA, COLDWRAP. COLDWRAP is derived from the repressed promoter of FLC and is necessary for the establishment of the stable repressed state of FLC by vernalization...
February 6, 2017: Developmental Cell
https://www.readbyqxmd.com/read/28131897/long-noncoding-rnas-and-sulforaphane-a-target-for-chemoprevention-and-suppression-of-prostate-cancer
#14
Laura M Beaver, Rachael Kuintzle, Alex Buchanan, Michelle W Wiley, Sarah T Glasser, Carmen P Wong, Gavin S Johnson, Jeff H Chang, Christiane V Löhr, David E Williams, Roderick H Dashwood, David A Hendrix, Emily Ho
Long noncoding RNAs (lncRNAs) have emerged as important in cancer development and progression. The impact of diet on lncRNA expression is largely unknown. Sulforaphane (SFN), obtained from vegetables like broccoli, can prevent and suppress cancer formation. Here we tested the hypothesis that SFN attenuates the expression of cancer-associated lncRNAs. We analyzed whole-genome RNA-sequencing data of normal human prostate epithelial cells and prostate cancer cells treated with 15 μM SFN or dimethylsulfoxide. SFN significantly altered expression of ~100 lncRNAs in each cell type and normalized the expression of some lncRNAs that were differentially expressed in cancer cells...
April 2017: Journal of Nutritional Biochemistry
https://www.readbyqxmd.com/read/28122578/bap1-dependent-expression-of-long-non-coding-rna-neat-1-contributes-to-sensitivity-to-gemcitabine-in-cholangiocarcinoma
#15
Mansi Parasramka, Irene K Yan, Xue Wang, Phuong Nguyen, Akiko Matsuda, Sayantan Maji, Catherine Foye, Yan Asmann, Tushar Patel
BACKGROUND: Genetic alterations in chromatin modulators such as BRCA-1 associated protein-1 (BAP1) are the most frequent genetic alteration in intrahepatic cholangiocarcinomas (CCA). We evaluated the contribution of BAP1 expression on tumor cell behavior and therapeutic sensitivity to identify rationale therapeutic strategies. METHODS: The impact of BAP1 expression on sensitivity to therapeutic agents was evaluated in CCA cells with a 7-fold difference in BAP1 expression (KMBC-low, HuCCT1-high) and genetically engineered haplo-insufficient BAP1 knockout cells...
January 25, 2017: Molecular Cancer
https://www.readbyqxmd.com/read/28122024/long-non-coding-rna-hotair-regulates-the-proliferation-self-renewal-capacity-tumor-formation-and-migration-of-the-cancer-stem-like-cell-csc-subpopulation-enriched-from-breast-cancer-cells
#16
Jia Deng, Mengchang Yang, Rong Jiang, Ning An, Xiaoshan Wang, Bin Liu
PURPOSE: Long non-coding RNAs (lncRNAs) play important roles in the malignant behavior of cancer. HOTAIR, a well-studied lncRNA, contributes to breast cancer development, and overexpression of HOTAIR predicts a poor prognosis. However, the regulatory role of HOTAIR in the cancer stem-like cell (CSC) subpopulation remains largely unknown. Our goal was to determine the regulatory functions of HOTAIR in the processes of self-renewal capacity, tumor formation and proliferation of CSCs derived from breast cancer...
2017: PloS One
https://www.readbyqxmd.com/read/28041882/lncrna-functional-networks-in-oligodendrocytes-reveal-stage-specific-myelination-control-by-an-lncol1-suz12-complex-in-the-cns
#17
Danyang He, Jincheng Wang, Yulan Lu, Yaqi Deng, Chuntao Zhao, Lingli Xu, Yinhuai Chen, Yueh-Chiang Hu, Wenhao Zhou, Q Richard Lu
Long noncoding RNAs (lncRNAs) are emerging as important regulators of cellular functions, but their roles in oligodendrocyte myelination remain undefined. Through de novo transcriptome reconstruction, we establish dynamic expression profiles of lncRNAs at different stages of oligodendrocyte development and uncover a cohort of stage-specific oligodendrocyte-restricted lncRNAs, including a conserved chromatin-associated lncOL1. Co-expression network analyses further define the association of distinct oligodendrocyte-expressing lncRNA clusters with protein-coding genes and predict lncRNA functions in oligodendrocyte myelination...
January 18, 2017: Neuron
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
#18
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
#19
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-β (TGF-β)-induced EMT of human lung cancer cell lines...
January 6, 2017: 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
#20
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
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