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Chromatin-associated LncRNA

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https://www.readbyqxmd.com/read/29778422/sp1-induced-upregulation-of-lncrna-pandar-predicts-adverse-phenotypes-in-retinoblastoma-and-regulates-cell-growth-and-apoptosis-in-vitro-and-in-vivo
#1
Lijie Sheng, Jing Wu, Xuewu Gong, Duo Dong, Xiaoxue Sun
Retinoblastoma (RB) is an intraocular malignancy for children and has a high mortality rate. Long non-coding RNAs (lncRNAs) are emerging as gene regulators and biomarkers in various malignancies. PANDAR is a novel cancer-related lncRNA that dysregulated in several types of cancers. However, its clinical value and potential effects on RB remains unclear. RT-qPCR was used to assess the relative expression of PANDAR in RB tissues and cells. Additionally, chromatin immunoprecipitation (ChIP) and luciferase reporter assays were performed to investigate whether SP1 could bind to the promoter region of PANDAR and activate its transcription...
May 17, 2018: Gene
https://www.readbyqxmd.com/read/29774079/long-non-coding-rnas-ac026904-1-and-uca1-a-one-two-punch-for-tgf-%C3%AE-induced-snai2-activation-and-epithelial-mesenchymal-transition-in-breast-cancer
#2
Guo-Yin Li, Wei Wang, Jian-Yong Sun, Bo Xin, Xiang Zhang, Ting Wang, Qian-Feng Zhang, Li-Bo Yao, Hua Han, Dai-Ming Fan, An-Gang Yang, Lin-Tao Jia, Lei Wang
Transforming growth factor-β (TGF-β) has received much attention as a major inducer of epithelial-mesenchymal transition (EMT) during cancer progression, mainly by activating a set of pleiotropic transcription factors including SNAI2/Slug. However, the involvement of long non-coding RNAs (lncRNAs) in TGF-β-induced Slug activation and EMT remains largely unknown. Methods: In this study, we used microarray analysis to compare lncRNA expression profiles between TGF-β treated and untreated breast cancer cells...
2018: Theranostics
https://www.readbyqxmd.com/read/29772549/long-non-coding-rna-and-polycomb-an-intricate-partnership-in-cancer-biology
#3
Cyrinne Achour, Francesca Aguilo
High-throughput analyses have revealed that the vast majority of the transcriptome does not code for proteins. These non-translated transcripts, when larger than 200 nucleotides, are termed long non-coding RNAs (lncRNAs), and play fundamental roles in diverse cellular processes. LncRNAs are subject to dynamic chemical modification, adding another layer of complexity to our understanding of the potential roles that lncRNAs play in health and disease. Many lncRNAs regulate transcriptional programs by influencing the epigenetic state through direct interactions with chromatin-modifying proteins...
June 1, 2018: Frontiers in Bioscience (Landmark Edition)
https://www.readbyqxmd.com/read/29765519/long-noncoding-rnas-are-associated-with-metabolic-and-cellular-processes-in-the-jejunum-mucosa-of-pre-weaning-calves-in-response-to-different-diets
#4
Rosemarie Weikard, Frieder Hadlich, Harald M Hammon, Doerte Frieten, Caroline Gerbert, Christian Koch, Georg Dusel, Christa Kuehn
Long noncoding RNAs (lncRNAs) emerged as important regulatory component of mechanisms involved in gene expression, chromatin modification and epigenetic processes, but they are rarely annotated in the bovine genome. Our study monitored the jejunum transcriptome of German Holstein calves fed two different milk diets using transcriptome sequencing (RNA-seq). To identify potential lncRNAs within the pool of unknown transcripts, four bioinformatic lncRNA prediction tools were applied. The intersection of the alignment-free lncRNA prediction tools (CNCI, PLEK and FEELnc) predicted 1,812 lncRNA transcripts concordantly comprising a catalogue of 1,042 putative lncRNA loci expressed in the calves' intestinal mucosa...
April 20, 2018: Oncotarget
https://www.readbyqxmd.com/read/29743621/colon-cancer-upregulated-long-non-coding-rna-lincdusp-regulates-cell-cycle-genes-and-potentiates-resistance-to-apoptosis
#5
Megan E Forrest, Alina Saiakhova, Lydia Beard, David A Buchner, Peter C Scacheri, Thomas LaFramboise, Sanford Markowitz, Ahmad M Khalil
Long non-coding RNAs (lncRNAs) are frequently dysregulated in many human cancers. We sought to identify candidate oncogenic lncRNAs in human colon tumors by utilizing RNA sequencing data from 22 colon tumors and 22 adjacent normal colon samples from The Cancer Genome Atlas (TCGA). The analysis led to the identification of ~200 differentially expressed lncRNAs. Validation in an independent cohort of normal colon and patient-derived colon cancer cell lines identified a novel lncRNA, lincDUSP, as a potential candidate oncogene...
May 9, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29734178/long-non-coding-rna-sh3pxd2a-as1-promotes-cell-progression-partly-through-epigenetic-silencing-p57-and-klf2-in-colorectal-cancer
#6
Zhonghua Ma, Peng Peng, Jing Zhou, Bingqing Hui, Hao Ji, Juan Wang, Keming Wang
BACKGROUND/AIMS: Colorectal cancer (CRC) is one of the most commonly diagnosed malignancies worldwide. Current evidence has revealed the key roles of long non-coding RNAs (IncRNAs) in multiple cancers, including CRC. In this study we identified the lncRNA SH3PXD2A-AS1 as a novel molecule associated with CRC progression by analyzing the publicly available data from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) datasets. METHODS: Quantitative real-time polymerase chain reaction (qRT-PCR) assays were performed to examine the expression levels of SH3PXD2A-AS1 in CRC tissue samples and CRC cell lines...
May 3, 2018: Cellular Physiology and Biochemistry
https://www.readbyqxmd.com/read/29708552/rna-pull-down-procedure-to-identify-rna-targets-of-a-long-non-coding-rna
#7
Manon Torres, Denis Becquet, Séverine Guillen, Bénédicte Boyer, Mathias Moreno, Marie-Pierre Blanchard, Jean-Louis Franc, Anne-Marie François-Bellan
Long non-coding RNA (lncRNA), which are sequences of more than 200 nucleotides without a defined reading frame, belong to the regulatory non-coding RNA's family. Although their biological functions remain largely unknown, the number of these lncRNAs has steadily increased and it is now estimated that humans may have more than 10,000 such transcripts. Some of these are known to be involved in important regulatory pathways of gene expression which take place at the transcriptional level, but also at different steps of RNA co- and post-transcriptional maturation...
April 10, 2018: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/29706346/an-osteoporosis-risk-snp-at-1p36-12-acts-as-an-allele-specific-enhancer-to-modulate-linc00339-expression-via-long-range-loop-formation
#8
Xiao-Feng Chen, Dong-Li Zhu, Man Yang, Wei-Xin Hu, Yuan-Yuan Duan, Bing-Jie Lu, Yu Rong, Shan-Shan Dong, Ruo-Han Hao, Jia-Bin Chen, Yi-Xiao Chen, Shi Yao, Hlaing Nwe Thynn, Yan Guo, Tie-Lin Yang
Genome-wide association studies (GWASs) have reproducibly associated variants within intergenic regions of 1p36.12 locus with osteoporosis, but the functional roles underlying these noncoding variants are unknown. Through an integrative functional genomic and epigenomic analyses, we prioritized rs6426749 as a potential causal SNP for osteoporosis at 1p36.12. Dual-luciferase assay and CRISPR/Cas9 experiments demonstrate that rs6426749 acts as a distal allele-specific enhancer regulating expression of a lncRNA (LINC00339) (∼360 kb) via long-range chromatin loop formation and that this loop is mediated by CTCF occupied near rs6426749 and LINC00339 promoter region...
April 14, 2018: American Journal of Human Genetics
https://www.readbyqxmd.com/read/29669339/upregulation-of-lncdq-is-associated-with-poor-prognosis-and-promotes-tumor-progression-via-epigenetic-regulation-of-the-emt-pathway-in-hcc
#9
Bing Zeng, Zewei Lin, Huilin Ye, Di Cheng, Guangtao Zhang, Jindu Zhou, Zhifeng Huang, Meng Wang, Canfeng Cai, Jun Zeng, Chaoming Tang, Jikui Liu
BACKGROUND/AIMS: Long noncoding RNAs (lncRNAs) are key regulators of cancer initiation and progression. In this study, we investigated the clinical value and functional role of LncRNA DQ786243 (LncDQ) in the pathogenesis of hepatocellular carcinoma (HCC). METHODS: To investigate the expression level of LncDQ in HCC, we performed quantitative real-time PCR using total RNA extracted from HCC tumor tissues and their matched non-neoplastic counterparts, as well as from the serum of HCC patients and healthy volunteers...
April 13, 2018: Cellular Physiology and Biochemistry
https://www.readbyqxmd.com/read/29661885/the-long-non-coding-rna-paupar-promotes-kap1-dependent-chromatin-changes-and-regulates-olfactory-bulb-neurogenesis
#10
Ioanna Pavlaki, Farah Alammari, Bin Sun, Neil Clark, Tamara Sirey, Sheena Lee, Dan J Woodcock, Chris P Ponting, Francis G Szele, Keith W Vance
Many long non-coding RNAs (lncRNAs) are expressed during central nervous system (CNS) development, yet their in vivo roles and mechanisms of action remain poorly understood. Paupar , a CNS-expressed lncRNA, controls neuroblastoma cell growth by binding and modulating the activity of transcriptional regulatory elements in a genome-wide manner. We show here that the Paupar lncRNA directly binds KAP1, an essential epigenetic regulatory protein, and thereby regulates the expression of shared target genes important for proliferation and neuronal differentiation...
April 16, 2018: EMBO Journal
https://www.readbyqxmd.com/read/29644006/the-long-non-coding-rna-hotair-is-transcriptionally-activated-by-hoxa9-and-is-an-independent-prognostic-marker-in-patients-with-malignant-glioma
#11
Ana Xavier-Magalhães, Céline S Gonçalves, Anne Fogli, Tatiana Lourenço, Marta Pojo, Bruno Pereira, Miguel Rocha, Maria Celeste Lopes, Inês Crespo, Olinda Rebelo, Herminio Tão, João Lima, Ricardo Moreira, Afonso A Pinto, Chris Jones, Rui M Reis, Joseph F Costello, Philippe Arnaud, Nuno Sousa, Bruno M Costa
The lncRNA HOTAIR has been implicated in several human cancers. Here, we evaluated the molecular alterations and upstream regulatory mechanisms of HOTAIR in glioma, the most common primary brain tumors, and its clinical relevance. HOTAIR gene expression, methylation, copy-number and prognostic value were investigated in human gliomas integrating data from online datasets and our cohorts. High levels of HOTAIR were associated with higher grades of glioma, particularly IDH wild-type cases. Mechanistically, HOTAIR was overexpressed in a gene dosage-independent manner, while DNA methylation levels of particular CpGs in HOTAIR locus were associated with HOTAIR expression levels in GBM clinical specimens and cell lines...
March 20, 2018: Oncotarget
https://www.readbyqxmd.com/read/29642935/sp1-induced-upregulation-of-lncrna-spry4-it1-exerts-oncogenic-properties-by-scaffolding-ezh2-lsd1-dnmt1-and-sponging-mir-101-3p-in-cholangiocarcinoma
#12
Yi Xu, Yue Yao, Xingming Jiang, Xiangyu Zhong, Zhidong Wang, Chunlong Li, Pengcheng Kang, Kaiming Leng, Daolin Ji, Zhenglong Li, Lining Huang, Wei Qin, Yunfu Cui
BACKGROUND: Accumulating evidence has indicated that long non-coding RNAs (lncRNAs) behave as a novel class of transcription products during multiple cancer processes. However, the mechanisms responsible for their alteration in cholangiocarcinoma (CCA) are not fully understood. METHODS: The expression of SPRY4-IT1 in CCA tissues and cell lines was determined by RT-qPCR, and the association between SPRY4-IT1 transcription and clinicopathologic features was analyzed...
April 11, 2018: Journal of Experimental & Clinical Cancer Research: CR
https://www.readbyqxmd.com/read/29617930/impact-of-car-agonist-ligand-tcpobop-on-mouse-liver-chromatin-accessibility
#13
Nicholas J Lodato, Andy Rampersaud, David J Waxman
Activation of the nuclear receptor and transcription factor CAR (Nr1i3) by its specific agonist ligand TCPOBOP (1,4-bis[2-(3,5-dichloropyridyloxy)]benzene) dysregulates hundreds of genes in mouse liver and is linked to male-biased hepatocarcinogenesis. To elucidate the genomic organization of CAR-induced gene responses, we investigated the distribution of TCPOBOP-responsive RefSeq coding and long non-coding RNA (lncRNA) genes across the megabase-scale topologically associating domains (TADs) that segment the genome, and which provide a structural framework that functionally constrains enhancer-promoter interactions...
April 2, 2018: Toxicological Sciences: An Official Journal of the Society of Toxicology
https://www.readbyqxmd.com/read/29615150/lncrna-bcar4-increases-viability-invasion-and-migration-non-small-cell-lung-cancer-cells-by-targeting-glioma-associated-oncogene-2-gli2
#14
Hongliang Yang, Lei Yan, Kai Sun, Xiaodong Sun, Xudong Zhang, Kerui Cai, Tiejun Song
OBJECTIVE: This study was aimed to explore the effects of lncRNA BCAR4 on the viability and aggressiveness of non-smallcell lung cancer (NSCLC) cells. METHODS: qRTPCR was used to determine the expression of lncRNA BCAR4 and GLI2 downstream genes in NSCLC tissues and cell lines. Chromatin isolation by RNA purification (CHIRP) and western blot were employed to measure the expression of GLI2 downstream proteins. Ki67 expression in nude mice tumors was tested by immunohistochemistry...
April 3, 2018: Oncology Research
https://www.readbyqxmd.com/read/29588351/a-g3bp1-interacting-lncrna-promotes-ferroptosis-and-apoptosis-in-cancer-via-nuclear-sequestration-of-p53
#15
Chao Mao, Xiang Wang, Yating Liu, Min Wang, Bin Yan, Yiqun Jiang, Ying Shi, Yi Shen, Xiaoli Liu, Weiwei Liai, Rui Yang, Desheng Xiao, Yan Cheng, Shuang Liu, Hu Zhou, Ya Cao, Weishi Yu, Kathrin Muegge, Herbert Yu, Yongguang Tao
Long non-coding RNAs (lncRNA) have been associated with various types of cancer, however, the precise role of many lncRNAs in tumorigenesis remains elusive. Here we demonstrate that the cytosolic lncRNA P53RRA is downregulated in cancers and functions as a tumor suppressor by inhibiting cancer progression. Chromatin remodeling proteins LSH and Cfp1 silenced or increased P53RRA expression respectively. P53RRA bound Ras GTPase-activating protein-binding protein 1 (G3BP1) using nucleotides 1 and 871 of P53RRA and the RRM interaction domain of G3BP1 (aa 177-466)...
March 27, 2018: Cancer Research
https://www.readbyqxmd.com/read/29540241/genomic-positional-conservation-identifies-topological-anchor-point-rnas-linked-to-developmental-loci
#16
Paulo P Amaral, Tommaso Leonardi, Namshik Han, Emmanuelle Viré, Dennis K Gascoigne, Raúl Arias-Carrasco, Magdalena Büscher, Luca Pandolfini, Anda Zhang, Stefano Pluchino, Vinicius Maracaja-Coutinho, Helder I Nakaya, Martin Hemberg, Ramin Shiekhattar, Anton J Enright, Tony Kouzarides
BACKGROUND: The mammalian genome is transcribed into large numbers of long noncoding RNAs (lncRNAs), but the definition of functional lncRNA groups has proven difficult, partly due to their low sequence conservation and lack of identified shared properties. Here we consider promoter conservation and positional conservation as indicators of functional commonality. RESULTS: We identify 665 conserved lncRNA promoters in mouse and human that are preserved in genomic position relative to orthologous coding genes...
March 15, 2018: Genome Biology
https://www.readbyqxmd.com/read/29537884/current-status-of-sperm-functional-genomics-and-its-diagnostic-potential-of-fertility-in-bovine-bos-taurus
#17
Sellappan Selvaraju, Sivashanmugam Parthipan, Lakshminarayana Somashekar, B Krishnan Binsila, Atul P Kolte, Arunachalam Arangasamy, Janivara Parameshwaraiah Ravindra, Stephen A Krawetz
With artificial insemination (AI) and other precision dependent assisted reproductive technologies (ART) being followed in large scale in human and animal reproduction, assessing semen quality and fertilizability is under continuous scrutiny. Various tests have been developed to predict semen quality, but so far no single, highly reliable test is available. In this regard, transcriptomic profiling of spermatozoa assumes significance as it carries the information about spermatogenesis, sperm function, and paternal roles in post-fertilization events...
March 14, 2018: Systems Biology in Reproductive Medicine
https://www.readbyqxmd.com/read/29511340/lncrna-casc9-promotes-esophageal-squamous-cell-carcinoma-metastasis-through-upregulating-lamc2-expression-by-interacting-with-the-creb-binding-protein
#18
Yan Liang, Xuedan Chen, Yuanyuan Wu, Juan Li, Shixin Zhang, Kai Wang, Xingying Guan, Kang Yang, Yun Bai
Esophageal squamous cell carcinoma (ESCC) is the main subtype of esophageal cancer. Long noncoding RNAs (lncRNAs) are thought to play a critical role in cancer development. Recently, lncRNA CASC9 was shown to be dysregulated in many cancer types, but the mechanisms whereby this occurs remain largely unknown. In this study, we found that CASC9 was significantly upregulated in ESCC tissues, with further analysis revealing that elevated CASC9 expression was associated with ESCC prognosis and metastasis. Furthermore, we found that CASC9 knockdown significantly repressed ESCC migration and invasion in vitro and metastasis in nude mice in vivo...
March 6, 2018: Cell Death and Differentiation
https://www.readbyqxmd.com/read/29504936/efficient-termination-of-nuclear-lncrna-transcription-promotes-mitochondrial-genome-maintenance
#19
Dorine Jeanne Mariëtte du Mee, Maxim Ivanov, Joseph Paul Parker, Stephen Buratowski, Sebastian Marquardt
Most DNA in the genomes of higher organisms does not code for proteins. RNA Polymerase II (Pol II) transcribes non-coding DNA into long non-coding RNAs (lncRNAs), but biological roles of lncRNA are unclear. We find that mutations in the yeast lncRNA CUT60 result in poor growth. Defective termination of CUT60 transcription causes read-through transcription across the ATP16 gene promoter. Read-through transcription localizes chromatin signatures associated with Pol II elongation to the ATP16 promoter. The act of Pol II elongation across this promoter represses functional ATP16 expression by a Transcriptional Interference (TI) mechanism...
March 5, 2018: ELife
https://www.readbyqxmd.com/read/29467285/angiogenic-patterning-by-steel-an-endothelial-enriched-long-noncoding-rna
#20
H S Jeffrey Man, Aravin N Sukumar, Gabrielle C Lam, Paul J Turgeon, Matthew S Yan, Kyung Ha Ku, Michelle K Dubinsky, J J David Ho, Jenny Jing Wang, Sunit Das, Nora Mitchell, Peter Oettgen, Michael V Sefton, Philip A Marsden
Endothelial cell (EC)-enriched protein coding genes, such as endothelial nitric oxide synthase (eNOS), define quintessential EC-specific physiologic functions. It is not clear whether long noncoding RNAs (lncRNAs) also define cardiovascular cell type-specific phenotypes, especially in the vascular endothelium. Here, we report the existence of a set of EC-enriched lncRNAs and define a role for s pliced- t ranscript e ndothelial- e nriched lncRNA (STEEL) in angiogenic potential, macrovascular/microvascular identity, and shear stress responsiveness...
March 6, 2018: Proceedings of the National Academy of Sciences of the United States of America
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