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Chromatin-associated LncRNA

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https://www.readbyqxmd.com/read/28904641/histone-code-and-long-non-coding-rnas-lncrnas-aberrations-in-lung-cancer-implications-in-the-therapy-response
#1
REVIEW
Abril Marcela Herrera-Solorio, Leonel Armas-López, Oscar Arrieta, Joaquín Zúñiga, Patricia Piña-Sánchez, Federico Ávila-Moreno
Respiratory diseases hold several genome, epigenome, and transcriptional aberrations as a cause of the accumulated damage promoted by, among others, environmental risk factors. Such aberrations can also come about as an adaptive response when faced with therapeutic oncological drugs. In epigenetic terms, aberrations in DNA methylation patterns, histone code marks balance, and/or chromatin-remodeling complexes recruitment, among Polycomb Repressive Complex-2 (PRC2) versus Trithorax (TRX) Activator Complex, have been proposed to be affected by several previously characterized functional long non-coding RNAs (lncRNAs)...
2017: Clinical Epigenetics
https://www.readbyqxmd.com/read/28882595/upregulation-of-sox2-activated-lncrna-pvt1-expression-promotes-breast-cancer-cell-growth-and-invasion
#2
Yan Wang, Jun Zhou, Zhaoxin Wang, Peishun Wang, Shuqin Li
Increasing evidences indicated that Long noncoding RNAs (lncRNAs) played pivotal roles during tumorigenesis in multiple types of cancers, including breast cancer. This study aimed to investigate the role and function of long noncoding RNA PVT1 in the progression of breast cancer and explore the transcription factor which contributes to the regulation of PVT1 in breast cancer. Our results indicated that the expression of PVT1 was significantly upregulated in breast cancer tissues, compared with adjacent normal tissues (ANTs)...
September 4, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28881724/the-pseudogene-derived-long-noncoding-rna-duxap8-promotes-gastric-cancer-cell-proliferation-and-migration-via-epigenetically-silencing-plekho1-expression
#3
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 8, 2017: Oncotarget
https://www.readbyqxmd.com/read/28867247/yin-yang-1-suppresses-pancreatic-ductal-adenocarcinoma-cell-proliferation-and-tumor-growth-by-regulating-sox2ot-sox2-axis
#4
Jing-Jing Zhang, Yi Zhu, Xiong-Fei Zhang, Dong-Fang Liu, Yan Wang, Chuang Yang, Guo-Dong Shi, Yun-Peng Peng, Kai Zhang, Lei Tian, Yi Miao, Kui-Rong Jiang
The transcription regulator Yin Yang-1 (YY1) serves as a tumor suppressor in pancreatic ductal adenocarcinoma (PDAC). However, the function of YY1 in proliferation of PDAC cells remains to be clarified. In this study, we found that overexpression of YY1 suppressed proliferation and decreased the expression of long non-coding RNA (lncRNA) SOX2OT and its potential target gene SOX2 in PDAC cells. Luciferase reporter, electrophoretic mobility shift (EMSA), and chromatin immunoprecipitation (ChIP) assays revealed binding of YY1 to the SOX2OT promoter...
September 1, 2017: Cancer Letters
https://www.readbyqxmd.com/read/28865451/genome-wide-computational-analysis-of-potential-long-noncoding-rna-mediated-dna-dna-rna-triplexes-in-the-human-genome
#5
Saakshi Jalali, Amrita Singh, Souvik Maiti, Vinod Scaria
BACKGROUND: Only a handful of long noncoding RNAs have been functionally characterized. They are known to modulate regulation through interacting with other biomolecules in the cell: DNA, RNA and protein. Though there have been detailed investigations on lncRNA-miRNA and lncRNA-protein interactions, the interaction of lncRNAs with DNA have not been studied extensively. In the present study, we explore whether lncRNAs could modulate genomic regulation by interacting with DNA through the formation of highly stable DNA:DNA:RNA triplexes...
September 2, 2017: Journal of Translational Medicine
https://www.readbyqxmd.com/read/28858731/lncrna-fezf1-as1-enhances-epithelial-mesenchymal-transition-emt-through-suppressing-e-cadherin-and-regulating-wnt-pathway-in-non-small-cell-lung-cancer-nsclc
#6
Rong He, Fei Hu Zhang, Ning Shen
OBJECTIVE: Recent discoveries verify that long non-coding RNAs (lncRNAs) are important functional regulators involved in non-small cell lung cancer (NSCLC) progression. However, long non-coding RNA FEZF1-AS1 was not been investigated in NSCLC so for. METHODS: We applied the quantitative real time polymerase chain reaction (qRT-PCR) assays to detect the expression of lncRNA FEZF1-AS1 in NSCLC tissues and adjacent normal tissues. Cell proliferation and invasion capacities were evaluated by MTT, colony formation, and cell invasion assays...
August 28, 2017: Biomedicine & Pharmacotherapy, Biomédecine & Pharmacothérapie
https://www.readbyqxmd.com/read/28840663/chromatin-associated-noncoding-rnas-in-development-and-inheritance
#7
REVIEW
Sreemukta Acharya, Mark Hartmann, Sylvia Erhardt
Noncoding RNAs (ncRNAs) have emerged as crucial players in chromatin regulation. Their diversity allows them to partake in the regulation of numerous cellular processes across species. During development, long and short ncRNAs act in conjunction with each other where long ncRNAs (lncRNAs) are best understood in establishing appropriate gene expression patterns, while short ncRNAs (sRNAs) are known to establish constitutive heterochromatin and suppress mobile elements. Additionally, increasing evidence demonstrates roles of sRNAs in several typically lncRNA-mediated processes such as dosage compensation, indicating a complex regulatory network of noncoding RNAs...
August 25, 2017: Wiley Interdisciplinary Reviews. RNA
https://www.readbyqxmd.com/read/28839111/super-lncrnas-identification-of-lncrnas-that-target-super-enhancers-via-rna-dna-dna-triplex-formation
#8
Benjamin Soibam
Super-enhancers are characterized by high levels of Mediator binding and are major contributors to the expression of their associated genes. They exhibit high levels of local chromatin interactions and higher order of local chromatin organization. On the other hand, LncRNAs can localize to specific DNA sites by forming a RNA:DNA:DNA triplex, which in turn can contribute to local chromatin organization. In this paper, we characterize a new class of lncRNAs called super-lncRNAs that target super-enhancers and which can contribute to the local chromatin organization of the super-enhancers...
August 24, 2017: RNA
https://www.readbyqxmd.com/read/28815539/long-noncoding-rnas-in-plants
#9
Hsiao-Lin V Wang, Julia A Chekanova
The eukaryotic genomes are pervasively transcribed. In addition to protein-coding RNAs, thousands of long noncoding RNAs (lncRNAs) modulate key molecular and biological processes. Most lncRNAs are found in the nucleus and associate with chromatin, but lncRNAs can function in both nuclear and cytoplasmic compartments. Emerging work has found that many lncRNAs regulate gene expression and can affect genome stability and nuclear domain organization both in plant and in the animal kingdom. Here, we describe the major plant lncRNAs and how they act, with a focus on research in Arabidopsis thaliana and our emerging understanding of lncRNA functions in serving as molecular sponges and decoys, functioning in regulation of transcription and silencing, particularly in RNA-directed DNA methylation, and in epigenetic regulation of flowering time...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/28810927/stat3-mediated-upregulation-of-lncrna-hoxd-as1-as-a-cerna-facilitates-liver-cancer-metastasis-by-regulating-sox4
#10
Hui Wang, Xisong Huo, Xin-Rong Yang, Jia He, Lijun Cheng, Na Wang, Xuan Deng, Haojie Jin, Ning Wang, Cun Wang, Fangyu Zhao, Jingyuan Fang, Ming Yao, Jia Fan, Wenxin Qin
BACKGROUND: Several of the thousands of human long noncoding RNAs (lncRNAs) have been functionally characterized, yet their potential involvement in hepatocellular carcinoma (HCC) remains poorly understood. METHODS: LncRNA-HOXD-AS1 was identified by microarray and validated by real-time PCR. The clinicopathological significance of HOXD-AS1 was analyzed by Kaplan-Meier method. Chromatin immunoprecipitation was conducted to examine the mechanism of HOXD-AS1 upregulation...
August 14, 2017: Molecular Cancer
https://www.readbyqxmd.com/read/28800314/long-noncoding-rna-pvt1-promotes-hepatocellular-carcinoma-progression-through-regulating-mir-214
#11
Xun Gou, Xiyan Zhao, Zhengrong Wang
BACKGROUND: Long noncoding RNAs (lncRNA) have been verified to be involved in hepatocellular carcinoma (HCC) progression. However, the potential biologic function of PVT1 in HCC is not still fully known. METHODS: PVT1 and miR-214 were detected by qRT-PCR assays in HCC tissues and adjacent normal tissues. CCK8, cell colony and transwell invasion assays were performed to evaluate cell proliferation and invasion abilities. Western-blot assay was performed to detect the protein of E-cadherin and Vimentin...
July 31, 2017: Cancer Biomarkers: Section A of Disease Markers
https://www.readbyqxmd.com/read/28783101/analysis-of-argonaute-4-associated-long-non-coding-rna-in-arabidopsis-thaliana-sheds-novel-insights-into-gene-regulation-through-rna-directed-dna-methylation
#12
Phil Chi Khang Au, Elizabeth S Dennis, Ming-Bo Wang
RNA-directed DNA methylation (RdDM) is a plant-specific de novo DNA methylation mechanism that requires long noncoding RNA (lncRNA) as scaffold to define target genomic loci. While the role of RdDM in maintaining genome stability is well established, how it regulates protein-coding genes remains poorly understood and few RdDM target genes have been identified. In this study, we obtained sequences of RdDM-associated lncRNAs using nuclear RNA immunoprecipitation against ARGONAUTE 4 (AGO4), a key component of RdDM that binds specifically with the lncRNA...
August 7, 2017: Genes
https://www.readbyqxmd.com/read/28759577/modular-function-of-long-noncoding-rna-coldair-in-the-vernalization-response
#13
Dong-Hwan Kim, Yanpeng Xi, Sibum Sung
The long noncoding RNA COLDAIR is necessary for the repression of a floral repressor FLOWERING LOCUS C (FLC) during vernalization in Arabidopsis thaliana. The repression of FLC is mediated by increased enrichment of Polycomb Repressive Complex 2 (PRC2) and subsequent trimethylation of Histone H3 Lysine 27 (H3K27me3) at FLC chromatin. In this study we found that the association of COLDAIR with chromatin occurs only at the FLC locus and that the central region of the COLDAIR transcript is critical for this interaction...
July 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28699365/activating-the-chromatin-by-noncoding-rnas
#14
Nihay Laham-Karam, Pia Laitinen, Tiia A Turunen, Seppo Ylä-Herttuala
SIGNIFICANCE: The extent and breadth of transcription have recently been uncovered and this has revealed an extensive array of noncoding RNAs (ncRNAs). The biological role and significance of these ncRNAs have been realized and to date it appears that ncRNAs may have many important regulatory functions. ncRNAs are multifaceted and they induce a complexity of different types of transcriptional and posttranscriptional regulation, including gene activation. Recent Advances: Association of ncRNAs with gene activation is an important finding...
August 10, 2017: Antioxidants & Redox Signaling
https://www.readbyqxmd.com/read/28683446/lncrna-snhg6-is-associated-with-poor-prognosis-of-gastric-cancer-and-promotes-cell-proliferation-and-emt-through-epigenetically-silencing-p27-and-sponging-mir-101-3p
#15
Kai Yan, Jie Tian, Wenzheng Shi, Hao Xia, Yuanfang Zhu
Background/Amis: Long non-coding RNAs (lncRNAs), a novel class of transcripts, have been shown to play critical roles in diverse cellular biological processes, including tumorigenesis. Small nucleolar RNA host gene 6 (SNHG6) regulates various biological processes in cancer cells. However, the biological role of SNHG6 in gastric cancer still remains to be explored. The aim of this study is to investigate the characteristic of the SNHG6 in gastric cancer. METHODS: Quantitative real-time polymerase chain reaction (qRT-PCR) was used to measure the expression of SNHG6 in gastric cancer tissues and cell lines...
June 27, 2017: Cellular Physiology and Biochemistry
https://www.readbyqxmd.com/read/28659173/long-noncoding-rna-mrccat1-promotes-metastasis-of-clear-cell-renal-cell-carcinoma-via-inhibiting-npr3-and-activating-p38-mapk-signaling
#16
Jia-Kuan Li, Cheng Chen, Jia-Yi Liu, Jia-Zi Shi, Shu-Peng Liu, Bing Liu, Deng-Shuang Wu, Zi-Yu Fang, Yi Bao, Ming-Ming Jiang, Ji-Hang Yuan, Le Qu, Lin-Hui Wang
BACKGROUND: Recent evidences showed that long noncoding RNAs (lncRNAs) are frequently dysregulated and play important roles in various cancers. Clear cell renal cell carcinoma (ccRCC) is one of the leading cause of cancer-related death, largely due to the metastasis of ccRCC. However, the clinical significances and roles of lncRNAs in metastatic ccRCC are still unknown. METHODS: lncRNA expression microarray analysis was performed to search the dysregulated lncRNA in metastatic ccRCC...
June 28, 2017: Molecular Cancer
https://www.readbyqxmd.com/read/28652379/the-mutant-p53-id4-complex-controls-vegfa-isoforms-by-recruiting-lncrna-malat1
#17
Magdalena Pruszko, Elisa Milano, Mattia Forcato, Sara Donzelli, Federica Ganci, Silvia Di Agostino, Simone De Panfilis, Francesco Fazi, David O Bates, Silvio Bicciato, Maciej Zylicz, Alicja Zylicz, Giovanni Blandino, Giulia Fontemaggi
The abundant, nuclear-retained, metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) has been associated with a poorly differentiated and aggressive phenotype of mammary carcinomas. This long non-coding RNA (lncRNA) localizes to nuclear speckles, where it interacts with a subset of splicing factors and modulates their activity. In this study, we demonstrate that oncogenic splicing factor SRSF1 bridges MALAT1 to mutant p53 and ID4 proteins in breast cancer cells. Mutant p53 and ID4 delocalize MALAT1 from nuclear speckles and favor its association with chromatin...
August 2017: EMBO Reports
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
#18
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
#19
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
#20
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
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