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Chromatin-associated LncRNA

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https://www.readbyqxmd.com/read/29339785/the-lncrna-gata6-as-epigenetically-regulates-endothelial-gene-expression-via-interaction-with-loxl2
#1
Philipp Neumann, Nicolas Jaé, Andrea Knau, Simone F Glaser, Youssef Fouani, Oliver Rossbach, Marcus Krüger, David John, Albrecht Bindereif, Phillip Grote, Reinier A Boon, Stefanie Dimmeler
Impaired or excessive growth of endothelial cells contributes to several diseases. However, the functional involvement of regulatory long non-coding RNAs in these processes is not well defined. Here, we show that the long non-coding antisense transcript of GATA6 (GATA6-AS) interacts with the epigenetic regulator LOXL2 to regulate endothelial gene expression via changes in histone methylation. Using RNA deep sequencing, we find that GATA6-AS is upregulated in endothelial cells during hypoxia. Silencing of GATA6-AS diminishes TGF-β2-induced endothelial-mesenchymal transition in vitro and promotes formation of blood vessels in mice...
January 16, 2018: Nature Communications
https://www.readbyqxmd.com/read/29328452/hif%C3%A2-1%C3%AE-%C3%A2-induced-upregulation-of-lncrna-uca1-promotes-cell-growth-in-osteosarcoma-by-inactivating-the-pten-akt-signaling-pathway
#2
Tengfei Li, Yang Xiao, Tunsheng Huang
Increasing evidence indicates that long non‑coding RNAs (lncRNAs) play an important role in multiple biological processes including cell growth, differentiation, proliferation and invasion. Urothelial carcinoma associated 1 (UCA1) is a highly conserved nuclear ncRNA and a key regulator of cell proliferation and apoptosis in several types of cancers. However, its role in osteosarcoma progression is not well known. In the present study, we aimed to determine the biological role of UCA1 in osteosarcoma progression...
January 3, 2018: Oncology Reports
https://www.readbyqxmd.com/read/29325547/paracrine-and-epigenetic-control-of-caf-induced-metastasis-the-role-of-hotair-stimulated-by-tgf-%C3%A3-1-secretion
#3
Yu Ren, Huan-Huan Jia, Yi-Qi Xu, Xuan Zhou, Xiao-Hui Zhao, Yun-Fei Wang, Xin Song, Zhi-Yan Zhu, Ting Sun, Yan Dou, Wei-Ping Tian, Xiu-Lan Zhao, Chun-Sheng Kang, Mei Mei
BACKGROUND: The communication between carcinoma associated fibroblasts (CAFs) and cancer cells facilitate tumor metastasis. In this study, we further underlying the epigenetic mechanisms of CAFs feed the cancer cells and the molecular mediators involved in these processes. METHODS: MCF-7 and MDA-MB-231 cells were treated with CAFs culture conditioned medium, respectively. Cytokine antibody array, enzyme-linked immunosorbent assay, western blotting and immunofluorescence were used to identify the key chemokines...
January 11, 2018: Molecular Cancer
https://www.readbyqxmd.com/read/29277325/sirt1-regulates-inflammation-response-of-macrophages-in-sepsis-mediated-by-long-noncoding-rna
#4
Yanhui Jia, Zhenzhen Li, Weixia Cai, Dan Xiao, Shichao Han, Fu Han, Xiaozhi Bai, Kejia Wang, Yang Liu, Xiaoqiang Li, Hao Guan, Dahai Hu
Molecular mechanisms for macrophage immune responses modulated by SIRT1 during sepsis remain unclear. Here, we show that SIRT1 expression is down-regulated in macrophages from mouse sepsis model or LPS stimulation. SIRT1 expression in macrophages correlates with low levels of a long noncoding RNA (lncRNA)-NONMMUT003701 [named as lncRNA-CCL2]. SIRT1 inhibits lncRNA-CCL2 expression via sustaining a repressive chromatin state in the lncRNA-CCL2 locus. The inflammation cytokines expression is downregulated by knockdown of lncRNA-CCL2...
December 19, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/29275200/long-non-coding-rna-ccal-promotes-hepatocellular-carcinoma-progression-by-regulating-ap-2%C3%AE-and-wnt-%C3%AE-catenin-pathway
#5
Yu Liu, Ye Yang, Tianlong Wang, Li Wang, Xin Wang, Tiemin Li, Yue Shi, Yawei Wang
OBJECTIVE: Long non-coding RNAs are emerging as key molecules in cancer progression. LncRNA-CCAL has shown to be highly expressed and important in regulating CRC and osteosarcoma development. Nevertheless, the expression and mechanism of CCAL in HCC is still not well understood. METHODS: qRT-PCR and ISH were used to evaluate CCAL expression in HCC tissues and cell lines. Histone H3 methylation and acetylation levels across CCAL promoter region were examined by chromatin immunoprecipitation assays...
December 21, 2017: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/29249332/nuclear-long-noncoding-rnas-key-regulators-of-gene-expression
#6
REVIEW
Qinyu Sun, Qinyu Hao, Kannanganattu V Prasanth
A significant portion of the human genome encodes genes that transcribe long nonprotein-coding RNAs (lncRNAs). A large number of lncRNAs localize in the nucleus, either enriched on the chromatin or localized to specific subnuclear compartments. Nuclear lncRNAs participate in several biological processes, including chromatin organization, and transcriptional and post-transcriptional gene expression, and also act as structural scaffolds of nuclear domains. Here, we highlight recent studies demonstrating the role of lncRNAs in regulating gene expression and nuclear organization in mammalian cells...
December 14, 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/29227193/ddx5-p68-associated-lncrna-loc284454-is-differentially-expressed-in-human-cancers-and-modulates-gene-expression
#7
Monalisa Das, Arun Renganathan, Shrinivas Nivrutti Dighe, Utsa Bhaduri, Abhijith Shettar, Geetashree Mukherjee, Paturu Kondaiah, Manchanahalli R Satyanarayana Rao
Long non-coding RNAs (lncRNAs) are emerging as important players in regulation of gene expression in higher eukaryotes. DDX5/p68 RNA helicase protein which is involved in splicing of precursor mRNAs also interacts with lncRNAs like, SRA and mrhl, to modulate gene expression. We performed RIP-seq analysis in HEK293T cells to identify the complete repertoire of DDX5/p68 interacting transcripts including 73 single exonic (SE) lncRNAs. The LOC284454 lncRNA is the second top hit of the list of SE lncRNAs which we have characterized in detail for its molecular features and cellular functions...
December 11, 2017: RNA Biology
https://www.readbyqxmd.com/read/29137412/long-non-coding-rna-snhg15-inhibits-p15-and-klf2-expression-to-promote-pancreatic-cancer-proliferation-through-ezh2-mediated-h3k27me3
#8
Zhonghua Ma, Hesuyuan Huang, Jirong Wang, Yan Zhou, Fuxing Pu, Qinghong Zhao, Peng Peng, Bingqing Hui, Hao Ji, Keming Wang
Long non-coding RNA (lncRNA) is emerging as an critical regulator in multiple cancers, including pancreatic cancer (PC). Recently, lncRNA SNHG15 was found to be up-regulated in gastric cancer and hepatocellular carcinoma, exerting oncogenic effects. Nevertheless, the biological function and regulatory mechanism of SNHG15 remain unclear in pancreatic cancer (PC). In this study, we reported that SNHG15 expression was also upregulated in PC tissues, and its overexpression was remarkably associated with tumor size, tumor node metastasis (TNM) stage and lymph node metastasis in patients with PC...
October 13, 2017: Oncotarget
https://www.readbyqxmd.com/read/29126220/catching-rnas-on-chromatin-using-hybridization-capture-methods
#9
Martin Machyna, Matthew D Simon
The growing appreciation of the importance of long noncoding RNAs (lncRNAs), together with the awareness that some of these RNAs are associated with chromatin, has inspired the development of methods to detect their sites of interaction on a genome-wide scale at high resolution. Hybridization capture methods combine antisense oligonucleotide hybridization with enrichment of RNA from cross-linked chromatin extracts. These techniques have provided insight into lncRNA localization and the interactions of lncRNAs with protein to better understand biological roles of lncRNAs...
November 8, 2017: Briefings in Functional Genomics
https://www.readbyqxmd.com/read/29081216/long-noncoding-rna-heih-promotes-colorectal-cancer-tumorigenesis-via-counteracting-mir-939%C3%A2-mediated-transcriptional-repression-of-bcl-xl
#10
Chunhui Cui, Duanyang Zhai, Lianxu Cai, Qiaobin Duan, Lang Xie, Jinlong Yu
Purpose: Studies have found that long noncoding RNA HEIH (lncRNA-HEIH) is upregulated and facilitates hepatocellular carcinoma tumor growth. However, its clinical significances, roles and action mechanism in colorectal cancer (CRC) remains unidentified. Materials and Methods: lncRNA-HEIH expression in CRC tissues and cell lines was measured by quantitative real-time polymerase chain reaction. Cell Counting Kit-8, ethynyl deoxyuridine incorporation assay, terminal deoxynucleotidyl transferase dUTP nick end labeling staining, and nude mice xenografts assays were performed to investigate the roles of lncRNA-HEIH...
October 30, 2017: Cancer Research and Treatment: Official Journal of Korean Cancer Association
https://www.readbyqxmd.com/read/29027165/chromatin-rna-immunoprecipitation-chrip
#11
Tanmoy Mondal, Santhilal Subhash, Chandrasekhar Kanduri
Researchers have recently had a growing interest in understanding the functional role of long noncoding RNAs (lncRNAs) in chromatin organization. Accumulated evidence suggests lncRNAs could act as interphase molecules between chromatin and chromatin remodelers to define the epigenetic code. However, it is not clear how lncRNAs target chromatin remodelers to specific chromosomal regions in order to establish a functionally distinct epigenetic state of chromatin. We developed and optimized chromatin RNA immunoprecipitation (ChRIP) technology to characterize the lncRNAs associated with active and inactive chromatin compartments...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29022920/the-lncrna-tug1-modulates-proliferation-in-trophoblast-cells-via-epigenetic-suppression-of-rnd3
#12
Yetao Xu, Zhiping Ge, Erbao Zhang, Qing Zuo, Shiyun Huang, Nana Yang, Dan Wu, Yuanyuan Zhang, Yanzi Chen, Haoqin Xu, Huan Huang, Zhiyan Jiang, Lizhou Sun
Due to limited treatment options, pre-eclampsia (PE) is associated with fetal perinatal and maternal morbidity and mortality. During the causes of PE, failure of uterine spiral artery remodeling which might be related to functioning abnormally of trophoblast cells, result in the occurrence and progression of PE. Recently, abnormal expression of long non-coding RNAs (lncRNAs), as imperative regulators involved in human diseases progression (included PE), which has been indicated by increasing evidence. In this research, we found that TUG1, a lncRNA, was markedly reduced in placental samples from patients with PE...
October 12, 2017: Cell Death & Disease
https://www.readbyqxmd.com/read/28979716/epigenetics-of-gastroenteropancreatic-neuroendocrine-tumors-a-clinicopathologic-perspective
#13
REVIEW
Brendan M Finnerty, Katherine D Gray, Maureen D Moore, Rasa Zarnegar, Thomas J Fahey Iii
Gastroenteropancreatic neuroendocrine tumors (GEP-NETs) are a heterogeneous group of rare tumors whose site-specific tumor incidence and clinical behavior vary widely. Genetic alterations associated with familial inherited syndromes have been well defined; however, the genetic profile of sporadic tumors is less clear as their tumorigenesis does not appear to be controlled by classic oncogenes such as P53, RB, or KRAS. Even within GEP-NETs, there are no common oncogenic drivers; for example, DAXX/ATRX mutations are strongly implicated in the tumorigenesis of pancreatic but not small bowel NETs...
September 15, 2017: World Journal of Gastrointestinal Oncology
https://www.readbyqxmd.com/read/28947655/mechanistic-insights-in-x-chromosome-inactivation
#14
REVIEW
Zhipeng Lu, Ava C Carter, Howard Y Chang
X-chromosome inactivation (XCI) is a critical epigenetic mechanism for balancing gene dosage between XY males and XX females in eutherian mammals. A long non-coding RNA (lncRNA), XIST, and its associated proteins orchestrate this multi-step process, resulting in the inheritable silencing of one of the two X-chromosomes in females. The XIST RNA is large and complex, exemplifying the unique challenges associated with the structural and functional analysis of lncRNAs. Recent technological advances in the analysis of macromolecular structure and interactions have enabled us to systematically dissect the XIST ribonucleoprotein complex, which is larger than the ribosome, and its place of action, the inactive X-chromosome...
November 5, 2017: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/28904641/histone-code-and-long-non-coding-rnas-lncrnas-aberrations-in-lung-cancer-implications-in-the-therapy-response
#15
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
#16
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)...
November 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
#17
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
#18
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...
November 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
#19
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
#20
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...
November 2017: Biomedicine & Pharmacotherapy, Biomédecine & Pharmacothérapie
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