Long non-coding RNAs in cancer

Gong, Zhaojian; Zhang, ShanShan S.; Zhang, WenLing L.; Huang, Hong; Li, Qiao; Deng, Hao; Ma, Jian; Zhou, Ming; Xiang, Juanjuan; Wu, Minghua; Li, XiaYu Y.; Wang, Xiong; Li, XiaoLing L.; Li, Yong; Zeng, Zhaoyang; Li, GuiYuan Y.

doi:10.1007/s11427-012-4413-9

Cited by 72 publications

(61 citation statements)

References 73 publications

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“…LncRNAs compose a large set of RNA molecules that exceed 200 nt in length, completely lack or possess limited protein-coding capacity, and represent a substantial portion of the transcriptome [65][66][67][68][69][70][71][72]. LncRNAs widely regulate gene expression at the epigenetic, transcriptional, and post-transcriptional levels.…”

Section: Discussionmentioning

confidence: 99%

Integrating ChIP-sequencing and digital gene expression profiling to identify BRD7 downstream genes and construct their regulating network

Xiong

Zhou

et al. 2015

Mol Cell Biochem

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BRD7 is a single bromodomain-containing protein that functions as a subunit of the SWI/SNF chromatin-remodeling complex to regulate transcription. It also interacts with the well-known tumor suppressor protein p53 to trans-activate genes involved in cell cycle arrest. In this paper, we report an integrative analysis of genome-wide chromatin occupancy of BRD7 by chromatin immunoprecipitation coupled with high-throughput sequencing (ChIP-seq) and digital gene expression (DGE) profiling by RNA-sequencing upon the overexpression of BRD7 in human cells. We localized 156 BRD7-binding peaks representing 184 genes by ChIP-sequencing, and most of these peaks were co-localized with histone modification sites. Four novel motifs were significantly represented in these BRD7-enriched regions. Ingenuity pathway analysis revealed that 22 of these BRD7 target genes were involved in a network regulating cell death and survival. DGE profiling identified 560 up-regulated genes and 1088 down-regulated genes regulated by BRD7. Using Gene Ontology and pathway analysis, we found significant enrichment of the cell cycle and apoptosis pathway genes. For the integrative analysis of the ChIP-seq and DEG data, we constructed a regulating network of BRD7 downstream genes, and this network suggests multiple feedback regulations of the pathways. Furthermore, we validated BIRC2, BIRC3, TXN2, and NOTCH1 genes as direct, functional BRD7 targets, which were involved in the cell cycle and apoptosis pathways. These results provide a genome-wide view of chromatin occupancy and the gene regulation network of the BRD7 signaling pathway.

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Section: Discussionmentioning

confidence: 99%

Integrating ChIP-sequencing and digital gene expression profiling to identify BRD7 downstream genes and construct their regulating network

Xiong

Zhou

et al. 2015

Mol Cell Biochem

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“…Accumulating evidence confirmed that lncRNAs contribute to cancer initiation and progression [6][7][8][9][10]. The dysregulation of lncRNAs are a primary feature of some human cancers, including prostate cancer, breast cancer, colon cancer, and lung cancer, and so on.…”

Section: Introductionmentioning

confidence: 98%

“…It could be achieved by mining previously published gene expression microarray data because a large group of lncRNA-specific probes were fortuitously represented on the commonly used microarray platforms, for example, the Affymetrix gene expression microarray platform [9].…”

Section: Introductionmentioning

confidence: 99%

AFAP1-AS1, a long noncoding RNA upregulated in lung cancer and promotes invasion and metastasis

et al. 2015

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Long noncoding RNAs (lncRNAs) have emerged as a major regulator of cancer. Significant fraction of lncRNAs is represented on widely used microarray platforms; however, many of which have no known function. To discover novel lung cancer-related lncRNAs, we analyzed the lncRNA expression patterns in five sets of previously published lung cancer gene expression profile data that were represented on Affymetrix HG-U133 Plus 2.0 array, and identified dysregulated lncRNAs in lung cancer. One lncRNA, actin filament associated protein 1 antisense RNA1 (AFAP1-AS1), was the most significantly upregulated in lung cancer and associated with poor prognosis. In vitro experiments demonstrated that AFAP1-AS1 knockdown significantly inhibited the cell invasive and migration capability in lung cancer cells. AFAP1-AS1 knockdown also increased the expression of its antisense protein coding gene, actin filament associated protein 1 (AFAP1), and affected the expression levels of several small GTPase family members and molecules in the actin cytokeratin signaling pathway, which suggested that AFAP1-AS1 promoted cancer cell metastasis via regulation of actin filament integrity. Our findings extend the number of noncoding RNAs functionally implicated in lung cancer progression and highlight the role of AFAP1-AS1 as potential prognostic biomarker and therapeutic target of lung cancer.

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“…In tumor cells, EBV expresses a limited set of latent proteins, such as LMP1 [7], LMP2A [8], EBNA1-6, and a few non-coding RNAs (EBERs) [9]. EBV also expresses 44 mature microRNAs (miRNAs) from 25 miRNA precursors encoded by two primary transcripts (BHRF1 and BART) [2,10].…”

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confidence: 99%

Regulation network and expression profiles of Epstein-Barr virus-encoded microRNAs and their potential target host genes in nasopharyngeal carcinomas

Zeng

Huang

et al. 2014

Sci. China Life Sci.

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Epstein-Barr virus (EBV) is associated with nasopharyngeal carcinoma (NPC) tumorigenesis. However, the mechanism(s) connecting EBV infection and NPC remain unclear. Recently, a new class of EBV microRNAs (miRNAs) has been described. To determine how EBV miRNAs control the expression of host genes, and to understand their potential role in NPC tumorigenesis, we profiled the expression of 44 mature EBV miRNAs and potential host genes in NPC and non-tumor nasopharyngeal epithelial tissues. We found that 40 EBV miRNAs from the BART transcript were highly expressed in NPC. Analysis of potential BART miRNA target genes revealed that 3140 genes and several important pathways might be involved in the carcinogenesis of NPC. A total of 105 genes with potential EBV miRNA binding sites were significantly downregulated, suggesting that EBV miRNAs may regulate these genes and contribute to NPC carcinogenesis. An EBV miRNA and host gene regulation network was generated to provide useful clues for validating of EBV miRNA functions in NPC tumorigenesis.

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Long non-coding RNAs in cancer

Cited by 72 publications

References 73 publications

Integrating ChIP-sequencing and digital gene expression profiling to identify BRD7 downstream genes and construct their regulating network

Integrating ChIP-sequencing and digital gene expression profiling to identify BRD7 downstream genes and construct their regulating network

AFAP1-AS1, a long noncoding RNA upregulated in lung cancer and promotes invasion and metastasis

Regulation network and expression profiles of Epstein-Barr virus-encoded microRNAs and their potential target host genes in nasopharyngeal carcinomas

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