A long noncoding RNA cluster-based genomic locus maintains proper development and visual function

Wang, Fei; Ren, Da-long; Liao, Xiaolin; Ke, Shengwei; Zhang, Bowen; Hu, Bing; Song, Xiaoyuan; Wang, Xiangting

doi:10.1093/nar/gkz444

Cited by 13 publications

(16 citation statements)

References 83 publications

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“…In functional assays, knockdown of 7SK in cell and xenograft experiments showed a tumor suppressor role of 7SK in TSCC. Numerous reports have linked non-coding RNAs with cancer ( Wapinski and Chang, 2011 ; Wang et al, 2019 ; Huang et al, 2020 ). For example, HOTAIR is found to be associated with tumor metastasis in breast cancer through binding with polycomb repressive complex 2 (PRC2) and the lysine-specific demethylase1 (LSD1) to regulate gene expression ( Burd et al, 2010 ; Tsai et al, 2010 ).…”

Section: Discussionmentioning

confidence: 99%

7SK Acts as an Anti-tumor Factor in Tongue Squamous Cell Carcinoma

et al. 2021

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Increasing evidence has shown the mechanistic insights about non-coding RNA 7SK in controlling the transcription. However, the biological function and mechanism of 7SK in cancer are largely unclear. Here, we show that 7SK is down-regulated in human tongue squamous carcinoma (TSCC) and acts as a TSCC suppressor through multiple cell-based assays including a migration assay and a xenograft mouse model. The expression level of 7SK was negatively correlated with the size of tumors in the 73 in-house collected TSCC patients. Through combined analysis of 7SK knockdown of RNA-Seq and available published 7SK ChIRP-seq data, we identified 27 of 7SK-regulated genes that were involved in tumor regulation and whose upstream regulatory regions were bound by 7SK. Motif analysis showed that the regulatory sequences of these genes were enriched for transcription factors FOXJ3 and THRA, suggesting a potential involvement of FOXJ3 and THRA in 7SK-regulated genes. Interestingly, the augmented level of FOXJ3 in TSCC patients and previous reports on THRA in other cancers have suggested that these two factors may promote TSCC progression. In support of this idea, we found that 21 out of 27 aforementioned 7SK-associated genes were regulated by FOXJ3 and THRA, and 12 of them were oppositely regulated by 7SK and FOXJ3/THRA. We also found that FOXJ3 and THRA dramatically promoted migration in SCC15 cells. Collectively, we identified 7SK as an antitumor factor and suggested a potential involvement of FOXJ3 and THRA in 7SK-mediated TSCC progression.

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Section: Discussionmentioning

confidence: 99%

7SK Acts as an Anti-tumor Factor in Tongue Squamous Cell Carcinoma

et al. 2021

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“…Our previous RNA-Seq data showed that GAS5 had differential expression patterns in young and old mice brains, which suggested that it may participate in brain aging ( Wang et al, 2019 ). Further examination using RT-qPCR on four different brain tissues confirmed that GAS5 is expressed significantly higher in the old mouse brain hippocampus region comparing with that of a young mouse.…”

Section: Discussionmentioning

confidence: 99%

“…Our previous RNA-Seq data showed that GAS5 exhibits differential expression patterns in young and old mice brain tissues, which suggested that it may play a role in brain aging ( Wang et al, 2019 ). Thus, we conducted various experiments on mice brain tissues and brain-derived cell lines to explore the role and underlying mechanism of GAS5 in senescence and brain aging.…”

Section: Introductionmentioning

confidence: 99%

Functional Network of the Long Non-coding RNA Growth Arrest-Specific Transcript 5 and Its Interacting Proteins in Senescence

Wang

et al. 2021

Front. Genet.

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Increasing studies show that long non-coding RNAs (lncRNAs) play essential roles in various fundamental biological processes. Long non-coding RNA growth arrest-specific transcript 5 (GAS5) showed differential expressions between young and old mouse brains in our previous RNA-Seq data, suggesting its potential role in senescence and brain aging. Examination using quantitative reverse transcription-polymerase chain reaction revealed that GAS5 had a significantly higher expression level in the old mouse brain hippocampus region than the young one. Cellular fractionation using hippocampus-derived HT22 cell line confirmed its nucleoplasm and cytoplasm subcellular localization. Overexpression or knockdown of GAS5 in HT22 cell line revealed that GAS5 inhibits cell cycle progression and promotes cell apoptosis. RNA-Seq analysis of GAS5-knockdown HT22 cells identified differentially expressed genes related to cell proliferation (e.g., DNA replication and nucleosome assembly biological processes). RNA pull-down assay using mouse brain hippocampus tissues showed that potential GAS5 interacting proteins could be enriched into several Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, and some of them are involved in senescence-associated diseases such as Parkinson’s and Alzheimer’s diseases. These results contribute to understand better the underlying functional network of GAS5 and its interacting proteins in senescence at brain tissue and brain-derived cell line levels. Our study may also provide a reference for developing diagnostic and clinic biomarkers of GAS5 in senescence and brain aging.

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“…The lncRNA Pnky is a trans-acting regulator of cortical development in vivo [26]. Wang et al demonstrate that conserved lncRNAs at the nonimprinting regions in brain are essential for zebra sh development [27].…”

Section: Introductionmentioning

confidence: 99%

Identification and characteristics of postnatal development-related long non-coding RNAs under microbiota dependent condition

Zheng¹,

Zhang²,

Zhang³

et al. 2020

Preprint

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BackgroundThe interplay of long-non coding RNAs (lncRNAs) and the intestinal microbiota may serve as an essential role in intestinal development and homeostasis. Microbiota could regulate a large numbers of lncRNAs expression in intestinal epithelial cells. However, the associations between lncRNAs and microbiota during early postnatal development stages are still need to understand. MethodsIn present study, the microbial effects on lncRNA of intestinal epithelial cells (IECs) during postnatal development stage were investigated. ResultsWe identified gut microbiota-specific lncRNAs in diverse postnatal development stages including week 1, week 4 and week 12/16 of mice. A large proportion of gut microbiota-specific lncRNAs only were differential expressed in a single postnatal development stage. Up- and down-regulated gut microbiota-specific lncRNAs both showed consistent expression pattern. We also constructed gut microbiota-specific lncRNAs and coding genes interacted co-expressed networks. Functional analysis indicated that gut microbiota-specific lncRNAs were associated with ABC transporters. ConclusionsIn summary, the present study characterizes the landscape of lncRNAs associated with gut microbiota in different postnatal development stages. It provide assistance for exploring the relationships among lncRNAs, gut microbiota and postnatal development stages.

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A long noncoding RNA cluster-based genomic locus maintains proper development and visual function

Cited by 13 publications

References 83 publications

7SK Acts as an Anti-tumor Factor in Tongue Squamous Cell Carcinoma

7SK Acts as an Anti-tumor Factor in Tongue Squamous Cell Carcinoma

Functional Network of the Long Non-coding RNA Growth Arrest-Specific Transcript 5 and Its Interacting Proteins in Senescence

Identification and characteristics of postnatal development-related long non-coding RNAs under microbiota dependent condition

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