LncBook: a curated knowledgebase of human long non-coding RNAs

Ma, Lijiao; Cao, Jiabao; Liu, Lin; Du, Qiang; Zhao, Li; Zou, Dong; Bajic, Vladimir B.; Zhang, Zhang

doi:10.1093/nar/gkz073

Cited by 128 publications

(41 citation statements)

References 43 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…mitranscriptome.org) [33] breast cancer databases were used to compare the expression of LINC00673 in normal and breast cancer tissues by using R software. The LncBook (https://bigd.big.ac.cn/lncbook) [34] and TargetScan (http://www.targetscan.org/) [35] databases were used to examine putative miRNA interactions between LINC00673 and MARK4. The YY1 binding motif in the promoter region of LINC00673 was identified by JASPAR (http://jaspar.genereg.net/) [36] and TRAN SFAC (http://gene-regulation.com/).…”

Section: Bioinformatics Analysismentioning

confidence: 99%

LINC00673 is activated by YY1 and promotes the proliferation of breast cancer cells via the miR-515-5p/MARK4/Hippo signaling pathway

Qiao

Ning

Wan

et al. 2019

J Exp Clin Cancer Res

135

103

View full text Add to dashboard Cite

Background An increasing number of studies have shown that long noncoding RNAs (lncRNAs) play essential roles in tumor initiation and progression. LncRNAs act as tumor promoters or suppressors by targeting specific genes via epigenetic modifications and competing endogenous RNA (ceRNA) mechanisms. In this study, we explored the function and detailed mechanisms of long intergenic nonprotein coding RNA 673 (LINC00673) in breast cancer progression. Methods Quantitative real-time PCR (qRT-PCR) was used to examine the expression of LINC00673 in breast cancer tissues and in adjacent normal tissues. Gain-of-function and loss-of function experiments were conducted to investigate the biological functions of LINC00673 in vitro and in vivo. We also explored the potential role of LINC00673 as a therapeutic target using antisense oligonucleotide (ASO) in vivo. RNA sequencing (RNA-seq), dual-luciferase reporter assays, chromatin immunoprecipitation (ChIP) assay, and rescue experiments were performed to uncover the detailed mechanism of LINC00673 in promoting breast cancer progression. Results In the present study, LINC00673 displayed a trend of remarkably increased expression in breast cancer tissues and was associated with poor prognosis in breast cancer patients. Importantly, LINC00673 depletion inhibited breast cancer cell proliferation by inhibiting the cell cycle and increasing apoptosis. Furthermore, ASO therapy targeting LINC00673 substantially suppressed breast cancer cell proliferation in vivo. Mechanistically, LINC00673 was found to act as a ceRNA by sponging miR-515-5p to regulate MARK4 expression, thus inhibiting the Hippo signaling pathway. Finally, ChIP assay showed that the transcription factor Yin Yang 1 (YY1) could bind to the LINC00673 promoter and increase its transcription in cis. Conclusions YY1-activated LINC00673 may exert an oncogenic function by acting as a sponge for miR-515-5p to upregulate the MARK4 and then inhibit Hippo signaling pathway, and may serve as a potential therapeutic target.

show abstract

Section: Bioinformatics Analysismentioning

confidence: 99%

LINC00673 is activated by YY1 and promotes the proliferation of breast cancer cells via the miR-515-5p/MARK4/Hippo signaling pathway

Qiao

Ning

Wan

et al. 2019

J Exp Clin Cancer Res

135

103

View full text Add to dashboard Cite

show abstract

“…The laborious process of functionally characterizing lncRNAs has remained a major limitation to lncRNA functional discovery. For example, while~16,000 long noncoding RNAs (lncRNAs) have been identified in the human genome, only 3% of all validated lncRNAs have an ascribed function [47,91,151]. For more than two decades since its discovery, RNA interference (RNAi) has been the method of choice for loss of function studies.…”

Section: Rna Interference (Rnai)mentioning

confidence: 99%

The how and why of lncRNA function: An innate immune perspective

Robinson

Covarrubias

2020

Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanism

226

192

View full text Add to dashboard Cite

“…Sequence matched exactly more than one place with equally quality were discarded to avoid bias (78). The reads that were not mapped to the genome were utilized to map against the transcriptome (junctions mapping LncBook (85). The viral proteins that bind to proteins with lncRNA interactors were also identified.…”

Section: Identification Of Differentially Expressed Lncrnasmentioning

confidence: 99%

Perversely expressed long noncoding RNAs can alter host response and viral proliferation in SARS-CoV-2 infection

Turjya

Khan

Islam

2020

Preprint

View full text Add to dashboard Cite

AbstractBackgroundSince December 2019, the world is experiencing an unprecedented crisis due to a novel coronavirus, SARS-CoV-2. Owing to poor understanding of pathogenicity, the virus is eluding treatment and complicating recovery. Regulatory roles of long non-coding RNAs (lncRNAs) during viral infection and associated antagonism of host antiviral immune responses has become more evident in last decade. To elucidate possible functions of lncRNAs in the COVID-19 pathobiology, we have utilized RNA-seq dataset of SARS-CoV-2 infected lung epithelial cells.ResultsOur analyses uncover 21 differentially expressed lncRNAs whose functions are broadly involved in cell survival and regulation of gene expression. By network enrichment analysis we find that these lncRNAs can directly interact with differentially expressed protein-coding genes ADAR, EDN1, KYNU, MALL, TLR2 and YWHAG; and also AKAP8L, EXOSC5, GDF15, HECTD1, LARP4B, LARP7, MIPOL1, UPF1, MOV10 and PRKAR2A, host genes that interact with SARS-CoV-2 proteins. These genes are involved in cellular signaling, metabolism, immune response and RNA homeostasis. Since lncRNAs have been known to sponge microRNAs and protect expression of upregulated genes, we also identified 9 microRNAs that are induced in viral infections; however, some lncRNAs are able to block their usual suppressive effect on overexpressed genes and consequently contribute to host defense and cell survival.ConclusionsOur investigation determines that deregulated lncRNAs in SARS-CoV-2 infection are involved in viral proliferation, cellular survival, and immune response, ultimately determining disease outcome and this information could drive the search for novel RNA therapeutics as a treatment option.

show abstract

LncBook: a curated knowledgebase of human long non-coding RNAs

Cited by 128 publications

References 43 publications

LINC00673 is activated by YY1 and promotes the proliferation of breast cancer cells via the miR-515-5p/MARK4/Hippo signaling pathway

LINC00673 is activated by YY1 and promotes the proliferation of breast cancer cells via the miR-515-5p/MARK4/Hippo signaling pathway

The how and why of lncRNA function: An innate immune perspective

Perversely expressed long noncoding RNAs can alter host response and viral proliferation in SARS-CoV-2 infection

Contact Info

Product

Resources

About