The Antisense Transcriptomes of Human Cells

He, Yiping; Vogelstein, Bert; Velculescu, Victor E.; Papadopoulos, Nickolas; Kinzler, Kenneth W.

doi:10.1126/science.1163853

Cited by 481 publications

(432 citation statements)

References 25 publications

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“…Antisense lncRNAs may form sense‐antisense pairs by pairing with a protein‐coding gene on the opposite strand and subsequently regulating epigenetic silencing, transcription, and mRNA stability 25, 26, 27…”

Section: Discussionmentioning

confidence: 99%

ARHGAP42 promotes cell migration and invasion involving PI3K/Akt signaling pathway in nasopharyngeal carcinoma

Lin

Ding

et al. 2018

Cancer Medicine

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Rho GTPase‐activating protein 42 was identified as an inhibitor of RhoA to maintain normal blood pressure homeostasis. However, the effect of ARHGAP42 in promoting cell malignancy in nasopharyngeal carcinoma is demonstrated in this study. Microarray and real‐time quantitative PCR were used for a mRNA profiling of ARHGAP42 in nasopharyngeal primary and metastatic carcinoma tissues. Western blot and immunohistochemical staining were used for detecting the expression of ARHGAP42 protein in nasopharyngeal carcinoma tissues and cell lines. The overexpression and silence experiments of ARHGAP42 were performed in NPC cell lines using siRNA and expressive plasmid for evaluating cancer cell migration and invasion in vitro. Real‐time quantitative PCR, western blot, and transwell test were employed for with the function of ARHGAP42 and its antisense lncRNA uc010rul. We confirmed the elevated expression of ARHGAP42 in metastatic NPC tissues of mRNA and protein for the first time. Immunohistochemical analysis indicated that NPC patients with highly ARHGAP42 expression were significantly associated with shorter metastasis‐free survival. Knockdown of ARHGAP42 resulted in significant inhibition of nasopharyngeal cancer cell migration and invasion in vitro, and the overexpression of ARHGAP42 showed the opposite effects. In addition, the silence of uc010rul resulted in ARHGAP42 expression decrease and significant inhibition of nasopharyngeal cancer cell migration and invasion. High expression of ARHGAP42 is associated with poor metastasis‐free survival of nasopharyngeal carcinoma patients. ARHGAP42 promotes migration and invasion of nasopharyngeal carcinoma cells in vitro; the antisense lncRNA may be involved in this effect.

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Section: Discussionmentioning

confidence: 99%

ARHGAP42 promotes cell migration and invasion involving PI3K/Akt signaling pathway in nasopharyngeal carcinoma

Lin

Ding

et al. 2018

Cancer Medicine

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“…Knowing the strand orientation of the transcripts can lead to interesting findings about transcript structure (Core et al 2008;He et al 2008;Seila et al 2008). The strand specificity of the directional Tn-RNA-seq method comes from specific digestion of the second cDNA strand combined with novel transposome modifications to control the attachment of specific sequences to the template cDNA.…”

Section: Discussionmentioning

confidence: 99%

“…It enables the detection of noncanonical transcription start sites (Liu et al 2011) as well as termination sites , alternative splice isoforms Jiang and Wong 2009), transcript mutations/editing (Rosenberg et al 2011), and allelic biases in transcript abundance (Pickrell et al 2010). Methods that preserve the strand from which the transcript originated also allow for the identification of antisense transcription (He et al 2008;Perkins et al 2009), which can play a role in post-transcriptional regulation. Because of the power of RNA-seq and the prevalence of aberrant gene-expression patterns in many diseases, there is a growing need to construct libraries efficiently from low starting amounts of RNA in a high-throughput and reproducible fashion.…”

mentioning

confidence: 99%

Transposase mediated construction of RNA-seq libraries

Gertz¹,

Varley²,

Davis³

et al. 2011

Genome Res.

102

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RNA-seq has been widely adopted as a gene-expression measurement tool due to the detail, resolution, and sensitivity of transcript characterization that the technique provides. Here we present two transposon-based methods that efficiently construct high-quality RNA-seq libraries. We first describe a method that creates RNA-seq libraries for Illumina sequencing from double-stranded cDNA with only two enzymatic reactions. We generated high-quality RNA-seq libraries from as little as 10 pg of mRNA (~1 ng of total RNA) with this approach. We also present a strand-specific RNA-seq library construction protocol that combines transposon-based library construction with uracil DNA glycosylase and endonuclease VIII to specifically degrade the second strand constructed during cDNA synthesis. The directional RNA-seq libraries maintain the same quality as the nondirectional libraries, while showing a high degree of strand specificity, such that 99.5% of reads map to the expected genomic strand. Each transposon-based library construction method performed well when compared with standard RNA-seq library construction methods with regard to complexity of the libraries, correlation between biological replicates, and the percentage of reads that align to the genome as well as exons. Our results show that high-quality RNA-seq libraries can be constructed efficiently and in an automatable fashion using transposition technology.

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“…Even now, new non-coding transcripts with potential regulatory functions are being discovered through the NextGen technologies. A recent example is the study by He et al (2008), in which the human anti-sense transcriptome was characterised by a tag-based approach on the Illumina GA instrument (Illumina, Inc, San Diego, CA, USA). Evidence for anti-sense transcripts was observed for over 6000 human genes pointing towards potential roles in gene expression, again pointing to the value of deep sequencing approaches for establishing fundamental components of the transcriptional apparatus.…”

Section: The Cancer Transcriptomementioning

confidence: 99%