Microarray profiling of microRNAs reveals frequent coexpression with neighboring miRNAs and host genes

Baskerville, Scott; Bartel, David P.

doi:10.1261/rna.7240905

Cited by 1,304 publications

(1,168 citation statements)

References 38 publications

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“…TRPM3 encodes a cation channel, but its biological function is not known (Grimm et al, 2003;Oberwinkler et al, 2005). A subset of miRNAs is located within the introns of protein coding genes (Rodriguez et al, 2004), and analysis of microarray data has shown that the expression of several intronic miRNAs is correlated with the expression of the mRNA from the same locus (Baskerville and Bartel, 2005). However, in Drosophila, at least some intronic miRNAs may not be coregulated with the corresponding mRNA (Aboobaker et al, 2005).…”

Section: Discussionmentioning

confidence: 99%

Detection of mammalian microRNA expression by in situ hybridization with RNA oligonucleotides

Deo

Chung

et al. 2006

Developmental Dynamics

266

216

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We have developed an in situ hybridization procedure for the detection of microRNAs (miRNAs) in tissue sections from mouse embryos and adult organs. The method uses highly specific washing conditions for RNA oligonucleotide probes conjugated to a fluorescein hapten. We show that this method detects predominantly mature miRNAs rather than the miRNA precursors or primary transcripts. We have determined expression patterns for several miRNAs expressed in the developing and adult nervous system, including miR-124a, miR-9, miR-92, and miR-204. Whereas miR-124a is expressed in neurons, miR-9 is expressed in neural progenitors and some neurons, and miR-204 is expressed in the choroid plexus, retinal pigment epithelium, and ciliary body. miR-204 is located in an intron of the TRPM3 gene, and the TRPM3 mRNA is coexpressed with miR-204 in the choroid plexus. We also find that primary transcripts for miR-124a and miR-9 genes are expressed in patterns similar to their respective mature miRNAs. The ability to visualize expression of specific miRNAs in embryos and tissues should aid studies on miRNA function.

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Section: Discussionmentioning

confidence: 99%

Detection of mammalian microRNA expression by in situ hybridization with RNA oligonucleotides

Deo

Chung

et al. 2006

Developmental Dynamics

266

216

View full text Add to dashboard Cite

show abstract

“…There are a few hundred experimentally sequenced and predicted human miRNAs [10][11][12][13], and together, they hold the potential to regulate thousands of genes impacting a large variety of biological processes. Expression of many miRNAs is regulated in a tissue-specific and temporal manner, the full biological relevance of which remains to be unraveled [13][14][15][16].…”

Section: Introductionmentioning

confidence: 99%

“…It is also not known whether they are in fact produced from the spliced intron or from an alternate internal promoter. In an early study, a number of intronic miRNAs were found to be co-expressed with their host transcripts [14], suggesting that an alternate transcription unit was unlikely. Regarding their processing, recent experimental studies of selected intronic miRNAs have suggested a potentially novel mechanism in which they are generated by a Drosha-mediated cleavage step between splicing commitment and excision, thereby ensuring both miRNA biogenesis and protein synthesis from a single primary transcript [23].…”

Section: Introductionmentioning

confidence: 99%

Ectopic expression of miR-126*, an intronic product of the vascular endothelial EGF-like 7 gene, regulates prostein translation and invasiveness of prostate cancer LNCaP cells

2008

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MicroRNAs (miRNAs) are endogenous noncoding RNAs that down-regulate gene expression by promoting cleavage or translational arrest of target mRNAs. While most miRNAs are transcribed from their own dedicated genes, some map to introns of 'host' transcripts, the biological significance of which remains unknown. Here, we show that prostate cells are naturally devoid of EGF-like domain 7 (Egfl7) transcripts and hence also deficient in a miRNA, miR-126*, generated from splicing and processing of its ninth intron. Use of recombinant and synthetic miRNAs or a specific antagomir established a role of miR-126* in silencing prostein in non-endothelial cells. We mapped two miR-126*-binding sites in the 3′UTR of the prostein mRNA required for translational repression. Transfection of synthetic miR-126* into prostate cancer LNCaP cells strongly reduced the translation of prostein. Interestingly, loss of prostein correlated with reduction of LNCaP cell migration and invasion. Thus, the robust expression of prostein protein in the prostate cells results from a combination of transcriptional activation of the prostein gene and absence of intronic miRNA-126* due to the prostate-specific repression of the Egfl7 gene. We conclude that intronic miRNAs from tissue-specific transcripts, or their natural absence, make cardinal contributions to cellular gene expression and phenotype. These findings also open the door to tissue-specific miRNA therapy.

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“…Relapse occurs easily, which leads to a poor prognosis (2). Previous studies have demonstrated that the differentially-expressed genes and miRNAs of adenocarcinoma may affect the development, transfer and treatment of cancer (3)(4)(5)(6)(7). In addition, there is a complex regulatory network between the TFs, miRNAs, and target and host genes in adenocarcinoma (3).…”

Section: Introductionmentioning

confidence: 99%

Construction and analysis of three networks of genes and microRNAs in adenocarcinoma

et al. 2015

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Abstract. Adenocarcinoma is one of the most serious diseases that threaten human health. Numerous studies have investigated adenocarcinoma and have obtained a considerable amount of data regarding genes and microRNA (miRNA) in adenocarcinoma. However, studies have only focused on one or a small number of genes and miRNAs, and the data is stored in a scattered form, making it challenging to summarize and assess the associations between the genes and miRNAs. In the present study, three networks of genes and miRNAs in adenocarcinoma were focused on. This enabled the construction of networks of elements involved in adenocarcinoma and the analysis of these networks, rather than only discussing one gene. Transcription factors (TFs), miRNAs, and target and host genes of miRNAs in adenocarcinoma, and the regulatory associations between these elements were identified in the present study. These elements and associations were then used to construct three networks, which consisted of the differentially-expressed, associated and global networks. The similarities and differences between the three networks were compared and analyzed. In total, 3 notable TFs, consisting of TP53, phosphatase and tensin homolog and SMAD4, were identified in adenocarcinoma. These TFs were able to regulate the differentially-expressed genes and the majority of the differentially-expressed miRNAs. Certain important regulatory associations were also found in adenocarcinoma, in addition to self-regulating associations between TFs and miRNAs. The upstream and downstream elements of the differentially-expressed genes and miRNAs were recorded, which revealed the regulatory associations between genes and miRNAs. The present study clearly revealed components of the pathogenesis of adenocarcinoma and the regulatory associations between the elements in adenocarcinoma. The present study may aid the investigation of gene therapy in adenocarcinoma and provides a theoretical basis for studies of gene therapy methods as a treatment for adenocarcinoma.

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Microarray profiling of microRNAs reveals frequent coexpression with neighboring miRNAs and host genes

Cited by 1,304 publications

References 38 publications

Detection of mammalian microRNA expression by in situ hybridization with RNA oligonucleotides

Detection of mammalian microRNA expression by in situ hybridization with RNA oligonucleotides

Ectopic expression of miR-126*, an intronic product of the vascular endothelial EGF-like 7 gene, regulates prostein translation and invasiveness of prostate cancer LNCaP cells

Construction and analysis of three networks of genes and microRNAs in adenocarcinoma

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