Many novel mammalian microRNA candidates identified by extensive cloning and RAKE analysis

Berezikov, Eugène; Tetering, Geert van; Verheul, Mark; Belt, José van de; Laake, Linda van; Vos, Joost B.; Verloop, Robert E.; Wetering, Marc van de; Guryev, Victor; Takada, Shuji; Zonneveld, Anton Jan van; Mano, Hiroyuki; Plasterk, Ronald H.A.; Cuppen, Edwin

doi:10.1101/gr.5159906

Cited by 244 publications

(196 citation statements)

References 39 publications

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“…Hundreds of candidates from other miRNA discovery efforts (Xie et al 2005;Berezikov et al 2006b) also failed to pass the filters, usually because no reads mapped to them.…”

Section: Experimental Evaluation Of Unconfirmed Mirnasmentioning

confidence: 99%

“…One set of studies predicted miRNAs based on phylogenetic conservation, and then tested these and additional murine-specific hairpins using RAKE and cloning (Berezikov et al , 2006b). Among the 322 candidates supported by these experiments, 11 were in our sets of miRNAs (two in our confirmed set, and nine in our novel set), and another nine did not satisfy our annotation criteria but had at least one read consistent with the predictions.…”

Section: Experimental Evaluation Of Unconfirmed Mirnasmentioning

confidence: 99%

“…Hundreds of mammalian miRNAs have been identified by Sanger sequencing of cloned small RNA-derived cDNAs (Lagos-Quintana et al 2001, 2002, 2003Houbaviy et al 2003;Berezikov et al 2006b;Landgraf et al 2007). Some miRNAs, however, are expressed only in a limited number of cells or through a limited portion of development, and their rarity makes them difficult to detect.…”

mentioning

confidence: 99%

“…Some miRNAs, however, are expressed only in a limited number of cells or through a limited portion of development, and their rarity makes them difficult to detect. Computational methods have been used to identify mammalian miRNAs initially missed by sequencing, and some of these predicted miRNAs have been evaluated experimentally-e.g., by rapid amplification of cDNA ends (RACE) (Lim et al 2003;Xie et al 2005), hybridization to RNA blots , microarrays (Bentwich et al 2005), and RNA-primed array-based Klenow extension (RAKE) (Berezikov et al 2006b). Each of these experimental methods, however, can yield false positives.…”

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confidence: 99%

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Mammalian microRNAs: experimental evaluation of novel and previously annotated genes

Chiang

Schoenfeld²,

Ruby³

et al. 2010

Genes Dev.

732

751

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MicroRNAs (miRNAs) are small regulatory RNAs that derive from distinctive hairpin transcripts. To learn more about the miRNAs of mammals, we sequenced 60 million small RNAs from mouse brain, ovary, testes, embryonic stem cells, three embryonic stages, and whole newborns. Analysis of these sequences confirmed 398 annotated miRNA genes and identified 108 novel miRNA genes. More than 150 previously annotated miRNAs and hundreds of candidates failed to yield sequenced RNAs with miRNA-like features. Ectopically expressing these previously proposed miRNA hairpins also did not yield small RNAs, whereas ectopically expressing the confirmed and newly identified hairpins usually did yield small RNAs with the classical miRNA features, including dependence on the Drosha endonuclease for processing. These experiments, which suggest that previous estimates of conserved mammalian miRNAs were inflated, provide a substantially revised list of confidently identified murine miRNAs from which to infer the general features of mammalian miRNAs. Our analyses also revealed new aspects of miRNA biogenesis and modification, including tissue-specific strand preferences, sequential Dicer cleavage of a metazoan precursor miRNA (pre-miRNA), consequential 59 heterogeneity, newly identified instances of miRNA editing, and evidence for widespread pre-miRNA uridylation reminiscent of miRNA regulation by Lin28.[Keywords: MicroRNA; miRNA biogenesis; noncoding RNA genes; high-throughput sequencing] Supplemental material is available at http://www.genesdev.org.

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“…Hundreds of candidates from other miRNA discovery efforts (Xie et al 2005;Berezikov et al 2006b) also failed to pass the filters, usually because no reads mapped to them.…”

Section: Experimental Evaluation Of Unconfirmed Mirnasmentioning

confidence: 99%

Section: Experimental Evaluation Of Unconfirmed Mirnasmentioning

confidence: 99%

mentioning

confidence: 99%

mentioning

confidence: 99%

See 2 more Smart Citations

Mammalian microRNAs: experimental evaluation of novel and previously annotated genes

Chiang

Schoenfeld²,

Ruby³

et al. 2010

Genes Dev.

732

751

View full text Add to dashboard Cite

show abstract

“…MiRNAs have been shown to function as post-transcriptional negative regulators of gene expression in a variety of systems [reviewed in 4,5 ]. There are about 500 known miRNAs in humans, although prediction algorithms suggest that the total number of miRNAs could be substantially larger [ 6 ], and experimental approaches suggest that new miRNAs still remain to be identified [ 7,8 ]. Thus, miRNAs appear likely to be a major component of gene regulation.…”

Section: Introductionmentioning

confidence: 99%

Analysis of microRNA expression by in situ hybridization with RNA oligonucleotide probes

Thompson

Deo

Turner

2007

Methods

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In situ hybridization is an important tool for analyzing gene expression and developing hypotheses about gene functions. The discovery of hundreds of microRNA (miRNA) genes in animals has provided new challenges for analyzing gene expression and functions. The small size of the mature miRNAs (∼20-24 nucleotides in length) presents difficulties for conventional in situ hybridization methods. However, we have developed a modified in situ hybridization method for detection of mammalian miRNAs in tissue sections, based upon the use of RNA oligonucleotide probes in combination with highly specific wash conditions. Here we present detailed procedures for detection of miRNAs in tissue sections or cultured cells. The methods described can utilize either nonradioactive hapten-conjugated probes that are detected by enzyme-coupled antibodies, or radioactively labeled probes that are detected by autoradiography. The ability to visualize miRNA expression patterns in tissue sections provides an additional tool for the analyses of miRNA expression and function. In addition, the use of radioactively labeled probes should facilitate quantitative analyses of changes in miRNA gene expression.

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RNA Secondary Structure Analysis Using The RNAshapes Package

Reeder

Giegerich

2009

CP in Bioinformatics

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Many novel mammalian microRNA candidates identified by extensive cloning and RAKE analysis

Cited by 244 publications

References 39 publications

Mammalian microRNAs: experimental evaluation of novel and previously annotated genes

Mammalian microRNAs: experimental evaluation of novel and previously annotated genes

Analysis of microRNA expression by in situ hybridization with RNA oligonucleotide probes

RNA Secondary Structure Analysis Using The RNAshapes Package

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