Identification of putative noncoding polyadenylated transcripts in
            <i>Drosophila melanogaster</i>

Tupy, Jonathan L.; Bailey, Adina; Dailey, Gina M; Evans-Holm, Martha; Siebel, Christian W.; Misra, Sima; Celniker, S; Rubin, Gerald M.

doi:10.1073/pnas.0501422102

Cited by 109 publications

(96 citation statements)

References 29 publications

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“…CR32777 corresponds to roX1, which is ubiquitously expressed at the blastoderm stage, hence it represents a false positive (20,21). The other two potential noncoding RNAs were recently identified independently in two other studies, and although the expression of CR32957 could not be detected by in situ hybridization (22), CR31972 transcripts are detected in the mesoderm (ref. 23; Table 8).…”

Section: Resultsmentioning

confidence: 99%

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Comprehensive identification of Drosophila dorsal–ventral patterning genes using a whole-genome tiling array

Biemar

Nix²,

Piel

et al. 2006

Proc. Natl. Acad. Sci. U.S.A.

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Dorsal-ventral (DV) patterning of the Drosophila embryo is initiated by Dorsal, a sequence-specific transcription factor distributed in a broad nuclear gradient in the precellular embryo. Previous studies have identified as many as 70 protein-coding genes and one microRNA (miRNA) gene that are directly or indirectly regulated by this gradient. A gene regulation network, or circuit diagram, including the functional interconnections among 40 Dorsal target genes and 20 associated tissue-specific enhancers, has been determined for the initial stages of gastrulation. Here, we attempt to extend this analysis by identifying additional DV patterning genes using a recently developed whole-genome tiling array. This analysis led to the identification of another 30 proteincoding genes, including the Drosophila homolog of Idax, an inhibitor of Wnt signaling. In addition, remote 5 exons were identified for at least 10 of the Ϸ100 protein-coding genes that were missed in earlier annotations. As many as nine intergenic uncharacterized transcription units were identified, including two that contain known microRNAs, miR-1 and -9a. We discuss the potential functions of these recently identified genes and suggest that intronic enhancers are a common feature of the DV gene network.gene network ͉ microRNA ͉ noncoding RNA D orsal-ventral (DV) asymmetry is established by complex interactions of at least 17 maternal genes that produce a localized ligand, Spätzle (Spz), in ventral regions of the perivitelline matrix surrounding the early embryo. Spz induces Toll signaling and the subsequent formation of a broad nuclear gradient of the Dorsal (Dl) protein, the Drosophila homolog of NF-B (1). The Dl nuclear gradient establishes the territories of the prospective mesoderm, neuroectoderm, and dorsal ectoderm by activating or repressing zygotic gene expression in a concentration-dependent manner. Previous genetic screens, subtractive hybridization assays, and microarray analyses identified as many as 70 protein-coding genes that are differentially expressed across the DV axis of early embryos undergoing cellularization and the initial phases of gastrulation. Most of those DV patterning genes encode transcription factors or components of cell signaling pathways, and many are likely to be direct targets of the Dorsal gradient (2).The advent of whole-genome tiling arrays provides a unique opportunity to identify microRNAs (miRNAs) and other noncoding RNAs that are regulated by the Dl gradient. In addition, these arrays present several opportunities for gene discovery not provided by traditional microarray screens. First, significant genes can be identified by using lower signal-to-noise cutoff values, because neighboring transcription units (TUs) serve as internal controls for even subtle elevations in tissue-specific expression. Second, there is no bias introduced by gene prediction models for the identification of protein-coding sequences. Third, it is possible to identify tissue-specific splicing isoforms for genes that display ubiquitous tra...

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Section: Resultsmentioning

confidence: 99%

“…A strategy similar to the one described by Tupy et al (22) was used to establish a likelihood of translation for previously unannotated transfrags. A 500-bp-long sequence from the second exon of the even-skipped (eve) gene was used as a positive control for protein-coding potential.…”

Section: Computational Analysis Of Likelihood Of Translationmentioning

confidence: 99%

Comprehensive identification of Drosophila dorsal–ventral patterning genes using a whole-genome tiling array

Biemar

Nix²,

Piel

et al. 2006

Proc. Natl. Acad. Sci. U.S.A.

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“…One example is the Sarcolamban (Scl) gene [48], previously annotated as a non-coding gene [49], but identified by a bioinformatics approach as a potential functional smORF in Drosophila (Table 1; [17]). Scl encodes for two 28 and 29aa transmembrane related-micropeptides which act as inhibitors of SERCA calcium pump and regulate heart muscle contraction (Figure 2A; [48]).…”

Section: Computational and Biochemical Strategies Unravel Novel Smorfmentioning

confidence: 99%

New Peptides Under the s(ORF)ace of the Genome

Pueyo

Magny

Couso

2016

Trends in Biochemical Sciences

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Hundreds of previously unidentified functional small peptides could exist in most genomes, but these sequences have been generally overlooked. The discovery of genes encoding small peptides with important functions in different organisms, has ignited the interest in these sequences, and led to an increasing amount of effort towards their identification.Here, we review the advances, both, computational, and biochemical, that are leading the way in the discovery of putatively functional smORFs, as well as the functional studies that have been carried out as a consequence of these searches. The evidence suggests that smORFs form a substantial part of our genomes, and that their encoded peptides could have important functions in a variety of cellular functions.

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“…These included genes annotated as CG18854, CG32207, CR32205 and pncr009 (also known as pncr009:3L), a series of 20 repeats that partially overlap the 3′ untranslated region (UTR) of CG4068, and an intergenic region adjacent to CG4770 (Supplementary Figs 2-7). Except for CG4068, the coding potential of all of these loci is limited 5,6 . Still, we chose to introduce an 'hp' prefix to these six loci to distinguish the small-RNA-generating hairpins ('hpRNAs') from the potential protein-encoding segments of these transcripts.…”

Section: -Nucleotide Cloning Range Indicative Of Degradation Fragmmentioning

confidence: 99%

The Drosophila hairpin RNA pathway generates endogenous short interfering RNAs

Okamura

Chung

Ruby

et al. 2008

Nature

362

379

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In contrast to microRNAs and Piwi-associated RNAs, short interfering RNAs (siRNAs) are seemingly dispensable for host-directed gene regulation in Drosophila. This notion is based on the fact that mutants lacking the core siRNA-generating enzyme Dicer-2 or the predominant siRNA effector Argonaute 2 are viable, fertile and of relatively normal morphology 1,2 . Moreover, endogenous Drosophila siRNAs have not yet been identified. Here we report that siRNAs derived from long hairpin RNA genes (hpRNAs) programme Slicer complexes that can repress endogenous target transcripts. The Drosophila hpRNA pathway is a hybrid mechanism that combines canonical RNA interference factors (Dicer-2, Hen1 (known as CG12367) and Argonaute 2) with a canonical microRNA factor (Loquacious) to generate ~21-nucleotide siRNAs. These novel regulatory RNAs reveal unexpected complexity in the sorting of small RNAs, and open a window onto the biological usage of endogenous RNA interference in Drosophila.Artificial, long-inverted repeat transcripts are efficiently processed by a Dicer-2 (Dcr-2)/ Argonaute 2 (AGO2)-driven RNA interference (RNAi) pathway in transgenic Drosophila 1 , 3 . We hypothesized that this might reflect the existence of an endogenous pathway that accepts long, inverted repeat transcripts. To test this idea, we searched for inverted repeats using EINVERTED 4 and selected putative hairpins containing mapped small RNA reads (see Methods). Out of 8,132 candidate regions, most consisted of the terminal inverted repeats of individual transposable elements or long terminal repeats of tandem inverted transposable elements. The remaining loci corresponded to inverted tandem duplications of messenger RNA-or transfer RNA-encoding genes, a microRNA (miRNA) gene (mir-997), a novel tandem pair of short hairpins (chou39-1 and chou39-2, Supplementary Fig. 1), and a handful of singlegene annotations and unannotated regions.We analysed the size distribution of cloned RNAs from all of the non-transposable-element EINVERTED hits. Although these mostly exhibited a broad length distribution across the ~18-

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Identification of putative noncoding polyadenylated transcripts in Drosophila melanogaster

Cited by 109 publications

References 29 publications

Comprehensive identification of Drosophila dorsal–ventral patterning genes using a whole-genome tiling array

Comprehensive identification of Drosophila dorsal–ventral patterning genes using a whole-genome tiling array

New Peptides Under the s(ORF)ace of the Genome

The Drosophila hairpin RNA pathway generates endogenous short interfering RNAs

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