Small Peptides Switch the Transcriptional Activity of Shavenbaby During
            <i>Drosophila</i>
            Embryogenesis

Kondo, Takefumi; Plaza, Serge; Zanet, Jennifer; Benrabah, E.; Valenti, Philippe; Hashimoto, Yoshiko; Kobayashi, Satoru; Payre, François; Kageyama, Yuji

doi:10.1126/science.1188158

Cited by 328 publications

(348 citation statements)

References 21 publications

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“…These transcripts have expression levels and tissue specificity similar to the stringent lincRNA set, but a significantly higher level of sequence conservation. Many could encode small peptides, similar to those that function in Drosophila melanogaster embryogenesis (Kondo et al 2010). Another 1533 TUCP transcripts are classified as pseudogenes, and may represent pseudogenes that have evolved to function as noncoding regulatory agents.…”

Section: Discussionmentioning

confidence: 99%

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Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses

Cabili¹,

Trapnell²,

Goff³

et al. 2011

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Large intergenic noncoding RNAs (lincRNAs) are emerging as key regulators of diverse cellular processes. Determining the function of individual lincRNAs remains a challenge. Recent advances in RNA sequencing (RNA-seq) and computational methods allow for an unprecedented analysis of such transcripts. Here, we present an integrative approach to define a reference catalog of >8000 human lincRNAs. Our catalog unifies previously existing annotation sources with transcripts we assembled from RNA-seq data collected from~4 billion RNA-seq reads across 24 tissues and cell types. We characterize each lincRNA by a panorama of >30 properties, including sequence, structural, transcriptional, and orthology features. We found that lincRNA expression is strikingly tissue-specific compared with coding genes, and that lincRNAs are typically coexpressed with their neighboring genes, albeit to an extent similar to that of pairs of neighboring protein-coding genes. We distinguish an additional subset of transcripts that have high evolutionary conservation but may include short ORFs and may serve as either lincRNAs or small peptides. Our integrated, comprehensive, yet conservative reference catalog of human lincRNAs reveals the global properties of lincRNAs and will facilitate experimental studies and further functional classification of these genes.

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Section: Discussionmentioning

confidence: 99%

“…5E,F). Thus, some of these transcripts may encode small functional peptides (Kondo et al 2010), whereas others may function as noncoding RNA.…”

Section: Novel Transcripts With Potential Coding Capacitymentioning

confidence: 99%

Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses

Cabili¹,

Trapnell²,

Goff³

et al. 2011

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show abstract

“…The peptides encoded by ORFs 1 to 4 of pri RNA were shown to regulate the transcription factor encoded by shavenbaby (svb) (Kondo et al, 2010), with expression of Svb target genes being greatly attenuated in pri-deficient mutants and mutation of svb resulting in an aberrant trichome pattern (Payre et al, 1999;Sucena et al, 2003;Zanet et al, 2015).…”

Section: (2) Polished Rice (Pri)mentioning

confidence: 99%

“…Although lncRNAs do not harbor apparent open reading frames (ORFs) for proteins of >100 amino acids, recent studies have identified a subset of lncRNAs that actually encode polypeptides of <100 amino acids (Fig. 1A) (Anderson et al, 2015;Kondo et al, 2010;Matsumoto et al, 2017;Nelson et al, 2016;Pauli et al, 2014).…”

Section: Introductionmentioning

confidence: 99%

Hidden Peptides Encoded by Putative Noncoding RNAs

Matsumoto

Nakayama

2018

Cell Struct. Funct.

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Although the definition of a noncoding RNA (ncRNA) is an RNA molecule that does not encode a protein, recent evidence has revealed that some ncRNAs are indeed translated to give rise to small polypeptides (usually containing fewer than 100 amino acids). Despite their small size, however, these peptides are often biologically relevant in that they are required for a variety of cellular processes. In this review, we summarize the production and functions of peptides that have been recently identified as translation products of putative ncRNAs.4

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“…The activation of Svb protein requires the truncation of its N-terminus. The details of this post-translational step are not yet completely understood, but this modification is mediated by products of the polished rice ( pri) gene, a polycistronic gene that encodes four short peptides [13]. Svb is required also for development of some of the trichomes on the adult cuticle [11] and for development of tarsal joints [14].…”

Section: Trichome Patterning Differences Betweenmentioning

confidence: 99%

The structure and evolution ofcis-regulatory regions: theshavenbabystory

Stern

Frankel

2013

Phil. Trans. R. Soc. B

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In this paper, we provide a historical account of the contribution of a single line of research to our current understanding of the structure of cis-regulatory regions and the genetic basis for morphological evolution. We revisit the experiments that shed light on the evolution of larval cuticular patterns within the genus Drosophila and the evolution and structure of the shavenbaby gene. We describe the experiments that led to the discovery that multiple genetic changes in the cis-regulatory region of shavenbaby caused the loss of dorsal cuticular hairs (quaternary trichomes) in first instar larvae of Drosophila sechellia. We also discuss the experiments that showed that the convergent loss of quaternary trichomes in D. sechellia and Drosophila ezoana was generated by parallel genetic changes in orthologous enhancers of shavenbaby. We discuss the observation that multiple shavenbaby enhancers drive overlapping patterns of expression in the embryo and that these apparently redundant enhancers ensure robust shavenbaby expression and trichome morphogenesis under stressful conditions. All together, these data, collected over 13 years, provide a fundamental case study in the fields of gene regulation and morphological evolution, and highlight the importance of prolonged, detailed studies of single genes.

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Small Peptides Switch the Transcriptional Activity of Shavenbaby During Drosophila Embryogenesis

Cited by 328 publications

References 21 publications

Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses

Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses

Hidden Peptides Encoded by Putative Noncoding RNAs

The structure and evolution ofcis-regulatory regions: theshavenbabystory

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