An Evolutionarily Conserved Domain of <i>roX2</i> RNA Is Sufficient for Induction of H4-Lys16 Acetylation on the Drosophila X Chromosome

Park, Seung Won; Kang, Yool Ie; Sypula, Joanna G.; Choi, Jiyeon; Oh, Hyangyee; Park, Yongkyu

doi:10.1534/genetics.107.071001

Cited by 49 publications

(85 citation statements)

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“…S3A; Ilik et al 2013;Quinn et al 2014). Looking at D3, the ∼450-nucleotide (nt) region of roX1 (∼3.7 kb) that can rescue male lethality up to ∼80% in the absence of any other roX RNA (highest rescue potential among any other region of roX1 except full-length roX1) (Quinn et al 2014), we saw evidence for R1H1 and also for the presence of a long-range stem-loop structure that we and others (Park et al 2007;Kelley et al 2008;Quinn et al 2014) predicted to form between the IRB element and roX1 box 1 ∼120 nt away (Supplemental Fig. S3B).…”

Section: Uvclap Provides An Efficient Methods To Capture Rna-protein Imentioning

confidence: 65%

“…For example, from the core MSL complex perspective, recent work on MSL2 has shown that MSL2 can recognize high-affinity sites (HASs) in the absence of other factors in vitro, but how would binding to HASs by MSL2 lead to the spreading of the complex to the rest of the X chromosome in a way that depends on roX RNAs and MLE (Villa et al 2016)? Moreover, from the roX lncRNA perspective, Park et al (2007) have shown that concatenating six copies of R2H5 without the sequence that is required to also form ASL can rescue only ∼17% male lethality. Therefore, we decided to evaluate the relative importance of the ASL-R2H5 structure in vivo using fly genetics by expressing several different roX RNA derivatives in the absence of endogenous roX expression.…”

Section: Mle Helicase Activity Is Important For Msl2 To Bind Rox2 In mentioning

confidence: 99%

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A mutually exclusive stem–loop arrangement in roX2 RNA is essential for X-chromosome regulation in Drosophila

et al. 2017

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The X chromosome provides an ideal model system to study the contribution of RNA-protein interactions in epigenetic regulation. In male flies, roX long noncoding RNAs (lncRNAs) harbor several redundant domains to interact with the ubiquitin ligase male-specific lethal 2 (MSL2) and the RNA helicase Maleless (MLE) for X-chromosomal regulation. However, how these interactions provide the mechanics of spreading remains unknown. By using the uvCLAP (UV cross-linking and affinity purification) methodology, which provides unprecedented information about RNA secondary structures in vivo, we identified the minimal functional unit of roX2 RNA. By using wild-type and various MLE mutant derivatives, including a catalytically inactive MLE derivative, MLE GET , we show that the minimal roX RNA contains two mutually exclusive stem-loops that exist in a peculiar structural arrangement: When one stem-loop is unwound by MLE, an alternate structure can form, likely trapping MLE in this perpetually structured region. We show that this functional unit is necessary for dosage compensation, as mutations that disrupt this formation lead to male lethality. Thus, we propose that roX2 lncRNA contains an MLE-dependent affinity switch to enable reversible interactions of the MSL complex to allow dosage compensation of the X chromosome.[Keywords: dosage compensation; H4K16ac; MLE; X chromosome; acetylation; roX RNA] Supplemental material is available for this article. RNA helicases are a large family of proteins that have important roles in many aspects of RNA biology. Although the name "helicase" suggests that the main function of these proteins is to destabilize and remove RNA secondary structures, there are several RNA helicases, especially of the DEAD-box subfamily, that use their helicase domains to simply interact with RNA (such as eIF4A3) and not for remodeling. On the other hand, a closely related RNA helicase, eIF4A1, can unwind RNA structures but only when they are relatively weak and short (Rogers et al. 2001). At the other extreme, several helicases are proposed to act as annealers that facilitate the formation of structured RNA rather than the other way around (Jankowsky 2011).Thus, although the helicase family is quite large, specific functions assigned to helicases that involve the actual removal of secondary structures in vivo are rather sparse. Maleless (MLE), known primarily for its role in Drosophila dosage compensation, is an RNA helicase of the DExH family, which is composed of relatively large multidomain helicases that (unlike the DEAD-box family) are thought to work as processive RNA helicases.

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Section: Uvclap Provides An Efficient Methods To Capture Rna-protein Imentioning

confidence: 65%

Section: Mle Helicase Activity Is Important For Msl2 To Bind Rox2 In mentioning

confidence: 99%

A mutually exclusive stem–loop arrangement in roX2 RNA is essential for X-chromosome regulation in Drosophila

et al. 2017

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“…Conserved RNA structures in roX2 recruit MSL. In an independent study 74 , we searched for conserved regions in the non-coding roX1 and roX2 (RNA on the X) genes to gain insights into their function. Both RNAs are components of the MSL (Male-specific lethal) complex and are crucial for dosage compensation in male flies, inducing lysine 16 acetylation of histone H4, leading to upregulation of hundreds of genes on the X chromosome 75 .…”

Section: Rna Genes and Structuresmentioning

confidence: 99%

Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures

Stark

Lin

Kheradpour³

et al. 2007

Nature

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Sequencing of multiple related species followed by comparative genomics analysis constitutes a powerful approach for the systematic understanding of any genome. Here, we use the genomes of 12 Drosophila species for the de novo discovery of functional elements in the fly. Each type of functional element shows characteristic patterns of change, or 'evolutionary signatures', dictated by its precise selective constraints. Such signatures enable recognition of new protein-coding genes and exons, spurious and incorrect gene annotations, and numerous unusual gene structures, including abundant stop-codon readthrough. Similarly, we predict non-protein-coding RNA genes and structures, and new microRNA (miRNA) genes. We provide evidence of miRNA processing and functionality from both hairpin arms and both DNA strands. We identify several classes of pre-and post-transcriptional regulatory motifs, and predict individual motif instances with high confidence. We also study how discovery power scales with the divergence and number of species compared, and we provide general guidelines for comparative studies.The sequencing of the human genome and the genomes of dozens of other metazoan species has intensified the need for systematic methods to extract biological information directly from DNA sequence. Comparative genomics has emerged as a powerful methodology for this endeavour 1,2 . Comparison of few (two-four) closely related genomes has proven successful for the discovery of protein-coding genes 3-5 , RNA genes 6,7 , miRNA genes 8-11 and catalogues of regulatory elements 3,4,12-14 . The resolution and discovery power of these studies should increase with the number of genomes [15][16][17][18][19][20] , in principle enabling the systematic discovery of all conserved functional elements.The fruitfly Drosophila melanogaster is an ideal system for developing and evaluating comparative genomics methodologies. Over the past century, Drosophila has been a pioneering model in which many of the basic principles governing animal development and population biology were established 21 . In the past decade, the genome sequence of D. melanogaster provided one of the first systematic views *These authors contributed equally to this work. {Lists of participants and affiliations appear at the end of the paper.

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“…1b, fragment E). Interestingly, this purine-rich region is located within stem-loop 6 (SL6) just upstream of a prominent, conserved stem-loop structure (SLroX2 or SL7) 12 that, when multimerized, is sufficient to restore the X-chromosomal targeting defects of a roX null mutant 13 . Pull-down assays using MS2-tagged RNA as bait confirmed that UNR bound with highest affinity to roX2 fragments containing SL6 (Fig.…”

Section: Resultsmentioning

confidence: 99%

UNR facilitates the interaction of MLE with the lncRNA roX2 during Drosophila dosage compensation

et al. 2014

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Dosage compensation is a regulatory process that balances the expression of X-chromosomal genes between males (XY) and females (XX). In Drosophila, this requires non-coding RNAs and RNA-binding proteins (RBPs) whose specific functions remain elusive. Here we show that the Drosophila RBP UNR promotes the targeting of the activating male-specific-lethal complex to the X-chromosome by facilitating the interaction of two crucial subunits: the RNA helicase MLE and the long non-coding RNA roX2.

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An Evolutionarily Conserved Domain of roX2 RNA Is Sufficient for Induction of H4-Lys16 Acetylation on the Drosophila X Chromosome

Cited by 49 publications

References 20 publications

A mutually exclusive stem–loop arrangement in roX2 RNA is essential for X-chromosome regulation in Drosophila

A mutually exclusive stem–loop arrangement in roX2 RNA is essential for X-chromosome regulation in Drosophila

Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures

UNR facilitates the interaction of MLE with the lncRNA roX2 during Drosophila dosage compensation

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