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An RNA Architectural Locus Control Region Involved in Dscam Mutually Exclusive Splicing

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An RNA Architectural Locus Control Region Involved in Dscam Mutually Exclusive Splicing ARTICLE Received 8 Aug 2012 | Accepted 7 Nov 2012 | Published 4 Dec 2012 DOI: 10.1038/ncomms2269 OPEN An RNA architectural locus control region involved in Dscam mutually exclusive splicing Xuebin Wang1,*, Guoli Li1,*, Yun Yang1, Wenfeng Wang1, Wenjing Zhang1, Huawei Pan1, Peng Zhang1, Yuan Yue1, Hao Lin1, Baoping Liu1, Jingpei Bi1, Feng Shi1, Jinping Mao1, Yijun Meng1, Leilei Zhan1 & Yongfeng Jin1 The most striking example of alternative splicing in a Drosophila melanogaster gene is observed in the Down syndrome cell adhesion molecule, which can generate 38,016 different isoforms. RNA secondary structures are thought to direct the mutually exclusive splicing of Down syndrome cell adhesion molecule, but the underlying mechanisms are poorly understood. Here we describe a locus control region that can activate the exon 6 cluster and specifically allow for the selection of only one exon variant in combination with docking site selector sequence interactions. Combining comparative genomic studies of 63 species with mutational analysis reveals that intricate, tandem multi-‘subunit’ RNA structures within the locus control region activate species-appropriate alternative variants. Importantly, strengthening the weak splice sites of the target exon can remove the locus control region dependence. Our findings not only provide a locus control region-dependent mechanism for mutually exclusive splicing, but also suggest a model for the evolution of increased complexity in a long-range RNA molecular machine. 1 Institute of Biochemistry, College of Life Sciences, Zhejiang University (Zijingang Campus), Hangzhou, Zhejiang ZJ310058, China. * These authors contributed equally to this work. Correspondence and requests for materials should be addressed to Y.J. (email: [email protected]). NATURE COMMUNICATIONS | 3:1255 | DOI: 10.1038/ncomms2269 | www.nature.com/naturecommunications 1 & 2012 Macmillan Publishers Limited. All rights reserved. ARTICLE NATURE COMMUNICATIONS | DOI: 10.1038/ncomms2269 lternative splicing is a widespread mechanism used by conservation in the reduction pattern for the various activation eukaryotes to expand protein diversity and to regulate constructs suggested a common activation pattern. Importantly, Agene expression1–3. Up to 95% of primary transcripts in the alternative exon 6.47 could be activated by locus replacement humans have been estimated to undergo alternative splicing4,5. of this region into the selector sequence IE47. Similarly, exon 6.48 The most striking example of alternative splicing is in the insect was frequently activated when the selector sequence IE48 was gene Down syndrome cell adhesion molecule (Dscam), which can replaced (Fig. 1g,h). Therefore, the large region upstream of the generate 38,016 different isoforms through mutually exclusive docking site could act as an activation element for efficient splicing of the four cassette exon clusters in D. melanogaster6,7. inclusion in exon 6. As this type of splicing of a cis-regulatory Mutually exclusive splicing is a strictly regulated form of element can specifically activate the target exons through long- alternative splicing in which the splicing machinery must distance interactions between docking site-selector sequences, we choose one of two or more candidate exons to include in each refer to it as an LCR by analogy with the well-characterised LCR messenger RNA (mRNA) isoform8. The most attractive model for in transcriptional regulation14–18. mutually exclusive splicing involves competition among RNA secondary structures. This mechanism was initially discovered RNA architecture and secondary structure of Drosophila LCR. within the exon 6 cluster of Dscam9,10. We recently observed The significant decrease observed in intron-wide scanning dele- similar structural arrangements in several clusters of mutually tions led us to hypothesize that this intronic region may form a exclusive exons, including the exon 4 and exon 9 clusters in long-range structure. Moreover, combining comparative geno- Dscam11. mics with structural predictions revealed that this intronic Although the docking site-selector sequence interactions have a sequence could potentially form a hexaleaf-shaped architecture key role in ensuring mutually exclusive splicing11,12, the role of consisting of six adjacent tandem stem–loop structures (I through these RNA structures remains poorly understood. A second VI, Fig. 2). Despite the relatively low sequence conservation, the component of this system involves the RNA-binding protein predicted RNA architecture and secondary structures are highly hrp36, which binds the exons throughout the exon 6 cluster and conserved in the 22 Drosophila species analysed (Fig. 2 and represses their inclusion in the mRNA isoform13. Nevertheless, Supplementary Fig. S3). Additionally, this double stranded RNA hrp36 has no effect on the inclusion of exon variants from Dscam (dsRNA) region showed clear evidence of multiple covariations exon clusters 4 and 9 (ref. 13). In the present study, we identified that maintain the structural integrity of the dsRNA a locus control region (LCR) that could activate the exon 6 (Supplementary Fig. S4). In each species, the 50 portion of the first cluster. Our findings not only provide an LCR-dependent dsRNA (I) was located an average of 54 nt downstream of the 50 mechanism for the selection of only one exon splice variant, splice site of exon 5, and the last dsRNA (VI) was located but also suggest a model for the evolution of increased complexity immediately upstream of the docking site (Fig. 2a,b). Importantly, in a long-range RNA molecular machine. as these six stem–loop structures were arranged in tandem, the ‘effective’ distance between the 50 and 30 ends was approximated Results to be o50 nt. To determine whether these RNA structures are essential for An LCR essential for Dscam exon 6 splicing. Our initial analysis exon 6 splicing, we tested the effects of disrupting and compen- indicated that sequences upstream of the docking site had satory mutations on splicing in transfection experiments. Muta- important roles in the activation of exon 6 through the generation tions M1 and M2 in stem I almost completely abolished the of a deletion construct with exon 6.2 fused to exon 6.46 inclusion of exon 6.47 in the mRNA isoform (Fig. 2c). A struc- (Supplementary Fig. S1). To further analyse the elements involved ture-restoring double mutation (M21) restored the efficiency of in exon 6 activation, we created a series of constructs designed to exon 6.47 inclusion to the wild-type (WT) level, thereby vali- mimic the approximation of sequences caused by RNA pairing dating predicted base–pair interactions. Likewise, the other five between the docking site and selector sequences (Fig. 1a). These RNA stems (II through VI) were confirmed by disruptive and data revealed that only the most proximal exon outside the loop compensatory mutation analysis (Fig. 2b,c). Thus, the data was activated, whereas the remaining exons were silenced obtained by disruptive and compensatory mutation analysis (Fig. 1b,c), implying an approximation-activation mechanism. strongly suggest that these RNA structures are essential for effi- Importantly, these constructs could be used to identify the ele- cient activation activity. ments necessary for exon 6 activation. Consequently, the deletion of the B200-bp sequences upstream of the docking site sub- stantially decreased or even abrogated the inclusion of the LCR architecture is evolutionarily conserved. Next, we explored proximal exon (data not shown). However, this sequence was not whether the intricate architecture found in the Drosophila LCR is sufficient for the activation of the exon 6.47 variant by locus conserved throughout insect or arthropod evolution. We expan- insertion, suggesting that other essential motif sequences are ded this analysis to other arthropod species from seven orders needed for efficient activation. (http://flybase.org/blast/). Together, these organisms encompass To identify other functional motifs, an B700-bp region several major taxonomic groups of insects and crustaceans that upstream of the docking site was scanned using by performing last shared a common ancestor B420 million years ago19. iterative deletions of 50–70-bp regions, and the effects of the Previous studies9,10,12,20, together with our current analysis, deletions on variant inclusion were quantitatively determined revealed that mutually exclusive splicing employed the docking/ (Fig. 1d). Unexpectedly, all of the deletions significantly decreased selector strategy in all of the species investigated. Remarkably, the the activation of the exon 6.47 variant. Most strikingly, 7 of 11 sequence comparison revealed eight conserved intronic elements deletions led to the almost exclusive omission of the 6.47 variant upstream of the docking site in exon cluster 6 among 15 (Fig. 1e,f). This outcome indicated that functional motifs may be hymenopteran species; the estimated divergence times ranged scattered throughout the intronic sequences upstream of the from 10 million to 150 million years ago (Fig. 3a). These docking site. A similar trend was observed in exons 6.48 and 6.43, Hymenoptera-specific intronic sequences form an architecture although the extent of the reduction of exons included in the similar to that observed in Drosophila, albeit with four-dsRNA mRNA isoforms from exons 6.48 and 6.43 differed from those tandem arrays (Fig. 3b and Supplementary Fig. S5). Structure- with exon 6.47 (Supplementary Fig. S2). This striking restoring
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