An RNA architectural locus control region involved in Dscam mutually exclusive splicing

Nature Communications

Volumn 3, Issue , 2012, Pages

  Wang, Xuebin ^a   Li, Guoli ^a   Yang, Yun ^a   Wang, Wenfeng ^a   Zhang, Wenjing ^a   Pan, Huawei ^a   Zhang, Peng ^a   Yue, Yuan ^a   Lin, Hao ^a   Liu, Baoping ^a   Bi, Jingpei ^a   Shi, Feng ^a   Mao, Jinping ^a   Meng, Yijun ^a   Zhan, Leilei ^a   Jin, Yongfeng ^a  

^a ZHEJIANG UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

CELL ADHESION MOLECULE; DSCAM PROTEIN; RNA; UNCLASSIFIED DRUG;

EVOLUTIONARY BIOLOGY; FLY; GENE EXPRESSION; GENOMICS; MOLECULAR ANALYSIS; MUTATION; RNA;

ALTERNATIVE RNA SPLICING; ANIMAL EXPERIMENT; ARTICLE; BINDING SITE; COMPARATIVE GENE MAPPING; CONTROLLED STUDY; DROSOPHILA MELANOGASTER; EXON; GENE CLUSTER; GENE TARGETING; GENETIC VARIABILITY; MOLECULAR DOCKING; MUTATIONAL ANALYSIS; NONHUMAN; REGULATOR GENE; RNA SEQUENCE; RNA STRUCTURE;

ALTERNATIVE SPLICING; ANIMALS; CELL ADHESION MOLECULES; CONSERVED SEQUENCE; DAPHNIA; DROSOPHILA MELANOGASTER; DROSOPHILA PROTEINS; ENHANCER ELEMENTS, GENETIC; EVOLUTION, MOLECULAR; EXONS; HYMENOPTERA; LOCUS CONTROL REGION; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; RNA;

DROSOPHILA MELANOGASTER;

EID: 84871753158     PISSN: None     EISSN: 20411723     Source Type: Journal    
DOI: 10.1038/ncomms2269     Document Type: Article

References (27)

1. Matlin, A. J., Clark, F. & Smith, C. W. Understanding alternative splicing: towards a cellular code. Nat. Rev. Mol. Cell Biol. 6, 386-398 (2005). (Pubitemid 40637856)
2. Chen, M. & Manley, J. Mechanisms of alternative splicing regulation: insights from molecular and genomics approaches. Nat. Rev. Mol. Cell Biol. 10, 741-754 (2009).
3. Nilsen, T. W. & Graveley, B. R. Expansion of the eukaryotic proteome by alternative splicing. Nature 463, 457-463 (2010).
4. Pan, Q., Shai, O., Lee, L. J., Frey, B. J. & Blencowe, B. J. Deep surveying of alternative splicing complexity in the human transcriptome by highthroughput sequencing. Nat. Genet. 40, 1413-1415 (2008).
5. Sultan, M. et al. A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome. Science 321, 956-960 (2008).
6. Schmucker, D. et al. Drosophila Dscam is an axon guidance receptor exhibiting extraordinary molecular diversity. Cell 101, 671-684 (2000).
7. Neves, G., Zucker, J., Daly, M. & Chess, A. Stochastic yet biased expression of multiple Dscam splice variants by individual cells. Nat. Genet. 36, 240-246 (2004). (Pubitemid 38282748)
8. Smith, C. W. Alternative splicing-when two's a crowd. Cell 123, 1-3 (2005). (Pubitemid 41414522)
9. Graveley, B. R. Mutually exclusive splicing of the insect Dscam pre-mRNA directed by competing intronic RNA secondary structures. Cell 123, 65-73 (2005). (Pubitemid 41414529)
10. Anastassiou, D., Liu, H. & Varadan, V. Variable window binding for mutually exclusive alternative splicing. Genome Biol. 7, R2 (2006).
11. Yang, Y. et al. RNA secondary structure in mutually exclusive splicing. Nat. Struct. Mol. Biol. 18, 159-168 (2011).
12. May, G. E., Olson, S., McManus, C. J. & Graveley, B. R. Competing RNA secondary structures are required for mutually exclusive splicing of the Dscam exon 6 cluster. RNA 17, 222-229 (2011).
13. Olson, S. et al. A regulator of Dscam mutually exclusive splicing fidelity. Nat. Struct. Mol. Biol. 14, 1134-1140 (2007). (Pubitemid 350223337)
14. Kioussis, D., Vanin, E., deLange, T., Flavell, R. A. & Grosveld, F. G. b-globin gene inactivation by DNA translocation in gb-thalassaemia. Nature 306, 662-666 (1983). (Pubitemid 14201849)
15. Bulger, M. et al. Conservation of sequence and structure flanking the mouse and human b-globin loci: the b-globin genes are embedded within an array of odorant receptor genes. Proc. Natl. Acad. Sci. USA 96, 5129-5134 (1999). (Pubitemid 29214547)
16. Tolhuis, B., Palstra, R. J., Splinter, E., Grosveld, F. & de Laat, W. Looping and interaction between hypersensitive sites in the active betaglobin locus. Mol. Cell 10, 1453-1465 (2002). (Pubitemid 36050885)
17. Serizawa, S. et al. Negative feedback regulation ensures the one receptor-one olfactory neuron rule in mouse. Science 302, 2088-2094 (2003). (Pubitemid 38017935)
18. Fuss, S. H., Omura, M. & Mombaerts, P. Local and cis effects of the H element on expression of odorant receptor genes in mouse. Cell 130, 373-384 (2007). (Pubitemid 47081139)
19. Glenner, H., Thomsen, P. F., Hebsgaard, M. B., Sørensen, M. V. & Willerslev, E. The origin of insects. Science 314, 1883-1884 (2006). (Pubitemid 46028498)
20. Brites, D. et al. The Dscam homologue of the crustacean Daphnia is diversified by alternative splicing like in insects. Mol. Biol. Evol. 25, 1429-1439 (2008). (Pubitemid 351882017)
21. Reese, M. G., Eeckman, F. H., Kulp, D. & Haussler, D. Improved splice site detection in genie. J. Comput. Biol. 4, 311-323 (1997). (Pubitemid 27355870)
22. Zhang, C., Hastings, M. L., Krainer, A. R. & Zhang, M. Q. Dual-specificity splice sites function alternatively as 50 and 30 splice sites. Proc. Natl Acad. Sci. USA 104, 15028-15033 (2007). (Pubitemid 47619587)
23. Kreahling, J. M. & Graveley, B. R. The iStem, a long-range RNA secondary structure element required for efficient exon inclusion in the Drosophila Dscam pre-mRNA. Mol. Cell. Biol. 25, 10251-10260 (2005). (Pubitemid 41681952)
24. Fox-Walsh, K. L. et al. The architecture of pre-mRNAs affects mechanisms of splice-site pairing. Proc. Natl Acad. Sci. USA 102, 16176-16181 (2005). (Pubitemid 41688887)
25. Hattori, D. et al. Robust discrimination between self and non-self neurites requires thousands of Dscam1 isoforms. Nature 461, 644-648 (2009).
26. Zuker, M. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 31, 3406-3415 (2003). (Pubitemid 37442169)
27. Regier, J. C. et al. Arthropod relationships revealed by phylogenomic analysis of nuclear protein-coding sequences. Nature 463, 1079-1083 (2010).