Evolution of hox post-transcriptional regulation by alternative polyadenylation and MicroRNA modulation within 12 drosophila genomes

Molecular Biology and Evolution

Volumn 28, Issue 9, 2011, Pages 2453-2460

  Patraquim, Pedro ^a   Warnefors, Maria ^a   Alonso, Claudio R ^a  

^a UNIVERSITY OF SUSSEX   (United Kingdom)

Author keywords

alternative polyadenylation; Drosophila evolution; Hox genes; microRNA evolution; post transcriptional regulation; RNA secondary structure

Indexed keywords

HOX PROTEIN; MICRORNA;

3' UNTRANSLATED REGION; ANTERIOR POSTERIOR AXIS; ARTICLE; DROSOPHILA MELANOGASTER; GENE EXPRESSION; GENE SEQUENCE; GENETIC CODE; GENETIC CONSERVATION; MOLECULAR EVOLUTION; NONHUMAN; POLYADENYLATION; PROTEIN PROCESSING; PROTEIN SECONDARY STRUCTURE; RNA STRUCTURE; TRANSCRIPTION REGULATION;

3' UNTRANSLATED REGIONS; ANIMALS; COMPUTATIONAL BIOLOGY; CONSERVED SEQUENCE; DROSOPHILA MELANOGASTER; DROSOPHILA PROTEINS; EVOLUTION, MOLECULAR; GENE EXPRESSION REGULATION; GENES, HOMEOBOX; GENOME, INSECT; HOMEODOMAIN PROTEINS; MICRORNAS; POLYADENYLATION; RNA PROCESSING, POST-TRANSCRIPTIONAL; RNA, MESSENGER; TRANSCRIPTION FACTORS;

ANIMALIA; DROSOPHILA MELANOGASTER; DROSOPHILIDAE;

EID: 80052168753     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msr073     Document Type: Article

References (22)

1. Alonso CR. 2002. Hox proteins: sculpting body parts by activating localized cell death. Curr Biol. 12:R776-R778. (Pubitemid 35426696)
2. Alonso CR. 2008. The molecular biology underlying developmental evolution. In: Minelli A, Fusco G, editors. Evolving pathways, key themes in evolutionary developmental biology. Cambridge, UK: Cambridge University Press. p. 80-99.
3. Alonso CR, Wilkins AS. 2005. The molecular elements that underlie developmental evolution. Nat Rev Genet. 6:709-715. (Pubitemid 41192322)
4. Bartel DP. 2004. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116:281-297.
5. Bartel DP, Chen C-Z. 2004. Micromanagers of gene expression: the potentially widespread influence of metazoan microRNAs. Nat Rev Genet. 5:396-400. (Pubitemid 38529411)
6. Bender W. 2008. MicroRNAs in the Drosophila bithorax complex. Genes Dev. 22:14-19.
7. Britten RJ, Davidson EH. 1969. Gene regulation for higher cells: a theory. Science 165:349-357.
8. Brudno M, Do CB, Cooper GM, Kim MF, Davydov E, Program NCS, Green ED, Sidow A, Batzoglou S. 2003. LAGAN and Multi-LAGAN: efficient tools for large-scale multiple alignment of genomic DNA. Genome Res. 13:721-731. (Pubitemid 36511930)
9. Hofacker IL. 2003. Vienna RNA secondary structure server. Nucleic Acids Res. 31:3429-3431. (Pubitemid 37442172)
10. Holland PW, Garcia-Fernàndez J. 1996. Hox genes and chordate evolution. Dev Biol. 173:382-395. (Pubitemid 26064864)
11. Kertesz M, Iovino N, Unnerstall U, Gaul U, Segal E. 2007. The role of site accessibility in microRNA target recognition. Nat Genet. 39:1278-1284. (Pubitemid 47482690)
12. Lewis EB. 1978. A gene complex controlling segmentation in Drosophila. Nature 276:565-570. (Pubitemid 9087758)
13. Li X, Quon G, Lipshitz HD, Morris Q. 2010. Predicting in vivo binding sites of RNA-binding proteins using mRNA secondary structure. RNA 16:1096-1107.
14. Long D, Lee R, Williams P, Chan CY, Ambros V, Ding Y. 2007. Potent effect of target structure on microRNA function. Nat Struct Mol Biol. 14:287-294. (Pubitemid 46608348)
15. McGinnis W, Krumlauf R. 1992. Homeobox genes and axial patterning. Cell 68:283-302.
16. Moore MJ. 2005. From birth to death: the complex lives of eukaryotic mRNAs. Science 309:1514-1518. (Pubitemid 41266467)
17. Pearson JC, Lemons D, McGinnis W. 2005. Modulating Hox gene functions during animal body patterning. Nat Rev Genet. 6:893-904. (Pubitemid 41782157)
18. Ronshaugen M, Biemar F, Piel J, Levine M, Lai EC. 2005. The Drosophila microRNA iab-4 causes a dominant homeotic transformation of halteres to wings. Genes Dev. 19: 2947-2952. (Pubitemid 41798111)
19. Ruby JG, Stark A, Johnston WK, Kellis M, Bartel DP, Lai EC. 2007. Evolution, biogenesis, expression, and target predictions of a substantially expanded set of Drosophila microRNAs. Genome Res. 17:1850-1864. (Pubitemid 351360008)
20. Stark A, Bushati N, Jan CH, Kheradpour P, Hodges E, Brennecke J, Bartel DP, Cohen SM, Kellis M. 2008. A single Hox locus in Drosophila produces functional microRNAs from opposite DNA strands. Genes Dev. 22:8-13.
21. Thomsen S, Azzam G, Kaschula R, Williams LS, Alonso CR. 2010. Developmental RNA processing of 3'UTRs in Hox mRNAs as a context-dependent mechanism modulating visibility to microRNAs. Development 137:2951-2960.
22. Tyler DM, Okamura K, Chung W-J, Hagen JW, Berezikov E, Hannon GJ, Lai EC. 2008. Functionally distinct regulatory RNAs generated by bidirectional transcription and processing of microRNA loci. Genes Dev. 22:26-36.