Long-distance regulation of Add2 pre-mRNA 3′ end processing

RNA Biology

Volumn 10, Issue 4, 2013, Pages 516-527

  Nedeljkovic, Mirjana ^a   Costessi, Luisa ^a   Iaconcig, Alessandra ^a   Porro, Fabiola ^a   Muro, Andrés F ^a  

^a INTERNATIONAL CENTRE FOR GENETIC ENGINEERING AND BIOTECHNOLOGY   (Italy)

Author keywords

3 end processing; Long distance; Mouse beta adducin (Add2); Non canonical; Upstream sequence element (USE)

Indexed keywords

ADDUCIN; BETA ADDUCIN; CIS ACTING ELEMENT; MESSENGER RNA PRECURSOR; UNCLASSIFIED DRUG;

3' UNTRANSLATED REGION; ARTICLE; ENHANCER REGION; IN VIVO STUDY; POLYADENYLATION; REGULATORY MECHANISM; RNA CLEAVAGE; SILENCER ELEMENT; STOP CODON;

EUKARYOTA;

EID: 84879027671     PISSN: 15476286     EISSN: 15558584     Source Type: Journal    
DOI: 10.4161/rna.23855     Document Type: Article

References (40)

1. Proudfoot NJ. Ending the message: poly(A) signals then and now. Genes Dev 2011; 25:1770-82; PMID:21896654; http://dx.doi.org/10.1101/gad.17268411.
2. Zhao J, Hyman L, Moore C. Formation of mRNA 3′ ends in eukaryotes: mechanism, regulation, and interrelationships with other steps in mRNA synthesis. Microbiol Mol Biol Rev 1999; 63:405-45; PMID:10357856.
3. Custódio N, Carmo-Fonseca M, Geraghty F, Pereira HS, Grosveld F, Antoniou M. Inefficient processing impairs release of RNA from the site of transcription. EMBO J 1999; 18:2855-66; PMID:10329631; http://dx.doi.org/10. 1093/emboj/18.10.2855.
4. Hilleren P, McCarthy T, Rosbash M, Parker R, Jensen TH. Quality control of mRNA 3′-end processing is linked to the nuclear exosome. Nature 2001; 413:538-42; PMID:11586364; http://dx.doi.org/10.1038/35097110.
5. Tian B, Hu J, Zhang H, Lutz CS. A large-scale analysis of mRNA polyadenylation of human and mouse genes. Nucleic Acids Res 2005; 33:201-12; PMID:15647503; http://dx.doi.org/10.1093/nar/gki158.
6. Zarudnaya MI, Kolomiets IM, Potyahaylo AL, Hovorun DM. Downstream elements of mammalian pre-mRNA polyadenylation signals: primary, secondary and higher-order structures. Nucleic Acids Res 2003; 31:1375-86; PMID:12595544; http://dx.doi.org/10.1093/nar/gkg241.
7. Dalziel M, Nunes NM, Furger A. Two G-rich regulatory elements located adjacent to and 440 nucleotides downstream of the core poly(A) site of the intronless melanocortin receptor 1 gene are critical for efficient 3′ end processing. Mol Cell Biol 2007; 27:1568-80; PMID:17189425; http://dx.doi.org/10. 1128/MCB.01821-06.
8. Fogel BL, McNally LM, McNally MT. Efficient polyadenylation of Rous sarcoma virus RNA requires the negative regulator of splicing element. Nucleic Acids Res 2002; 30:810-7; PMID:11809895; http://dx.doi.org/10.1093/nar/30.3.810.
9. Wilusz JE, Beemon KL. The negative regulator of splicing element of Rous sarcoma virus promotes polyadenylation. J Virol 2006; 80:9634-40; PMID:16973567; http://dx.doi.org/10.1128/JVI.00845-06.
10. Brown PH, Tiley LS, Cullen BR. Efficient polyadenylation within the human immunodeficiency virus type 1 long terminal repeat requires flanking U3-specific sequences. J Virol 1991; 65:3340-3; PMID:1851882.
11. Carswell S, Alwine JC. Efficiency of utilization of the simian virus 40 late polyadenylation site: effects of upstream sequences. Mol Cell Biol 1989; 9:4248-58; PMID:2573828.
12. Hall-Pogar T, Liang S, Hague LK, Lutz CS. Specific trans-acting proteins interact with auxiliary RNA polyadenylation elements in the COX-2 3′-UTR. RNA 2007; 13:1103-15; PMID:17507659; http://dx.doi.org/10.1261/rna.577707.
13. Moreira A, Takagaki Y, Brackenridge S, Wollerton M, Manley JL, Proudfoot NJ. The upstream sequence element of the C2 complement poly(A) signal activates mRNA 3′ end formation by two distinct mechanisms. Genes Dev 1998; 12:2522-34; PMID:9716405; http://dx.doi.org/10.1101/gad.12.16.2522.
14. Natalizio BJ, Muniz LC, Arhin GK, Wilusz J, Lutz CS. Upstream elements present in the 3′-untranslated region of collagen genes influence the processing efficiency of overlapping polyadenylation signals. J Biol Chem 2002; 277:42733-40; PMID:12200454; http://dx.doi.org/10.1074/jbc.M208070200.
15. Valsamakis A, Zeichner S, Carswell S, Alwine JC. The human immunodeficiency virus type 1 polyadenylylation signal: a 3′ long terminal repeat element upstream of the AAUAAA necessary for efficient polyadenylylation. Proc Natl Acad Sci USA 1991; 88:2108-12; PMID:1848693; http://dx.doi.org/10.1073/pnas.88.6.2108.
16. Costessi L, Porro F, Iaconcig A, Nedeljkovic M, Muro AF. Characterization of the distal polyadenylation site of the β-adducin (ADD2) pre-mRNA. PLoS One 2013; 8:e58879.
17. Costessi L, Devescovi G, Baralle FE, Muro AF. Brain-specific promoter and polyadenylation sites of the beta-adducin pre-mRNA generate an unusually long 3′-UTR. Nucleic Acids Res 2006; 34:243-53; PMID:16414955; http://dx.doi.org/10.1093/nar/gkj425.
18. Gilligan DM, Lozovatsky L, Gwynn B, Brugnara C, Mohandas N, Peters LL. Targeted disruption of the beta adducin gene (Add2) causes red blood cell spherocytosis in mice. Proc Natl Acad Sci USA 1999; 96:10717-22; PMID:10485892; http://dx.doi.org/10.1073/pnas.96.19.10717.
19. Muro AF, Marro ML, Gajovic S, Porro F, Luzzatto L, Baralle FE. Mild spherocytic hereditary elliptocytosis and altered levels of alpha- and gamma-adducins in beta-adducin-deficient mice. Blood 2000; 95:3978-85; PMID:10845937.
20. Porro F, Rosato-Siri M, Leone E, Costessi L, Iaconcig A, Tongiorgi E, et al. beta-adducin (Add2) KO mice show synaptic plasticity, motor coordination and behavioral deficits accompanied by changes in the expression and phosphorylation levels of the alpha- and gamma-adducin subunits. Genes Brain Behav 2010; 9:84-96; PMID:19900187; http://dx.doi.org/10.1111/j.1601-183X.2009. 00537.x.
21. Bednarek E, Caroni P. β-Adducin is required for stable assembly of new synapses and improved memory upon environmental enrichment. Neuron 2011; 69:1132-46; PMID:21435558; http://dx.doi.org/10.1016/j.neuron.2011.02.034.
22. Garneau NL, Wilusz J, Wilusz CJ. The highways and byways of mRNA decay. Nat Rev Mol Cell Biol 2007; 8:113-26; PMID:17245413; http://dx.doi.org/10.1038/ nrm2104.
23. Beaudoing E, Freier S, Wyatt JR, Claverie JM, Gautheret D. Patterns of variant polyadenylation signal usage in human genes. Genome Res 2000; 10:1001-10; PMID:10899149; http://dx.doi.org/10.1101/gr.10.7.1001.
24. Legendre M, Gautheret D. Sequence determinants in human polyadenylation site selection. BMC Genomics 2003; 4:7; PMID:12600277; http://dx.doi.org/10. 1186/1471-2164-4-7.
25. Kubo T, Wada T, Yamaguchi Y, Shimizu A, Handa H. Knock-down of 25 kDa subunit of cleavage factor Im in Hela cells alters alternative polyadenylation within 3′-UTRs. Nucleic Acids Res 2006; 34:6264-71; PMID:17098938; http://dx.doi.org/10.1093/nar/gkl794.
26. Mayr C, Bartel DP. Widespread shortening of 3′UTRs by alternative cleavage and polyadenylation activates oncogenes in cancer cells. Cell 2009; 138:673-84; PMID:19703394; http://dx.doi.org/10.1016/j.cell.2009.06.016.
27. Matsuoka Y, Li X, Bennett V. Adducin: structure, function and regulation. Cell Mol Life Sci 2000; 57:884-95; PMID:10950304; http://dx.doi.org/10.1007/ PL00000731.
28. Maciolek NL, McNally MT. Serine/arginine-rich proteins contribute to negative regulator of splicing element-stimulated polyadenylation in rous sarcoma virus. J Virol 2007; 81:11208-17; PMID:17670832; http://dx.doi.org/10. 1128/JVI.00919-07.
29. Brackenridge S, Proudfoot NJ. Recruitment of a basal polyadenylation factor by the upstream sequence element of the human lamin B2 polyadenylation signal. Mol Cell Biol 2000; 20:2660-9; PMID:10733568; http://dx.doi.org/10.1128/ MCB.20.8.2660-2669.2000.
30. Hall-Pogar T, Zhang H, Tian B, Lutz CS. Alternative polyadenylation of cyclooxygenase-2. Nucleic Acids Res 2005; 33:2565-79; PMID:15872218; http://dx.doi.org/10.1093/nar/gki544.
31. Moreira A, Wollerton M, Monks J, Proudfoot NJ. Upstream sequence elements enhance poly(A) site efficiency of the C2 complement gene and are phylogenetically conserved. EMBO J 1995; 14:3809-19; PMID:7641699.
32. Schek N, Cooke C, Alwine JC. Definition of the upstream efficiency element of the simian virus 40 late polyadenylation signal by using in vitro analyses. Mol Cell Biol 1992; 12:5386-93; PMID:1333042.
33. Hu J, Lutz CS, Wilusz J, Tian B. Bioinformatic identification of candidate cis-regulatory elements involved in human mRNA polyadenylation. RNA 2005; 11:1485-93; PMID:16131587; http://dx.doi.org/10.1261/rna.2107305.
34. Blencowe BJ. Exonic splicing enhancers: mechanism of action, diversity and role in human genetic diseases. Trends Biochem Sci 2000; 25:106-10; PMID:10694877; http://dx.doi.org/10.1016/S0968-0004(00)01549-8.
35. Lou H, Neugebauer KM, Gagel RF, Berget SM. Regulation of alternative polyadenylation by U1 snRNPs and SRp20. Mol Cell Biol 1998; 18:4977-85; PMID:9710581.
36. Lou H, Yang Y, Cote GJ, Berget SM, Gagel RF. An intron enhancer containing a 5′ splice site sequence in the human calcitonin/calcitonin gene-related peptide gene. Mol Cell Biol 1995; 15:7135-42; PMID:8524281.
37. McCracken S, Longman D, Johnstone IL, Cáceres JF, Blencowe BJ. An evolutionarily conserved role for SRm160 in 3′-end processing that functions independently of exon junction complex formation. J Biol Chem 2003; 278:44153-60; PMID:12944400; http://dx.doi.org/10.1074/jbc.M306856200.
38. Martinson HG. An active role for splicing in 3′-end formation. Wiley Interdiscip Rev RNA 2011; 2:459-70; PMID:21957037; http://dx.doi.org/10. 1002/wrna.68.
39. Boelens WC, Jansen EJ, van Venrooij WJ, Stripecke R, Mattaj IW, Gunderson SI. The human U1 snRNP-specific U1A protein inhibits polyadenylation of its own pre-mRNA. Cell 1993; 72:881-92; PMID:8458082; http://dx.doi.org/10.1016/0092- 8674(93)90577-D.
40. Brogna S, Wen J. Nonsense-mediated mRNA decay (NMD) mechanisms. Nat Struct Mol Biol 2009; 16:107-13; PMID:19190664; http://dx.doi.org/10.1038/nsmb. 1550.