Dissection of splicing regulation at an endogenous locus by Zinc-finger nuclease-mediated gene editing

PLoS ONE

Volumn 6, Issue 2, 2011, Pages

  Cristea, Sandra ^a   Gregory, Philip D ^a   Urnov, Fyodor D ^a   Cost, Gregory J ^a  

^a SANGAMO BIOSCIENCES INC   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA PRECURSOR; POLYPYRIMIDINE TRACT BINDING PROTEIN; PROTEIN BAX; UNCLASSIFIED DRUG; ZINC FINGER NUCLEASE PROTEIN; ZINC FINGER PROTEIN; RIBONUCLEASE;

ANIMAL CELL; ARTICLE; BINDING SITE; CHINESE HAMSTER; CONTROLLED STUDY; EXON; EXON SKIPPING; GENE LOCUS; GENE MUTATION; GENE TARGETING; INTRON; NONHUMAN; REGULATORY RNA SEQUENCE; RNA EDITING; RNA SPLICING; ANIMAL; CHEMISTRY; CHO CELL; CRICETULUS; GENETICS; HAMSTER; METABOLISM; MUTAGENESIS; NUCLEOTIDE SEQUENCE;

CRICETULUS GRISEUS; MAMMALIA;

ANIMALS; BASE SEQUENCE; BCL-2-ASSOCIATED X PROTEIN; CHO CELLS; CRICETINAE; CRICETULUS; GENETIC LOCI; MUTAGENESIS; RIBONUCLEASES; RNA SPLICE SITES; RNA SPLICING; ZINC FINGERS;

EID: 79951560263     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0016961     Document Type: Article

References (34)

1. Schwartz S, Ast G, (2010) Chromatin density and splicing destiny: on the cross-talk between chromatin structure and splicing. Embo J 29: 1629-1636.
2. Schwartz S, Meshorer E, Ast G, (2009) Chromatin organization marks exon-intron structure. Nat Struct Mol Biol 16: 990-995.
3. Tilgner H, Nikolaou C, Althammer S, Sammeth M, Beato M, et al. (2009) Nucleosome positioning as a determinant of exon recognition. Nat Struct Mol Biol 16: 996-1001.
4. Kolasinska-Zwierz P, Down T, Latorre I, Liu T, Liu XS, et al. (2009) Differential chromatin marking of introns and expressed exons by H3K36me3. Nat Genet 41: 376-381.
5. Luco RF, Pan Q, Tominaga K, Blencowe BJ, Pereira-Smith OM, et al. (2010) Regulation of alternative splicing by histone modifications. Science 327: 996-1000.
6. Maniatis T, Reed R, (2002) An extensive network of coupling among gene expression machines. Nature 416: 499-506.
7. Proudfoot NJ, Furger A, Dye MJ, (2002) Integrating mRNA processing with transcription. Cell 108: 501-512.
8. Neugebauer KM, (2002) On the importance of being co-transcriptional. J Cell Sci 115: 3865-3871.
9. Bentley D, (2002) The mRNA assembly line: transcription and processing machines in the same factory. Curr Opin Cell Biol 14: 336-342.
10. Kornblihtt AR, de la Mata M, Fededa JP, Munoz MJ, Nogues G, (2004) Multiple links between transcription and splicing. Rna 10: 1489-1498.
11. Hicks MJ, Yang CR, Kotlajich MV, Hertel KJ, (2006) Linking splicing to Pol II transcription stabilizes pre-mRNAs and influences splicing patterns. PLoS Biol 4: e147.
12. Das R, Yu J, Zhang Z, Gygi MP, Krainer AR, et al. (2007) SR proteins function in coupling RNAP II transcription to pre-mRNA splicing. Mol Cell 26: 867-881.
13. Luo MJ, Reed R, (1999) Splicing is required for rapid and efficient mRNA export in metazoans. Proc Natl Acad Sci U S A 96: 14937-14942.
14. Reed R, (2003) Coupling transcription, splicing and mRNA export. Curr Opin Cell Biol 15: 326-331.
15. Carothers AM, Urlaub G, Grunberger D, Chasin LA, (1993) Splicing mutants and their second-site suppressors at the dihydrofolate reductase locus in Chinese hamster ovary cells. Mol Cell Biol 13: 5085-5098.
16. Chen IT, Chasin LA, (1993) Direct selection for mutations affecting specific splice sites in a hamster dihydrofolate reductase minigene. Mol Cell Biol 13: 289-300.
17. O'Neill JP, Rogan PK, Cariello N, Nicklas JA, (1998) Mutations that alter RNA splicing of the human HPRT gene: a review of the spectrum. Mutat Res 411: 179-214.
18. Santiago Y, Chan E, Liu PQ, Orlando S, Zhang L, et al. (2008) Targeted gene knockout in mammalian cells by using engineered zinc-finger nucleases. Proc Natl Acad Sci U S A 105: 5809-5814.
19. Perez EE, Wang J, Miller JC, Jouvenot Y, Kim KA, et al. (2008) Establishment of HIV-1 resistance in CD4+ T cells by genome editing using zinc-finger nucleases. Nat Biotechnol 26: 808-816.
20. Liu PQ, Chan EM, Cost GJ, Zhang L, Wang J, et al. (2009) Generation of a triple-gene knockout mammalian cell line using engineered zinc-finger nucleases. Biotechnol Bioeng 106: 97-105.
21. Malphettes L, Freyvert Y, Chang J, Liu P-Q, Chan E, et al. (2010) Highly-efficient deletion of FUT8 in CHO cell lines using zinc-finger nucleases yields cells which produce completely nonfucosylated antibodies. Biotechnology and Bioengineering 106: 774-783.
22. Urnov FD, Miller JC, Lee YL, Beausejour CM, Rock JM, et al. (2005) Highly efficient endogenous human gene correction using designed zinc-finger nucleases. Nature 435: 646-651.
23. Hockemeyer D, Soldner F, Beard C, Gao Q, Mitalipova M, et al. (2009) Efficient targeting of expressed and silent genes in human ESCs and iPSCs using zinc-finger nucleases. Nat Biotechnol 27: 851-857.
24. Dekelver RC, Choi VM, Moehle EA, Paschon DE, Hockemeyer D, et al. (2010) Functional genomics, proteomics, and regulatory DNA analysis in isogenic settings using zinc finger nuclease-driven transgenesis into a safe harbor locus in the human genome. Genome Res.
25. Orlando SJ, Santiago Y, Dekelver RC, Freyvert Y, Boydston EA, et al. (2010) Zinc-finger nuclease-driven targeted integration into mammalian genomes using donors with limited chromosomal homology. Nucleic Acids Res.
26. Cost GJ, Freyvert Y, Vafiadis A, Santiago Y, Miller JC, et al. (2009) BAK and BAX deletion using zinc-finger nucleases yields apoptosis-resistant CHO cells. Biotechnol Bioeng 105: 330-340.
27. Kol G, Lev-Maor G, Ast G, (2005) Human-mouse comparative analysis reveals that branch-site plasticity contributes to splicing regulation. Hum Mol Genet 14: 1559-1568.
28. Gao K, Masuda A, Matsuura T, Ohno K, (2008) Human branch point consensus sequence is yUnAy. Nucleic Acids Res 36: 2257-2267.
29. Schwartz SH, Silva J, Burstein D, Pupko T, Eyras E, et al. (2008) Large-scale comparative analysis of splicing signals and their corresponding splicing factors in eukaryotes. Genome Res 18: 88-103.
30. Schwartz S, Hall E, Ast G, (2009) SROOGLE: webserver for integrative, user-friendly visualization of splicing signals. Nucleic Acids Res 37: W189-192.
31. Kotecki M, Reddy PS, Cochran BH, (1999) Isolation and characterization of a near-haploid human cell line. Exp Cell Res 252: 273-280.
32. Ruskin B, Greene JM, Green MR, (1985) Cryptic branch point activation allows accurate in vitro splicing of human beta-globin intron mutants. Cell 41: 833-844.
33. Hornig H, Aebi M, Weissmann C, (1986) Effect of mutations at the lariat branch acceptor site on beta-globin pre-mRNA splicing in vitro. Nature 324: 589-591.
34. Sickmier EA, Frato KE, Shen H, Paranawithana SR, Green MR, et al. (2006) Structural basis for polypyrimidine tract recognition by the essential pre-mRNA splicing factor U2AF65. Mol Cell 23: 49-59.