Transcriptome analyses to investigate the pathogenesis of RNA splicing factor retinitis pigmentosa

Advances in Experimental Medicine and Biology

Volumn 723, Issue , 2012, Pages 519-525

  Farkas, Michael H ^a   Grant, Greg R ^b   Pierce, Eric A ^a  

^a MASSACHUSETTS EYE AND EAR INFIRMARY   (United States)

^b UNIVERSITY OF PENNSYLVANIA   (United States)

Author keywords

Next Generation Sequencing; Prpf; Retinitis Pigmentosa; RNA Splicing Factors; RNA Seq; Transcriptome

Indexed keywords

MESSENGER RNA PRECURSOR; TRANSCRIPTOME;

BIOINFORMATICS; CONFERENCE PAPER; GENE; GENE MUTATION; GENETIC PROCEDURES; GENETIC TRANSCRIPTION; MOUSE MUTANT; NEXT GENERATION SEQUENCING; NONHUMAN; PATHOGENESIS; PIGMENT EPITHELIUM; PRIORITY JOURNAL; PRPF3 GENE; PRPF31 GENE; PRPF8 GENE; RETINITIS PIGMENTOSA; RNA PROCESSING; RNA SEQUENCE; RNA SPLICING; SMN1 GENE;

HUMANS; RETINITIS PIGMENTOSA; RNA PRECURSORS; RNA SPLICING; RNA-BINDING PROTEINS; TRANSCRIPTOME;

EID: 84855980533     PISSN: 00652598     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-4614-0631-0_65     Document Type: Conference Paper

References (32)

1. Ansorge WJ (2009) Next-generation DNA sequencing techniques. New Biotechnol 25:195-203
2. Beggs JD, Teigelkamp S, Newman AJ (1995) The role of PRP8 protein in nuclear pre-mRNA splicing in yeast. J Cell Sci Suppl 19:101-105
3. Blencowe BJ, Ahmad S, Lee LJ (2009) Current-generation high-throughput sequencing: deepening insights into mammalian transcriptomes. Genes Dev 23:1379-1386
4. Buchholz DE, Hikita ST, Rowland TJ et al (2009) Derivation of functional retinal pigmented epithelium from induced pluripotent stem cells. Stem Cells 27:2427-2434
5. Bult CJ, Eppig JT, Kadin JA et al (2008) The Mouse Genome Database (MGD): Mouse biology and model systems. Nuc Acid Res 36:D724-D728 (Pubitemid 351149814)
6. Bunker CH, Berson EL, Bromley WC et al (1984) Prevalence of retinitis pigmentosa in Maine. Am J Ophthalmol 97:357-365 (Pubitemid 14160551)
7. Carr AJ, Vugler AA, Hikita ST et al (2009) Protective effects of human iPS-derived retinal pigment epithelium cell transplantation in the retinal dystrophic rat. PLoS ONE 4:e8152
8. Farkas MH, Bujakowska K, Krishan, A et al (2010) Characterization of aberrant splicing by next generation high-throughput RNA-seq in mice with targeted mutations in Prpf3, Prpf8, and Prpf31 Invest Ophthalmol Vis Sci 51:ARVO E-Abstract 3667
9. Grainger RJ, Beggs JD (2005) Prp8 protein: At the heart of the spliceosome. RNA 11:533-557 (Pubitemid 40594322)
10. Graziotto JJ, Farkas MH, Bujakowska KM et al (2011) Three gene targeted mouse models of RNA splicing factor RP show late onset RPE and retinal degeneration. Invest Ophthalmol Vis Sci 52(1):190-198
11. Grondahl J (1987) Estimation of prognosis and prevalence of retinitis pigmentosa and Usher syndrome in Norway. Clin Genet 31:255-264 (Pubitemid 17057729)
12. Haim M, Holm NV, Rosenberg T (1992) Prevalence of retinitis pigmentosa and allied disorders in Denmark. I Main results. Acta Ophthalmol (Copenh) 70:178-186
13. Hartong DT, Berson EL, Dryja TP (2006) Retinitis pigmentosa. Lancet 368:1795-1809 (Pubitemid 44739028)
14. Kent WJ (2002) BLAT - the BLAST-like alignment tool. Genome Res 12:656-664 (Pubitemid 34308645)
15. Langmead B, Hansen K, Leek J (2010) Cloud-scale RNA-sequencing differential expression analysis with Myrna. Genome Biol 11:R83
16. Langmead B, Trapnell C, Pop M et al (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10:R25
17. Li H, Homer N (2010) A survey of sequence alignment algorithms for next-generation sequencing. Brief Bioinform 11:473-483
18. Maita H, Kitaura H, Ariga H, Iguchi-Ariga SM (2005) Association of PAP-1 and Prp3p, the products of causative genes of dominant retinitis pigmentosa, in the tri-snRNP complex. Exp Cell Res 302:61-68 (Pubitemid 39482369)
19. McKie AB, McHale JC, Keen TJ et al (2001) Mutations in the pre-mRNA splicing factor gene PRPC8 in autosomal dominant retinitis pigmentosa (RP13). Hum Mol Genet 10:1555-1562 (Pubitemid 32734307)
20. McPherson JD (2009) Next-generation gap. Nat Meth 6:S2-S5
21. Ozsolak F, Goren A, Gymrek M et al (2010) Digital transcriptome profiling from attomole-level RNA samples. Genome Res 20:519-525
22. RetNet (2009) RetNet Web site address. http://www.sph.uth.tmc.edu/Retnet/
23. Shendure J (2008) The beginning of the end for microarrays? Nat Meth 5:585-587 (Pubitemid 351911858)
24. Simon SA, Zhai J, Nandety RS et al (2009) Short-read sequencing technologies for transcriptional analyses. Annu Rev Plant Biol 60:305-333
25. Teng X, Xiao H (2009) Perspectives of DNA microarray and next-generation DNA sequencing technologies. Sci C Life Sci 52:7-16
26. Vithana EN, Abu-Safieh L, Allen MJ et al (2001) A human homolog of yeast pre-mRNA splicing gene, PRP31, underlies autosomal dominant retinitis pigmentosa on chromosome 19q13.4 (RP11). Mol Cell 8:375-381 (Pubitemid 32831554)
27. Wang Z, Gerstein M, Snyder M (2009) RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 10:57-63
28. Xu L, Hu L, Ma K, et al (2006) Prevalence of retinitis pigmentosa in urban and rural adult Chinese: The Beijing Eye Study. Eur J Ophthalmol 16:865-866 (Pubitemid 46174403)
29. Yu J, Hu K, Smuga-Otto K et al (2009) Human induced pluripotent stem cells free of vector and transgene sequences. Science 324:797-801
30. Yu J, Vodyanik MA, Smuga-Otto K et al (2007) Induced pluripotent stem cell lines derived from human somatic cells. Science 318:1917-1920
31. Zhang Z, Lotti F, Dittmar K et al (2008) SMN deficiency causes tissue-specific perturbations in the repertoire of snRNAs and widespread defects in splicing. Cell 133:585-600 (Pubitemid 351636302)
32. Zhao C, Bellur DL, Lu S et al (2009) Autosomal-dominant retinitis pigmentosa caused by a mutation in SNRNP200, a gene required for unwinding of U4/U6 snRNAs. Am J Hum Genet 85:617-627