» Literature references

Literature references

The purpose of this section is to provide some literature references and information related to the field of Alternative RNA Splicing. Six main themes have been selected:

 

> SpliceArray™ Publications by Clients and/or Collaborators
> Reviews
> Technology
> Diagnostics
> Biological/Functional Relevance
> Disease/Drug Discovery
> Bio-informatics

 

This selection is by no means exhaustive. Its main purpose is to sensitize the readers to the relevance of alternative RNA Splicing in various fields. ExonHit's authors will do their best effort to periodically update these pages.

 

SpliceArray™ Publications by Clients and/or Collaborators

 

• Hewetson A, Wright-Pastusek AE, Helmer RA, Wesley KA, Chilton BS: Conservation of inter-protein sites in RUSH and RFBP, an ATP11B isoform. Mol Cell Endocrinol. (2008) Sep 24;292(1-2):79-86. PMID: 18584949 

 

• Filippov V, Schmidt EL, Filippova M, Duerksen-Hughes PJ: Splicing and splice factor SRp55 participate in the response to DNA damage by changing isoform ratios of target genes. Gene. (2008) Aug 15;420(1):34-41.PMID: 18571879 

 

• Einstein R, Jordan H, Zhou W, Brenner M, Moses EG and Liggett SB: Alternative splicing of the G protein-coupled receptor superfamily in human airway smooth muscle diversifies the complement of receptors. Proc Natl Acad Sci U S A. (2008) Apr 1;105(13):5230-5. PMID: 18362331 Full Text (PDF)

 

• Lee JH, Horak CE, Khanna C, Meng Z, Yu LR, Veenstra TD and Steeg PS: Alterations in Gemin5 Expression Contribute to Alternative mRNA Splicing Patterns and Tumor Cell Motility. Cancer Res. (2008) Feb 1;68(3):639-44. PMID: 18245461 Full Text (PDF)

 

• Novoyatleva T, Heinrich B, Tang Y, Benderska N, Butchbach MER, Lorson CL, Lorson MA, Ben-Dov C, Fehlbaum P, Bracco L, Burghes AHM, Bollen M and Stamm S: Protein phosphatase 1 binds to the RNA recognition motif of several splicing factors and regulates alternative pre-mRNA processing. Hum Mol Genet. (2008) Jan 1;17(1):52-70. PMID: 17913700

 

• Heinzen EL , Yoon W, Weale ME , Sen A , Wood NW, Burke JR, Welsh-Bohmer KA, Hulette CM, Sisodiya SM and Goldstein DB: Alternative ion channel splicing in mesial temporal lobe epilepsy and Alzheimers disease. Genome Biology. (2007) 8:R32. PMID: 17343748 Full Text (PDF)

 

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Reviews

 

This section provides general review articles related to Alternative Splicing.

 

• Soller M: Pre-messenger RNA processing and its regulation: a genomic perspective. Cell Mol Life Sci. (2006) 63(7-8):796-819. PMID: 16465448

 

• Garcia-Blanco MA: Methods for the study of alternative splicing. Methods. (2005) 37(4):289-91. PMID: 16314257

 

• Stamm S, Ben-Ari S, Rafalska I et al. : Function of alternative splicing. Gene. (2005) 344:1-20. PMID: 15656968

 

• Garcia-Blanco MA, Baraniak AP, and Lasda EL: Alternative splicing in disease and therapy. Nat Biotechnol. (2004) 22(5):535-46. PMID: 15122293  

 

• Faustino NA and Cooper TA: Pre-mRNA splicing and human disease. Genes Dev. (2003) 17(4):419-37. PMID: 12600935

 

• Ladd, A. N., and Cooper, T. A.: Finding signals that regulate alternative splicing in the post-genomic era. Genome Biology (2002) 3 (11):reviews0008.1-0008.16. PMID: 12429065

 

• Maquat, L.E.: Molecular biology. Skiing toward nonstop mRNA decay. Science (2002) 295, 2221-2222. PMID: 11910094

 

• Moore, M.J.: RNA events. No end to nonsense. Science (2002) 298, 370-371. PMID: 12376689

 

• Wagner, E. et al.: mRNA surveillance: the perfect persist. J Cell Sci (2002) 115, 3033-3038. PMID: 12118059

 

• Venter, J.C. et al. : The sequence of the human genome. Science (2001) 291, 1304-1351. PMID: 11181995

 

• Lopez, A.J.: Alternative splicing of pre-mRNA: developmental consequences and mechanisms of regulation. Annu Rev Genet (1998) 32, 279-305. PMID: 9928482

 

• Burge, C. B., Tuschl, T., and Sharp, P. A.: Splicing of precursors to mRNAs by the spliceosomes. In The RNA World II (1999). R. F. Gesteland, T. R. Cech, and J. F. Atkins, eds. (Cold Spring Harbor, New York, Cold Spring Harbor Laboratory Press), pp. 525-560.

 

• Berget, S.M.: Exon recognition in vertebrate splicing. J Biol Chem (1995) 270, 2411-2414. PMID: 7852296

 

• Talerico, M. et al.: Intron definition in splicing of small Drosophila introns. Mol Cell Biol (1994) 14, 3434-3445. PMID: 8164690

 

• Robberson, B.L. et al.: Exon definition may facilitate splice site selection in RNAs with multiple exons. Mol Cell Biol (1990) 10, 84-94. PMID: 2136768  

 

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Technology

 

This section focuses on articles describing technological platforms dedicated to monitoring the expression of splice variants/events and deciphering their functional relevance.

 

• Zhou W, Calciano MA, Jordan H, Brenner M, Johnson S, Wu D, Lei L, Pallares D, Beurdeley P, Rouet F, Gill PS, Bracco L, Soucaille C, Einstein R. : High resolution analysis of the human transcriptome: detection of extensive alternative splicing independent of transcriptional activity. BMC Genet.(2009) Oct 5;10:63. PMID: 19804644

 

• Pando MP, Kotraiah V, McGowan K, Bracco L, and Einstein R: Alternative isoform discrimination by the next generation of expression profiling microarrays. Expert Opin Ther Targets. (2006) 10(4):613-25. PMID: 16848696

* A review of the next generation of microarray products designed to monitor alternative splicing.

 

• Gaur RK: RNA interference: a potential therapeutic tool for silencing splice isoforms linked to human diseases. Biotechniques. (2006) Suppl:15-22. PMID: 16629383

 

• Pan Q, Saltzman AL, Kim YK et al. : Quantitative microarray profiling provides evidence against widespread coupling of alternative splicing with nonsense-mediated mRNA decay to control gene expression. Genes Dev. (2006) 20(2):153-8. PMID: 16418482

* Premature termination codon production was analyzed in the context of alternative spliced events and found to generally be produced at fairly low levels and appear to be independent of nonsense mediated decay.

 

• Shai O, Morris QD, Blencowe BJ, and Frey BJ: Inferring global levels of alternative splicing isoforms using a generative model of microarray data. Bioinformatics. (2006) 22(5):606-13. PMID: 16403798

* Presents an algorithm know as GenASAP (a Bayesian learning method in an unsupervised probability model) that uses data from microarrays with exon body and junction probes to predict levels of alternative splicing.

 

• Kan Z, Garrett-Engele PW, Johnson JM, and Castle JC: Evolutionarily conserved and diverged alternative splicing events show different expression and functional profiles. Nucleic Acids Res. (2005) 33(17):5659-66. PMID: 16195578

* Used a bioinformatic approach by considering splice site conservation as a surrogate for functional significance, and found that alternative splicing plays an important role in enhancing the functional capacity of central nervous system.

 

• Mangasarian A: Alternative RNA splicing and drug target identification. IDrugs. (2005) 8(9):725-9. PMID: 16118693

* A review covering the importance of alternative splicing generating diversity and its impact on drug discovery.

 

• Fehlbaum P, Guihal C, Bracco L, and Cochet O: A microarray configuration to quantify expression levels and relative abundance of splice variants. Nucleic Acids Res. (2005) 33(5):e47. PMID: 15760843

* Demonstration that a microarray probe design consisting of junctions and exons was sufficient to accurately monitor alternative splice events.

 

• Huang X, Li J, Lu L et al. : Novel development-related alternative splices in human testis identified by cDNA microarrays. J Androl. (2005) 26(2):189-96. PMID: 15713825

 

• Zheng Y, Yuan W, Zhou Z, Xu M, and Sha JH: Molecular cloning and expression of a novel alternative splice variant of BRDT gene. Int J Mol Med. (2005) 15(2):315-21. PMID: 15647849

* A cDNA microarray was used to identify a novel alternative splice variant of BRDT gene, named BRDT-NY, presumably involved in testicular function.

 

• Relogio A, Ben-Dov C, Baum M et al. : Alternative splicing microarrays reveal functional expression of neuron-specific regulators in Hodgkin lymphoma cells. J Biol Chem. (2005) 280(6):4779-84. PMID: 15546866

* Using microarrays with exon body and junction probes, found the relative abundance of alternatively spliced isoforms correlates with transformation and tumor grade in Hodgkin lymphoma.

 

• Pan Q, Shai O, Misquitta C et al. : Revealing global regulatory features of mammalian alternative splicing using a quantitative microarray platform. Mol Cell. (2004) 16(6):929-41. PMID: 15610736

* This paper describes a microarray with exon body and junction probes, and a novel algorithm, Gen ASAP to identify significant events that are altered in experimental samples.

 

• Le K, Mitsouras K, Roy M et al. : NuDetecting tissue-specific regulation of alternative splicing as a qualitative change in microarray data. cleic Acids Res. (2004) 32(22):e180. PMID: 15598820

* Developed microarrays to detect alternative splicing using exon body and junction probes, and developed a analytical method to systematically detectdifferences in splicing based on the anti-correlation between the log-ratios of two different samples versus a pool containing both samples.

 

• Zheng Y, Zhou ZM, Yin LL, Li JM, and Sha JH: Molecular cloning and characterization of a novel splicing variant of PIASx. Acta Pharmacol Sin. (2004) 25(8):1058-64. PMID: 15301740

*A new isoform of PIAS family, named PIAS-NY was identified in expression studies on a human testis cDNA microarray and found predominantly expressed in testis, weakly in the pancreas, and almost imperceptibly in the other organs.

 

• Wang H, Hubbell E, Hu JS et al. : Gene structure-based splice variant deconvolution using a microarray platform. Bioinformatics. (2003) 19 Suppl 1:i315-22. PMID: 12855476

* Developed a gene based algorthim to determine variant specific expression values.

 

• Yeakley JM, Fan JB, Doucet D et al. : Profiling alternative splicing on fiber-optic arrays. Nat Biotechnol. (2002) 20(4):353-8. PMID: 11923840

* One of the earliest examples of using exon body probes and junctions to detect alternatively spliced events on a high throughput array platform.

 

• Celotto AM and Graveley BR: Exon-specific RNAi: a tool for dissecting the functional relevance of alternative splicing. Rna. (2002) 8(6):718-24. PMID: 12088145

 

• Hu, G.K. et al.: Predicting splice variant from DNA chip expression data. Genome Res (2001) 11, 1237-1245. PMID: 11435406

 

• Shoemaker, D.D. et al.: Experimental annotation of the human genome using microarray technology. Nature (2001) 409, 922-927. PMID: 11237012 

 

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Diagnostics

 

This section focuses on papers describing the characterization of splice variants with a potential utility as biomarkers for diagnostic, prognostic and pharmacogenomic applications.

 

• André F, Michiels S, Dessen P, Scott V, Suciu V, Uzan C, Lazar V, Lacroix L, Vassal G, Spielmann M, Vielh P, Delaloge S. Exonic expression profiling of breast cancer and benign lesions: a retrospective analysis. Lancet Oncol. (2009) 10(4):381-90. Epub 2009 Feb 25. . PMID: 19249242

 

• Ashida S, Furihata M, Katagiri T et al. : Expression of novel molecules, MICAL2-PV (MICAL2 prostate cancer variants), increases with high Gleason score and prostate cancer progression. Clin Cancer Res. (2006) 12(9):2767-73. PMID: 16675569

 

• Zhang C, Li HR, Fan JB et al. : Profiling alternatively spliced mRNA isoforms for prostate cancer classification. BMC Bioinformatics. (2006) 7:202. PMID: 16608523

 

• Rha SY, Jeung HC, Yang WI et al. : Alteration of hTERT full-length variant expression level showed different gene expression profiles and genomic copy number changes in breast cancer. Oncol Rep. (2006) 15(4):749-55. PMID: 16525654

 

• Pacifico MD, Grover R, Richman PI, Daley FM, Buffa F, and Wilson GD: CD44v3 levels in primary cutaneous melanoma are predictive of prognosis: Assessment by the use of tissue microarray. Int J Cancer. (2006) 118(6):1460-4. PMID: 16187282

 

• Maxwell CA, Rasmussen E, Zhan F et al. : RHAMM expression and isoform balance predict aggressive disease and poor survival in multiple myeloma. Blood. (2004) 104(4):1151-8. PMID: 15105292

 

• Bracco L and Kearsey J: The relevance of alternative RNA splicing to pharmacogenomics. Trends Biotechnol. (2003) 21(8):346-53. PMID: 12902171

 

• Ho L, Guo Y, Spielman L et al. : Altered expression of a-type but not b-type synapsin isoform in the brain of patients at high risk for Alzheimer's disease assessed by DNA microarray technique. Neurosci Lett. (2001) 298(3):191-4. PMID: 11165439  

 

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Biological/ Functional Relevance

 

These selected articles describe how alternative splicing can affect/modulate the function of a gene product and impact its signaling capabilities

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• Heinzen EL , Yoon W, Weale ME , Sen A , Wood NW, Burke JR, Welsh-Bohmer KA, Hulette CM, Sisodiya SM and Goldstein DB: Alternative ion channel splicing in mesial temporal lobe epilepsy and Alzheimers disease. Genome Biology. (2007) 8:R32. PMID: 17343748

* Identified a set of disease-associated alternatively-spliced gene products representing high priorities for detailed functional investigations into how these changes impact pathophysiology in Alzheimer's disease and mesial temporal lobe epilepsy.

 

• Ben-Ari S, Toiber D, Sas AS, Soreq H, and Ben-Shaul Y: Modulated splicing-associated gene expression in P19 cells expressing distinct acetylcholinesterase splice variants. J Neurochem. (2006) 97 Suppl 1:24-34. PMID: 16635247

* Deregulation of alternative splicing and gene expression of acetylcholinesterase (AChE) are both modified during neuronal stress. Overexpression studies of AChE alternative isoforms suggest causal involvement in global changes in neuronal splicing and target gene expression.

 

• Li C, Kato M, Shiue L, Shively JE, Ares M, Jr., and Lin RJ: Cell type and culture condition-dependent alternative splicing in human breast cancer cells revealed by splicing-sensitive microarrays. Cancer Res. (2006) 66(4):1990-9. PMID: 16488998

* The authors use splicing-sensitive microarrays to elucidate breast cancer associated splicing profiles between different cell lines or the same cell line grown in different environments. They clearly detect specific splicing differences between cell lines and growth conditions, illustrating the importance of carefully considering your experimental model.

 

• Ule J, Ule A, Spencer J et al. : Nova regulates brain-specific splicing to shape the synapse. Nat Genet. (2005) 37(8):844-52. PMID: 16041372

* This study describes the striking ability of Nova to specifically regulate the exon content of RNAs encoding proteins that interact in the synapse.

 

• Yoong LF, Peng ZN, Wan G, and Too HP: Tissue expression of alternatively spliced GFRalpha1, NCAM and RET isoforms and the distinct functional consequence of ligand-induced activation of GFRalpha1 isoforms. Brain Res Mol Brain Res. (2005) 139(1):1-12. PMID: 15979200

* This paper describes distinct and not overlapping expression profiles for cells transfected with individual GFRalpha1 isoforms and suggests that the combinatorial interactions of GFRalpha, RET, and NCAM alternative isoforms contribute to pleiotrophic biological responses associated with these genes.

 

• Otun HA, MacDougall MW, Bailey J, Europe-Finner GN, and Robson SC: Spatial and temporal expression of the myometrial mitogen-activated protein kinases p38 and ERK1/2 in the human uterus during pregnancy and labor. J Soc Gynecol Investig. (2005) 12(3):185-90. PMID: 15784503

* This study demonstrates that p38 and ERK1 are spatially regulated during pregnancy and are involved in regulating the activity of ATF2 isoforms.

 

• Hoey T, Zhang S, Schmidt N et al. : Distinct requirements for the naturally occurring splice forms Stat4alpha and Stat4beta in IL-12 responses. Embo J. (2003) 22(16):4237-48. PMID: 12912921

* The authors describe a novel isoform of Stat4, Stat4beta, which lacks a putative transactivation domain. This deletion event is show to have profound effects on gene induction and the regulation of physiological responses to IL-12.

 

• Matter, N., Herrlich, P., and Konig, H.: Signal-dependent regulation of splicing via phosphorylation of Sam68. Nature (2003) 420, 691-695. PMID: 12478298

 

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Disease / Drug Discovery

 

This section focuses on the relevance of splicing in disease and drug discovery.

 

• Montano M, Rarick M, Sebastiani P et al. : Gene-expression profiling of HIV-1 infection and perinatal transmission in Botswana. Genes Immun. (2006). PMID: 16691187

* This study found that HIV-1 infection not only cased initiation of innate response gene-sets but also genes that influence RNA processing and splicing.

 

• Sanchez-Aguilera A, Garcia JF, Sanchez-Beato M, and Piris MA: Hodgkin's lymphoma cells express alternatively spliced forms of HDM2 with multiple effects on cell cycle control. Oncogene. (2006) 25(18):2565-74. PMID: 16331255

* The authors describe multiple and at times apposing functions of various alternative isoforms of the HDM2 oncoprotein. These findings help to further elucidate the role of HDM2 in tumorigenesis.

 

• He B, Mirza M, and Weber GF: An osteopontin splice variant induces anchorage independence in human breast cancer cells. Oncogene. (2006) 25(15):2192-202. PMID: 16288209

* This study shows that a novel splice variant of osteopontin, osteopontin-c, no longer aggregates to promote cell adhesion and enhances clone formation in soft agar assays. They also demonstrate that the osteopontin-c splice variant is a highly specific marker for transformed cells.

 

• Soret J, Bakkour N, Maire S et al. : Selective modification of alternative splicing by indole derivatives that target serine-arginine-rich protein splicing factors. Proc Natl Acad Sci U S A. (2005) 102(24):8764-9. PMID: 15939885  

 

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Bio-informatics

 

This section describes bio-informatics analyses related to the prevalence or the regulation of alternative splicing.

 

• Xing Y, Wang Q, and Lee C: Evolutionary divergence of exon flanks: a dissection of mutability and selection. Genetics. (2006) 173(3):1787-91. PMID: 16702427

 

• Xing Y, Yu T, Wu YN, Roy M, Kim J, and Lee C: An expectation-maximization algorithm for probabilistic reconstructions of full-length isoforms from splice graphs. Nucleic Acids Res. (2006) 34(10):3150-60. PMID: 16757580

 

• Xing Y and Lee C: Alternative splicing and RNA selection pressure--evolutionary consequences for eukaryotic genomes. Nat Rev Genet. (2006) 7(7):499-509. PMID: 16770337

 

• Le Texier V, Riethoven JJ, Kumanduri V et al. : AltTrans: transcript pattern variants annotated for both alternative splicing and alternative polyadenylation. BMC Bioinformatics. (2006) 7:169. PMID: 16556303

 

• Holste D, Huo G, Tung V, and Burge CB: HOLLYWOOD: a comparative relational database of alternative splicing. Nucleic Acids Res. (2006) 34(Database issue):D56-62. PMID: 16381932

 

• Xing Y and Lee CJ: Protein modularity of alternatively spliced exons is associated with tissue-specific regulation of alternative splicing. PLoS Genet. (2005) 1(3):e34. PMID: 16170410

 

• Xing Y and Lee C: Evidence of functional selection pressure for alternative splicing events that accelerate evolution of protein subsequences. Proc Natl Acad Sci U S A. (2005) 102(38):13526-31. PMID: 16157889

 

• Wang J, Smith PJ, Krainer AR, and Zhang MQ: Distribution of SR protein exonic splicing enhancer motifs in human protein-coding genes. Nucleic Acids Res. (2005) 33(16):5053-62. PMID: 16147989

 

• Ohler U, Shomron N, and Burge CB: Recognition of unknown conserved alternatively spliced exons. PLoS Comput Biol. (2005) 1(2):113-22. PMID: 16110330

 

• Han K, Yeo G, An P, Burge CB, and Grabowski PJ: A combinatorial code for splicing silencing: UAGG and GGGG motifs. PLoS Biol. (2005) 3(5):e158. PMID: 15828859

 

• Yeo GW, Van Nostrand E, Holste D, Poggio T, and Burge CB: Identification and analysis of alternative splicing events conserved in human and mouse. Proc Natl Acad Sci U S A. (2005) 102(8):2850-5. PMID: 15708978

 

• Yeo G, Holste D, Kreiman G, and Burge CB: Variation in alternative splicing across human tissues. Genome Biol. (2004) 5(10):R74. PMID: 15461793

 

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