Global Analysis of MRNA Splicing

Overview

Journal RNA

Specialty Molecular Biology

Date 2007 Dec 18

PMID 18083834

Citations 38

Authors

Michael J Moore

Pamela A Silver

Affiliations

Soon will be listed here.

Abstract

Alternative mRNA splicing is a rich source of transcript diversity in eukaryotic cells with broad roles in development and disease. Systems-wide experimental methods have started to define how global splicing regulation shapes complex biological properties and pathways. Here, we review these approaches, describe recent insights they have yielded, and discuss avenues of future investigation.

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References

Paradis C, Cloutier P, Shkreta L, Toutant J, Klarskov K, Chabot B . hnRNP I/PTB can antagonize the splicing repressor activity of SRp30c. RNA. 2007; 13(8):1287-300. PMC: 1924885. DOI: 10.1261/rna.403607. View

Ni J, Grate L, Donohue J, Preston C, Nobida N, OBrien G . Ultraconserved elements are associated with homeostatic control of splicing regulators by alternative splicing and nonsense-mediated decay. Genes Dev. 2007; 21(6):708-18. PMC: 1820944. DOI: 10.1101/gad.1525507. View

Tardiff D, Lacadie S, Rosbash M . A genome-wide analysis indicates that yeast pre-mRNA splicing is predominantly posttranscriptional. Mol Cell. 2006; 24(6):917-29. PMC: 1828117. DOI: 10.1016/j.molcel.2006.12.002. View

Pan Q, Saltzman A, Kim Y, Misquitta C, Shai O, Maquat L . 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. PMC: 1356107. DOI: 10.1101/gad.1382806. View

Maniatis T, Reed R . An extensive network of coupling among gene expression machines. Nature. 2002; 416(6880):499-506. DOI: 10.1038/416499a. View

Mardis E . ChIP-seq: welcome to the new frontier. Nat Methods. 2007; 4(8):613-4. DOI: 10.1038/nmeth0807-613. View

Blanchette M, Green R, Brenner S, Rio D . Global analysis of positive and negative pre-mRNA splicing regulators in Drosophila. Genes Dev. 2005; 19(11):1306-14. PMC: 1142554. DOI: 10.1101/gad.1314205. View

Keene J, Komisarow J, Friedersdorf M . RIP-Chip: the isolation and identification of mRNAs, microRNAs and protein components of ribonucleoprotein complexes from cell extracts. Nat Protoc. 2007; 1(1):302-7. DOI: 10.1038/nprot.2006.47. View

Gama-Carvalho M, Barbosa-Morais N, Brodsky A, Silver P, Carmo-Fonseca M . Genome-wide identification of functionally distinct subsets of cellular mRNAs associated with two nucleocytoplasmic-shuttling mammalian splicing factors. Genome Biol. 2006; 7(11):R113. PMC: 1794580. DOI: 10.1186/gb-2006-7-11-r113. View

10.

Burckin T, Nagel R, Mandel-Gutfreund Y, Shiue L, Clark T, Chong J . Exploring functional relationships between components of the gene expression machinery. Nat Struct Mol Biol. 2005; 12(2):175-82. DOI: 10.1038/nsmb891. View

11.

Clark T, Sugnet C, Ares Jr M . Genomewide analysis of mRNA processing in yeast using splicing-specific microarrays. Science. 2002; 296(5569):907-10. DOI: 10.1126/science.1069415. View

12.

Sugnet C, Srinivasan K, Clark T, OBrien G, Cline M, Wang H . Unusual intron conservation near tissue-regulated exons found by splicing microarrays. PLoS Comput Biol. 2006; 2(1):e4. PMC: 1331982. DOI: 10.1371/journal.pcbi.0020004. View

13.

Blencowe B . Alternative splicing: new insights from global analyses. Cell. 2006; 126(1):37-47. DOI: 10.1016/j.cell.2006.06.023. View

14.

Okoniewski M, Yates T, Dibben S, Miller C . An annotation infrastructure for the analysis and interpretation of Affymetrix exon array data. Genome Biol. 2007; 8(5):R79. PMC: 1929135. DOI: 10.1186/gb-2007-8-5-r79. View

15.

Ule J, Jensen K, Ruggiu M, Mele A, Ule A, Darnell R . CLIP identifies Nova-regulated RNA networks in the brain. Science. 2003; 302(5648):1212-5. DOI: 10.1126/science.1090095. View

16.

Moore M, Schwartzfarb E, Silver P, Yu M . Differential recruitment of the splicing machinery during transcription predicts genome-wide patterns of mRNA splicing. Mol Cell. 2006; 24(6):903-15. DOI: 10.1016/j.molcel.2006.12.006. View

17.

Wang Z, Rolish M, Yeo G, Tung V, Mawson M, Burge C . Systematic identification and analysis of exonic splicing silencers. Cell. 2004; 119(6):831-45. DOI: 10.1016/j.cell.2004.11.010. View

18.

Black D . Mechanisms of alternative pre-messenger RNA splicing. Annu Rev Biochem. 2003; 72:291-336. DOI: 10.1146/annurev.biochem.72.121801.161720. View

19.

Xing Y, Kapur K, Wong W . Probe selection and expression index computation of Affymetrix Exon Arrays. PLoS One. 2006; 1:e88. PMC: 1762343. DOI: 10.1371/journal.pone.0000088. View

20.

Ule J, Stefani G, Mele A, Ruggiu M, Wang X, Taneri B . An RNA map predicting Nova-dependent splicing regulation. Nature. 2006; 444(7119):580-6. DOI: 10.1038/nature05304. View