Most highly expressed protein-coding genes have a single dominant isoform

Journal of Proteome Research

Volumn 14, Issue 4, 2015, Pages 1880-1887

  Ezkurdia, Iakes ^a   Rodriguez, Jose Manuel ^b   Carrillo De Santa Pau, Enrique ^b   Vázquez, Jesús ^a   Valencia, Alfonso ^b   Tress, Michael L ^b  

^a CENTRO NACIONAL DE INVESTIGACIONES CARDIOVASCULARES CNIC   (Spain)

^b Centro Nacional de Investigaciones Oncológicas   (Spain)

Author keywords

Alternative splicing; Dominant isoforms; Large scale proteomics; Protein function; Protein structure; RNAseq

Indexed keywords

ISOPROTEIN; PEPTIDE;

AMINO ACID SEQUENCE; ARTICLE; CONTROLLED STUDY; DATA BASE; GENE; GENE EXPRESSION; GENE MAPPING; PRIORITY JOURNAL; PROTEIN CODING GENE; PROTEIN FUNCTION; PROTEIN STRUCTURE; PROTEOMICS; RNA SEQUENCE; BIOLOGY; GENETICS; HUMAN; OPEN READING FRAME; PROCEDURES; PROTEIN DATABASE;

EUKARYOTA;

COMPUTATIONAL BIOLOGY; DATABASES, PROTEIN; HUMANS; OPEN READING FRAMES; PEPTIDES; PROTEIN ISOFORMS; PROTEOMICS;

EID: 84926443748     PISSN: 15353893     EISSN: 15353907     Source Type: Journal    
DOI: 10.1021/pr501286b     Document Type: Article

References (39)

1. Pan, Q.; Shai, O.; Lee, L. J.; Frey, B. J.; Blencowe, B. J. Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing Nat. Genet. 2008, 40, 1413-1415
2. Wang, E.; Sandberg, R.; Luo, S.; Khrebtukova, I.; Zhang, L.; Mayr, C.; Kingsmore, S.; Schroth, G.; Burge, C. Alternative isoform regulation in human tissue transcriptomes Nature 2008, 456, 470-476
3. Harrow, J.; Denoeud, F.; Frankish, A.; Reymond, A.; Chen, C. K.; Chrast, J.; Lagarde, J.; Gilbert, J. G.; Storey, R.; Swarbreck, D. GENCODE: producing a reference annotation for ENCODE Genome Biol. 2006, 7, S4
4. Johnson, J.; Castle, J.; Garrett-Engele, P.; Kan, Z.; Loerch, P.; Armour, C.; Santos, R.; Schadt, E.; Stoughton, R.; Shoemaker, D. Genome-Wide Survey of Human Alternative Pre-mRNA Splicing with Exon Junction Microarrays Science 2003, 302, 2141-2144
5. Harrow, J.; Frankish, A.; Gonzalez, J. M.; Tapanari, E.; Diekhans, M.; Kokocinski, F.; Aken, B. L.; Barrell, D.; Zadissa, A.; Searle, S. GENCODE: the reference human genome annotation for The ENCODE Project Genome Res. 2012, 22, 760-774
6. Ezkurdia, I.; del Pozo, A.; Frankish, A.; Rodriguez, J. M.; Harrow, J.; Ashman, K.; Valencia, A.; Tress, M. L. Comparative proteomics reveals a significant bias toward alternative protein isoforms with conserved structure and function Mol. Biol. Evol. 2012, 29, 2265-2283
7. Smith, C. W.; Valcárcel, J. Alternative pre-mRNA splicing: the logic of combinatorial control Trends Biochem. Sci. 2000, 25, 381-388
8. Taneri, B.; Snyder, B.; Gaasterland, T. Distribution of alternatively spliced transcript isoforms within human and mouse transcriptomes J. OMICS Res. 2011, 14, 1-5
9. Djebali, S.; Davis, C. A.; Merkel, A.; Dobin, A.; Lassmann, T.; Mortazavi, A.; Tanzer, A.; Lagarde, J.; Lin, W.; Schlesinger, F. Landscape of transcription in human cells Nature 2012, 14, 101-108
10. Gonzàlez-Porta, M.; Frankish, A.; Rung, J.; Harrow, J.; Brazma, A. Transcriptome analysis of human tissues and cell lines reveals one dominant transcript per gene Genome Biol. 2013, 14, R70
11. Gstaiger, M.; Aebersold, R. Applying mass spectrometry-based proteomics to genetics, genomics and network biology Nat. Rev. Genet. 2009, 10, 617
12. Chang, K.; Georgianna, D.; Heber, S.; Payne, G.; Muddiman, D. Detection of alternative splice variants at the proteome level in Aspergillus flavus J. Proteome Res. 2012, 9, 1209-1217
13. Low, T. Y.; van Heesch, S.; van den Toorn, H.; Giansanti, P.; Cristobal, A.; Toonen, P.; Schafer, S.; Hübner, N.; van Breukelen, B.; Mohammed, S. Quantitative and qualitative proteome characteristics extracted from in-depth integrated genomics and proteomics analysis Cell Rep. 2013, 5, 1469-1478
14. Sheynkman, G. M.; Shortreed, M. R.; Frey, B. L.; Smith, L. M. Discovery and mass spectrometric analysis of novel splice-junction peptides using RNA-Seq Mol. Cell Proteomics 2013, 12, 2341-2353
15. Ning, K.; Nesvizhskii, A. The utility of mass spectrometry-based proteomic data for validation of novel alternative splice forms reconstructed from RNA-Seq data: a preliminary assessment BMC Bioinf. 2010, 11, S14
16. Harte, R. A.; Farrell, C. M.; Loveland, J. E.; Suner, M. M.; Wilming, L.; Aken, B.; Barrell, D.; Frankish, A.; Wallin, C.; Searle, S. Tracking and coordinating an international curation effort for the CCDS Project Database 2012, bas008
17. Rodriguez, J. M.; Maietta, P.; Ezkurdia, I.; Pietrelli, A.; Wesselink, J. J.; Lopez, G.; Valencia, A.; Tress, M. L. APPRIS: annotation of principal and alternative splice isoforms Nucleic Acids Res. 2013, 41, D110-D117
18. Farrah, T.; Deutsch, E. W.; Hoopmann, M. R.; Hallows, J. L.; Sun, Z.; Huang, C. Y.; Moritz, R. L. The state of the human proteome in 2012 as viewed through PeptideAtlas J. Proteome Res. 2013, 12, 162-171
19. Munoz, J.; Low, T. Y.; Kok, Y. J.; Chin, A.; Frese, C. K.; Ding, V.; Choo, A.; Heck, A. J. The quantitative proteomes of human-induced pluripotent stem cells and embryonic stem cells Mol. Syst. Biol. 2011, 7, 550
20. Nagaraj, N.; Wisniewski, J. R.; Geiger, T.; Cox, J.; Kircher, M.; Kelso, J.; Pääbo, S.; Mann, M. Deep proteome and transcriptome mapping of a human cancer cell line Mol. Syst. Biol. 2011, 7, 548
21. Geiger, T.; Wehner, A.; Schaab, C.; Cox, J.; Mann, M. Comparative proteomic analysis of eleven common cell lines reveals ubiquitous but varying expression of most proteins Mol. Cell Proteomics. 2012, 11, M111.014050
22. Kim, M. S.; Pinto, S. M.; Getnet, D.; Nirujogi, R. S.; Manda, S. S.; Chaerkady, R.; Madugundu, A. K.; Kelkar, D. S.; Isserlin, R.; Jain, S. A draft map of the human proteome Nature 2014, 509, 575-581
23. Wilhelm, M.; Schlegl, J.; Hahne, H.; Moghaddas Gholami, A.; Lieberenz, M.; Savitski, M. M.; Ziegler, E.; Butzmann, L.; Gessulat, S.; Marx, H. Mass-spectrometry-based draft of the human proteome Nature 2014, 509, 582-587
24. Ezkurdia, I.; Vázquez, J.; Valencia, A.; Tress, M. L. Analyzing the first drafts of the human proteome. J. Proteome Res. 2014.
25. Shteynberg, D.; Nesvizhskii, A. I.; Moritz, R. L.; Deutsch, E. W. Combining results of multiple search engines in proteomics Mol. Cell Proteomics 2013, 12, 2383-2393
26. Cox, J.; Neuhauser, N.; Michalski, A.; Scheltema, R. A.; Olsen, J. V.; Mann, M. Andromeda: a peptide search engine integrated into the MaxQuant environment J. Proteome Res. 2011, 10, 1794-1805
27. Koenig, T.; Menze, B. H.; Kirchner, M.; Monigatti, F.; Parker, K. C.; Patterson, T.; Steen, J. J.; Hamprecht, F. A.; Steen, H. Robust prediction of the MASCOT score for an improved quality assessment in mass spectrometric proteomics J. Proteome Res. 2008, 7, 3708-3717
28. Lopez, G.; Maietta, P.; Rodriguez, J.-M.; Valencia, A.; Tress, M. L. firestar -advances in the prediction of functionally important residues Nucleic Acids Res. 2011, 39, W235-W241
29. Punta, M.; Coggill, P. C.; Eberhardt, R. Y.; Mistry, J.; Tate, J.; Boursnell, C.; Pang, N.; Forslund, K.; Ceric, G.; Clements, J. The Pfam protein families database Nucleic Acids Res. 2012, 40, D290-D301
30. Palumbo, E.; Djebali, S.; Breschi, A. Blueprint Project CRG Pipeline. February 18, 2013. ftp://ftp.ebi.ac.uk/pub/databases/blueprint//protocols/Analysis-protocols/README-rnaseq-analysis-crg.
31. Quinlan, A. R.; Hall, I. M. BEDTools: a flexible suite of utilities for comparing genomic features Bioinformatics 2010, 26, 841-842
32. Flicek, P.; Ahmed, I.; Amode, M. R.; Barrell, D.; Beal, K.; Brent, S.; Carvalho-Silva, D.; Clapham, P.; Coates, G.; Fairley, S. Ensembl 2013 Nucleic Acids Res. 2013, 41, D48-D55
33. Farajollahi, S.; Maas, S. Molecular diversity through RNA editing: a balancing act Trends Genet. 2010, 26, 221-230
34. Vogel, C.; Marcotte, E. M. Insights into the regulation of protein abundance from proteomic and transcriptomic analyses Nat. Rev. Genet. 2012, 13, 227-232
35. Tsui, S. K.; Chan, P. P.; Cheuk, C. W.; Liew, C. C.; Waye, M. M.; Fung, K. P.; Lee, C. Y. A novel cDNA encoding for a LIM domain protein located at human chromosome 14q32 as a candidate for leukemic translocation Biochem. Mol. Biol. Int. 1996, 4, 747-754
36. Berman, H. M.; Westbrook, J.; Feng, Z.; Gilliland, G.; Bhat, T. N.; Weissig, H.; Shindyalov, I. N.; Bourne, P. E. The Protein Data Bank Nucleic Acids Res. 2012, 28, 235-242
37. Hoffman, L.; Gorbea, C.; Rechsteiner, M. Identification; molecular cloning, and characterization of subunit 11 of the human 26S proteasome FEBS Lett. 1999, 449, 88-92
38. Steijger, T.; Abril, J. F.; Engström, P. G.; Kokocinski, F.; Hubbard, T. J.; Guigó, R.; Harrow, J.; Bertone, P. RGASP Consortium Assessment of transcript reconstruction methods for RNA-seq Nat. Methods. 2013, 10, 1177-1184
39. Lahens, N. F.; Kavakli, I. H.; Zhang, R.; Hayer, K.; Black, M. B.; Dueck, H.; Pizarro, A.; Kim, J.; Irizarry, R.; Thomas, R. S.; Grant, G. R.; Hogenesch, J. B. IVT-seq reveals extreme bias in RNA sequencing Genome Biol. 2014, 15, R86