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Alternative isoform regulation in human tissue transcriptomes
Open accessAbstract
Through alternative processing of pre-messenger RNAs, individual mammalian genes often produce multiple mRNA and protein isoforms that may have related, distinct or even opposing functions. Here we report an in-depth analysis of 15 diverse human tissue and cell line transcriptomes on the basis of deep sequencing of complementary DNA fragments, yielding a digital inventory of gene and mRNA isoform expression. Analyses in which sequence reads are mapped to exon-exon junctions indicated that 92-94% of human genes undergo alternative splicing, 86% with a minor isoform frequency of 15% or more. Differences in isoform-specific read densities indicated that most alternative splicing and alternative cleavage and polyadenylation events vary between tissues, whereas variation between individuals was approximately twofold to threefold less common. Extreme or 'switch-like' regulation of splicing between tissues was associated with increased sequence conservation in regulatory regions and with generation of full-length open reading frames. Patterns of alternative splicing and alternative cleavage and polyadenylation were strongly correlated across tissues, suggesting coordinated regulation of these processes, and sequence conservation of a subset of known regulatory motifs in both alternative introns and 3' untranslated regions suggested common involvement of specific factors in tissue-level regulation of both splicing and polyadenylation.
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“Direct sequencing of RNA libraries also provides the opportunity to explore alternative splicing, a key mechanism that contributes to transcriptome diversity (Pan et al., 2008;Wang et al., 2008).”
From An RNA-Sequencing Transcriptome and Splicing Database of Glia, Neurons, and Vascular Cells of the Cerebral Cortex (2014) · cites this paper as Wang et al., 2008
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“RNA sequencing (RNA-seq) studies indicate that ~93% of human genes undergo alternative splicing and about 86% have a minor isoform frequency above 15% (ref. 11).”
From How many human proteoforms are there? (2018) · cites this paper as [11]
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In the citing paper
“RNA sequencing (RNA-seq) studies indicate that ~93% of human genes undergo alternative splicing and about 86% have a minor isoform frequency above 15% (ref. 11).”
From How many human proteoforms are there? (2018) · cites this paper as [11]
In the citing paper
“RNA-seq experiments have discovered over 100,000 AS transcripts in the human genome (Pan et al., 2008; Wang et al., 2008)”
From Splice-Junction-Based Mapping of Alternative Isoforms in the Human Proteome (2019) · cites this paper as Wang et al., 2008
In the citing paper
“Transcripts from ∼95% of multi-exon human genes are alternatively spliced (Pan et al., 2008, Wang et al., 2008).”
From Impact of Alternative Splicing on the Human Proteome (2017) · cites this paper as Wang et al., 2008
In the citing paper
“Several recent findingspropose that Rbfox can also regulate alternative polyadenylation (Wang et al., 2008) and mRNA stability (Ray et al., 2013), based on analysis of Rbfox motif sites in 3′ UTRs that are correlated with transcript abundance in different tissues.”
From HITS-CLIP and integrative modeling define the Rbfox splicing-regulatory network linked to brain development and autism (2014) · cites this paper as Wang et al., 2008
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Cites
Initial sequencing and analysis of the human genome
International Human Genome Sequencing Consortium, Whitehead Institute for Biomedical Research, C. F. G. R., Lander, E. S., Linton, L. M., Birren, B., Nusbaum, C., Zody, M. C., Baldwin, J., Devon, K., Dewar, K., et al. (2001) · Nature · doi:10.1038/35057062 · Cited by 24,216
Mapping and quantifying mammalian transcriptomes by RNA-Seq
Mortazavi, A., Williams, B. A., McCue, K., Schaeffer, L., & Wold, B. (2008) · Nature Methods · doi:10.1038/nmeth.1226 · Cited by 13,696
Lewis, B. P., Burge, C. B., & Bartel, D. P. (2005) · Cell · doi:10.1016/j.cell.2004.12.035 · Cited by 11,855
Self-citationMechanisms of Alternative Pre-Messenger RNA Splicing
Black, D. L. (2003) · Annual Review of Biochemistry · doi:10.1146/annurev.biochem.72.121801.161720 · Cited by 2,704
MAQC Consortium, Shi, L., Shi, L., Reid, L. H., Jones, W. D., Shippy, R., Warrington, J. A., Baker, S. C., Collins, P. J., de Longueville, F., et al. (2006) · Nature Biotechnology · doi:10.1038/nbt1239 · Cited by 2,126
Self-citationXie, X., Lu, J., Kulbokas, E. J., Golub, T. R., Mootha, V., Lindblad-Toh, K., Lander, E. S., & Kellis, M. (2005) · Nature · doi:10.1038/nature03441 · Cited by 1,872
Genome-Wide Survey of Human Alternative Pre-mRNA Splicing with Exon Junction Microarrays
Johnson, J. M., Castle, J. C., Garrett-Engele, P. W., Kan, Z., Loerch, P., Armour, C. D., Santos, R., Schadt, E. E., Stoughton, R. B., & Shoemaker, D. D. (2003) · Science · doi:10.1126/science.1090100 · Cited by 1,418
HITS-CLIP yields genome-wide insights into brain alternative RNA processing
Licatalosi, D. D., Mele, A., Fak, J. J., Ule, J., Kayikci, M., Chi, S. W., Clark, T. A., Schweitzer, A. C., Blume, J. E., Wang, X., et al. (2008) · Nature · doi:10.1038/nature07488 · Cited by 1,352
Understanding alternative splicing: towards a cellular code
Matlin, A. J., Clark, F., & Smith, C. W. J. (2005) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm1645 · Cited by 1,299
Sultan, M., Schulz, M. H., Richard, H., Magen, A., Klingenhoff, A., Scherf, M., Seifert, M., Borodina, T., Soldatov, A., Parkhomchuk, D., et al. (2008) · Science · doi:10.1126/science.1160342 · Cited by 1,293
Research works printed but not linked: 2
- Schroth, G. P., Luo, S. & Khrebtukova, I. Transcriptome analysis using high-throughput DNA sequencing. Methods Mol. Biol. (in the press)
- Pan, Q., Shai, O., Lee, L. J., Frey, B. J. & Blencowe, B. J. Deep surveying of alternative splicing complexity in the human genome by next generation sequencing. Nature Genet. (in the press)
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Sessions, O. M., Tan, Y., Goh, K. C., Liu, Y., Tan, P. B. O., Rozen, S., & Ooi, E. E. (2013) · PLoS neglected tropical diseases · doi:10.1371/journal.pntd.0002107 · Cited by 84
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Mane, S. P., Evans, C., Cooper, K., Crasta, O. R., Folkerts, O., Hutchison, S. K., Harkins, T. T., Thierry‐Mieg, D., Thierry‐Mieg, J., & Jensen, R. V. (2009) · BMC Genomics · doi:10.1186/1471-2164-10-264 · Cited by 84
Shi, Y., & He, M. (2014) · Gene · doi:10.1016/j.gene.2014.01.031 · Cited by 84
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Wang, Y., Zhou, Z., Gao, J., Wu, Y., Xia, Z., Zhang, H., & Wu, J. (2016) · Frontiers in Plant Science · doi:10.3389/fpls.2016.01654 · Cited by 84
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Transcriptome of embryonic and neonatal mouse cortex by high-throughput RNA sequencing
Han, X., Wu, X., Chung, W.-Y., Li, T., Nekrutenko, A., Altman, N. S., Chen, G., & Ma, H. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0902417106 · Cited by 83
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Michalski, D., Valles, J. G. O., Russo, J., Charley, P. A., Anderson, J. R., Heck, A. M., Geiss, B. J., & Wilusz, J. (2019) · Journal of Biological Chemistry · doi:10.1074/jbc.ra119.009129 · Cited by 83
Nie, M., Chen, N., Pang, H., Jiang, T., Jiang, W., Tian, P., Yao, L., Chen, Y., DeBerardinis, R. J., Li, W., et al. (2022) · Journal of Clinical Investigation · doi:10.1172/jci160152 · Cited by 83
Oppenheim, S. J., Baker, R. H., Simon, S., & DeSalle, R. (2014) · Insect Molecular Biology · doi:10.1111/imb.12154 · Cited by 83
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Moran‐Jones, K., Grindlay, J., Jones, M. D., Smith, R., & Norman, J. C. (2009) · Cancer Research · doi:10.1158/0008-5472.can-09-1852 · Cited by 83
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Sharma, S., & Schiller, M. R. (2019) · Critical Reviews in Biochemistry and Molecular Biology · doi:10.1080/10409238.2019.1586828 · Cited by 83
Wang, G., Wu, Y., Wei, Y., Zhang, X., Li, Y., Li, L., Wen, B., Yin, P., Guo, L., & Cao, M. (2014) · ChemPlusChem · doi:10.1002/cplu.201300345 · Cited by 82
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Metadata
- Authors
- Wang, E. T., Sandberg, R., Luo, S., Khrebtukova, I., Zhang, L., Mayr, C., Kingsmore, S. F., Schroth, G. P., & Burge, C. B.
- Affiliations
- Massachusetts Institute of Technology (US)
- Karolinska Institutet (SE)
- Illumina (United States) (US)
- Whitehead Institute for Biomedical Research (US)
- National Center for Genome Resources (US)
- Corresponding author
- Burge, Christopher B.
- ORCID
- Venue
- Nature
- Published
- 2008-11
- Volume
- 456
- Issue
- 7221
- Pages
- 470-476
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- PMC
- PMC2593745
- OpenAlex
- W2155804510
- Cited by
- 5,181
- References
- 41
- Citations by year
- 2026: 172 · 2025: 222 · 2024: 253 · 2023: 254 · 2022: 317 · 2021: 364 · 2020: 294 · 2019: 304 · 2018: 266 · 2017: 262 · 2016: 294 · 2015: 316 · 2014: 345 · 2013: 347 · 2012: 376
- FWCI
- 108.59
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- Funders
- National Human Genome Research Institute (R01HG002439)
- National Cancer Institute (P30CA008748)
- National Institute of General Medical Sciences (R01GM085319)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA regulation and disease
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Keywords
- alternative splicing, mRNA isoforms, tissue-specific gene expression, exon-exon junctions, sequence conservation, 3' untranslated region, human transcriptome, human cell lines, splicing regulation
- MeSH terms
- RNA Splicing Factors, Base Sequence, Cell Line, Exons, Humans, Organ Specificity, Repressor Proteins, RNA, Messenger, Open Reading Frames, RNA-Binding Proteins, Alternative Splicing, Protein Isoforms, Gene Expression Profiling, Polyadenylation
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