A Global View of Gene Activity and Alternative Splicing by Deep Sequencing of the Human Transcriptome
Abstract
The functional complexity of the human transcriptome is not yet fully elucidated. We report a high-throughput sequence of the human transcriptome from a human embryonic kidney and a B cell line. We used shotgun sequencing of transcripts to generate randomly distributed reads. Of these, 50% mapped to unique genomic locations, of which 80% corresponded to known exons. We found that 66% of the polyadenylated transcriptome mapped to known genes and 34% to nonannotated genomic regions. On the basis of known transcripts, RNA-Seq can detect 25% more genes than can microarrays. A global survey of messenger RNA splicing events identified 94,241 splice junctions (4096 of which were previously unidentified) and showed that exon skipping is the most prevalent form of alternative splicing.
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RNA-seq provides a powerful tool to decipher global gene expression patterns far beyond the limitations of microarrays.
“RNA deep-sequencing (RNA-seq) provides a powerful tool to decipher global gene expression patterns far beyond the limitations of microarrays, including an unprecedented capability to discover novel genes, alternative transcript variants, chimeric transcripts, and expressed sequence variants as well as allele-specific expression [8–12].”
From Comparison of RNA-seq and microarray-based models for clinical endpoint prediction (2015) · cites this paper as [11]
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- Authors
- Sultan, M., Schulz, M. H., Richard, H., Magen, A., Klingenhoff, A., Scherf, M., Seifert, M., Borodina, T., Soldatov, A., Parkhomchuk, D., Schmidt, D., O'Keeffe, S., Haas, S., Vingron, M., Lehrach, H., & Yaspo, M.-L.
- Affiliations
- Max Planck Society (DE)
- Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Ihnestrasse 73, 14195 Berlin, Germany.
- Corresponding author
- Sultan, Marc
- Schulz, Marcel H.
- Richard, Hugues
- Yaspo, Marie-Laure
- ORCID
- Venue
- Science
- Published
- 2008-08-15
- Volume
- 321
- Issue
- 5891
- Pages
- 956-960
- ISSN
- 0036-8075 (ISSN-L)
- 1095-9203
- OpenAlex
- W2097117811
- Cited by
- 1,293
- References
- 28
- Citations by year
- 2026: 13 · 2025: 27 · 2024: 24 · 2023: 17 · 2022: 44 · 2021: 36 · 2020: 35 · 2019: 64 · 2018: 49 · 2017: 53 · 2016: 66 · 2015: 96 · 2014: 98 · 2013: 125 · 2012: 145
- FWCI
- 54.65
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Science (publishedVersion)
- PubMed (publishedVersion)
- Max Planck Institute for Plasma Physics (submittedVersion)
- MPG.PuRe (Max Planck Society) (submittedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Single-cell and spatial transcriptomics
- Keywords
- human transcriptome, alternative splicing, exon skipping, splice junctions, mRNA expression profiling, gene expression, polyadenylated transcripts, human embryonic kidney cells, B-cell lines
- MeSH terms
- Cell Line, Exons, Humans, Introns, RNA Polymerase II, RNA, Messenger, Genome, Human, Alternative Splicing, Sequence Analysis, RNA, DNA, Complementary, Computational Biology, Oligonucleotide Array Sequence Analysis, Gene Expression Profiling, DNA, Intergenic, RNA Splice Sites, Cell Line, Tumor
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