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RNA sequencing: advances, challenges and opportunities
Open accessAbstract
In the few years since its initial application, massively parallel cDNA sequencing, or RNA-seq, has allowed many advances in the characterization and quantification of transcriptomes. Recently, several developments in RNA-seq methods have provided an even more complete characterization of RNA transcripts. These developments include improvements in transcription start site mapping, strand-specific measurements, gene fusion detection, small RNA characterization and detection of alternative splicing events. Ongoing developments promise further advances in the application of RNA-seq, particularly direct RNA sequencing and approaches that allow RNA quantification from very small amounts of cellular materials.
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“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 [10]
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“Furthermore, RNAseq is considered the best currently available technique to detect not only the expression of novel genes, but also of genes expressed a very low or extremely high levels [23].”
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“RNA-Seq technology, also known as whole transcriptome shotgun sequencing, is a genome-wide sequencing technology that increases the coverage of DNA sequences (Ozsolak and Milos, 2011; Van Verk et al., 2013; Yi et al., 2018).”
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“Importantly, this method is unbiased, since it can quantify both known and unknown isoforms and transcripts for a given mRNA (Ozsolak and Milos, 2011).”
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“It also provides a more precise digital signal and high-throughput analysis with a broader scope, and is a powerful tool for studying transcriptome complexity (10,13).”
Metadata
- Authors
- Ozsolak, F., & Milos, P. M.
- Affiliations
- Helicos Biosciences (United States) (US)
- Corresponding author
- Ozsolak, Fatih
- Milos, Patrice M.
- Venue
- Nature Reviews Genetics
- Published
- 2010-12-30
- Volume
- 12
- Issue
- 2
- Pages
- 87-98
- ISSN
- 1471-0056 (ISSN-L)
- 1471-0064
- PMC
- PMC3031867
- OpenAlex
- W2060842569
- Semantic Scholar
- cf2841f590819568ab156862c2506ab633493747
- Cited by
- 2,135
- References
- 105
- Citations by year
- 2026: 52 · 2025: 108 · 2024: 113 · 2023: 98 · 2022: 131 · 2021: 152 · 2020: 146 · 2019: 134 · 2018: 141 · 2017: 173 · 2016: 163 · 2015: 169 · 2014: 169 · 2013: 168 · 2012: 152
- FWCI
- 10.78
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature Reviews Genetics (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Funders
- National Human Genome Research Institute (R01HG005230, R44HG005279)
- Topics
- 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
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
- Keywords
- RNA sequencing, transcriptome, direct RNA sequencing, RNA quantification, strand-specific RNA-seq, fusion gene detection, small RNA, alternative splicing
- MeSH terms
- Animals, Humans, RNA, Transcription, Genetic, Alternative Splicing, Sequence Analysis, RNA
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