The DOI matches its Crossref record; 62 of the 62 references it cites were found in a registry or an index.
Isoform Diversity and Regulation in Peripheral and Central Neurons Revealed through RNA-Seq
Open accessAbstract
To fully understand cell type identity and function in the nervous system there is a need to understand neuronal gene expression at the level of isoform diversity. Here we applied Next Generation Sequencing of the transcriptome (RNA-Seq) to purified sensory neurons and cerebellar granular neurons (CGNs) grown on an axonal growth permissive substrate. The goal of the analysis was to uncover neuronal type specific isoforms as a prelude to understanding patterns of gene expression underlying their intrinsic growth abilities. Global gene expression patterns were comparable to those found for other cell types, in that a vast majority of genes were expressed at low abundance. Nearly 18% of gene loci produced more than one transcript. More than 8000 isoforms were differentially expressed, either to different degrees in different neuronal types or uniquely expressed in one or the other. Sensory neurons expressed a larger number of genes and gene isoforms than did CGNs. To begin to understand the mechanisms responsible for the differential gene/isoform expression we identified transcription factor binding sites present specifically in the upstream genomic sequences of differentially expressed isoforms, and analyzed the 3' untranslated regions (3' UTRs) for microRNA (miRNA) target sites. Our analysis defines isoform diversity for two neuronal types with diverse axon growth capabilities and begins to elucidate the complex transcriptional landscape in two neuronal populations.
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“Therefore, genes expressed at FPKM values Ͼ0.1 are expressed at statistically significant levels (Ͼ99% confidence)”
From An RNA-Sequencing Transcriptome and Splicing Database of Glia, Neurons, and Vascular Cells of the Cerebral Cortex (2014) · cites this paper as Lerch et al., 2012
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Zhang, Y., Chen, K., Sloan, S. A., Bennett, M. L., Scholze, A. R., O'Keeffe, S., Phatnani, H. P., Guarnieri, P., Caneda, C., Ruderisch, N., et al. (2014) · The Journal of Neuroscience · doi:10.1523/jneurosci.1860-14.2014 · Cited by 4,875
“…assess the accuracy and reliability of our RNA-Seq experiments, we applied a widely used procedure to determine the threshold for reliable FPKM estimation based on optimizing the intersection of falsepositive and false-negative rates (Ramskold et al., 2009; Lerch et al., 2012; Chen et al., 2013).”
BackgroundMethodInfluentialEvolution to the rescue: using comparative genomics to understand long non-coding RNAs
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Transcriptome Analysis of the Human Striatum in Tourette Syndrome
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Zhu, Y., Lyapichev, K. A., Lee, D. H., Motti, D., Ferraro, N. M., Zhang, Y., Yahn, S. L., Soderblom, C., Zha, J., Bethea, J. R., et al. (2017) · Journal of Neuroscience · doi:10.1523/jneurosci.2751-16.2017 · Cited by 130
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Metadata
- Authors
- Lerch, J. K., Kuo, F., Motti, D., Morris, R., Bixby, J. L., & Lemmon, V. P.
- Affiliations
- University of Miami (US)
- Corresponding author
- Bixby, John L.
- Lemmon, Vance P.
- Venue
- PLoS ONE
- Publisher
- Public Library of Science (PLoS)
- Published
- 2012-01-17
- Volume
- 7
- Issue
- 1
- Pages
- e30417
- ISSN
- 1932-6203 (ISSN-L)
- PMC
- PMC3260295
- OpenAlex
- W2064384407
- Cited by
- 50
- References
- 62
- Citations by year
- 2026: 1 · 2023: 4 · 2022: 3 · 2021: 3 · 2020: 5 · 2018: 3 · 2017: 5 · 2016: 7 · 2015: 6 · 2014: 6 · 2013: 4 · 2012: 3
- FWCI
- 2.44
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- PLoS ONE (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
- Figshare (submittedVersion, cc-by)
- Funders
- National Institutes of Health (W81XWH, HD057632)
- National Institute of Neurological Disorders and Stroke (NS059866, R01NS059866)
- Eunice Kennedy Shriver National Institute of Child Health and Human Development (R01HD057632, HD057632)
- 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
- alternative splicing, isoform diversity, sensory neurons, neuronal gene expression, axon growth, transcription factor binding sites, microRNA binding sites, 3' untranslated region, cell type-specific gene expression, transcriptome
- MeSH terms
- Animals, Binding Sites, Cells, Cultured, Central Nervous System, Cerebellum, Ganglia, Spinal, Gene Expression Regulation, Mice, Inbred C57BL, Neurons, Sensory Receptor Cells, Transcription Factors, Cluster Analysis, Logistic Models, Open Reading Frames, Peripheral Nervous System, Protein Isoforms, 5' Untranslated Regions, Gene Expression Profiling, Transcription Initiation Site, MicroRNAs, Mice, Gene Regulatory Networks, High-Throughput Nucleotide Sequencing, Transcriptome
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