Alternative TSSs are co‐regulated in single cells in the mouse brain
Open accessAbstract
Alternative transcription start sites (TSSs) have been extensively studied genome‐wide for many cell types and have been shown to be important during development and to regulate transcript abundance between cell types. Likewise, single‐cell gene expression has been extensively studied for many cell types. However, how single cells use TSSs has not yet been examined. In particular, it is unknown whether alternative TSSs are independently expressed, or whether they are co‐activated or even mutually exclusive in single cells. Here, we use a previously published single‐cell RNA‐seq dataset, comprising thousands of cells, to study alternative TSS usage. We find that alternative TSS usage is a regulated process, and the correlation between two TSSs expressed in single cells of the same cell type is surprisingly high. Our findings indicate that TSSs generally are regulated by common factors rather than being independently regulated or stochastically expressed.
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Most alternative promoters might be co-expressed in the same cell.
“which suggests that most alternative promoters might be co-expressed in the same cell”
From Alternative promoters in CpG depleted regions are prevalently associated with epigenetic misregulation of liver cancer transcriptomes (2023) · cites this paper as [63]
The Discussion (page unavailable) reports that alternative TSSs were almost always co-expressed in single cells, supporting the general idea. But it distinguishes alternative promoters—TSSs more than 1 kb apart—and says few genes expressed them; the Results (page unavailable) identify only six potential alternative-promoter pairs in the analyzed cells. The paper therefore does not establish that most alternative promoters are co-expressed. (LLM, conf=0.84)
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Self-citationCounting absolute numbers of molecules using unique molecular identifiers
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Nepal, C., & Andersen, J. B. (2023) · Nature Communications · doi:10.1038/s41467-023-38272-4 · Cited by 39 · see citing works
- Authors
- Karlsson, K., Lönnerberg, P., & Linnarsson, S.
- Affiliations
- Stanford Medicine (US)
- Karolinska Institutet (SE)
- Corresponding author
- Linnarsson, Sten
- Venue
- Molecular Systems Biology
- Published
- 2017-05-01
- Volume
- 13
- Issue
- 5
- Pages
- 930-930
- ISSN
- 1744-4292 (ISSN-L)
- PMC
- PMC5448164
- OpenAlex
- W2613027773
- Cited by
- 32
- References
- 4
- Citations by year
- 2026: 1 · 2025: 3 · 2024: 1 · 2023: 3 · 2022: 3 · 2021: 14 · 2020: 2 · 2019: 1 · 2018: 3 · 2017: 1
- FWCI
- 0.78
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Molecular Systems Biology (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)
- Funders
- Vetenskapsrådet (STARGET)
- EC|European Research Council (261063)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- 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
- alternative transcription start sites, single-cell gene expression, co-regulation, mouse brain, cell-type-specific transcription, single-cell RNA sequencing
- MeSH terms
- Animals, Base Sequence, Brain, Gene Expression, Transcription Initiation Site, Mice, Cystatin C, Single-Cell Analysis
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