ArticleMolecular systems biology2017
Alternative TSSs are co-regulated in single cells in the mouse brain.
Article in Molecular systems biology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed, 32 citations in OpenAlex.
- The patterns of alternative TSS usage explain the highly heterogeneous landscape of 5'UTR lengths in eukaryotes.NAR genomics and bioinformatics · 2025Article
- Quantification of single cell-type-specific alternative transcript initiation.bioRxiv : the preprint server for biology · 2025Article
- Multi-landmark alignment of genomic signals reveals conserved expression patterns across transcription start sites.Scientific reports · 2023Article
- Alternative promoters in CpG depleted regions are prevalently associated with epigenetic misregulation of liver cancer transcriptomes.Nature communications · 2023Article
- Article
- Alternative Transcription Start Site Usage and Functional Implications in Pathogenic Fungi.Journal of fungi (Basel, Switzerland) · 2022Review
- Virtual Gene Concept and a Corresponding Pragmatic Research Program in Genetical Data Science.Entropy (Basel, Switzerland) · 2021Review
- Promoter switching in response to changing environment and elevated expression of protein-coding genes overlapping at their 5' ends.Scientific reports · 2021Article
- Deletion of a non-canonical regulatory sequence causes loss of Scn1a expression and epileptic phenotypes in mice.Genome medicine · 2021Article
- Computing the Role of Alternative Splicing in Cancer.Trends in cancer · 2021Review
- High-resolution analysis of cell-state transitions in yeast suggests widespread transcriptional tuning by alternative starts.Genome biology · 2021Article
- Mobile genomics: tools and techniques for tackling transposons.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2020Review
- Article
- NanoPARE: parallel analysis of RNA 5' ends from low-input RNA.Genome research · 2018Article
- Single-cell RNAseq for the study of isoforms-how is that possible?Genome biology · 2018Review
- Consistent inverse correlation between DNA methylation of the first intron and gene expression across tissues and species.Epigenetics & chromatin · 2018Article
- Alternative TSSs are co-regulated in single cells in the mouse brain.Molecular systems biology · 2017Article
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 2 countries.
Funding
Abstract
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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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.