Alternative TSSs are co‐regulated in single cells in the mouse brain
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 m...
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| Format: | Article |
| Language: | English |
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Springer Nature
2017-05-01
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| Series: | Molecular Systems Biology |
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| Online Access: | https://doi.org/10.15252/msb.20167374 |
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| _version_ | 1849234302248681472 |
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| author | Kasper Karlsson Peter Lönnerberg Sten Linnarsson |
| author_facet | Kasper Karlsson Peter Lönnerberg Sten Linnarsson |
| author_sort | Kasper Karlsson |
| collection | DOAJ |
| description | 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. |
| format | Article |
| id | doaj-art-2e1e0de139fa4ebbb69d3a7fa228dba9 |
| institution | Kabale University |
| issn | 1744-4292 |
| language | English |
| publishDate | 2017-05-01 |
| publisher | Springer Nature |
| record_format | Article |
| series | Molecular Systems Biology |
| spelling | doaj-art-2e1e0de139fa4ebbb69d3a7fa228dba92025-08-20T04:03:12ZengSpringer NatureMolecular Systems Biology1744-42922017-05-0113511010.15252/msb.20167374Alternative TSSs are co‐regulated in single cells in the mouse brainKasper Karlsson0Peter Lönnerberg1Sten Linnarsson2Stanford Cancer Institute, Stanford University School of MedicineLaboratory for Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska InstitutetLaboratory for Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska InstitutetAbstract 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.https://doi.org/10.15252/msb.20167374alternative TSS usageneuronssingle‐cell RNA sequencingtranscriptionUMI |
| spellingShingle | Kasper Karlsson Peter Lönnerberg Sten Linnarsson Alternative TSSs are co‐regulated in single cells in the mouse brain Molecular Systems Biology alternative TSS usage neurons single‐cell RNA sequencing transcription UMI |
| title | Alternative TSSs are co‐regulated in single cells in the mouse brain |
| title_full | Alternative TSSs are co‐regulated in single cells in the mouse brain |
| title_fullStr | Alternative TSSs are co‐regulated in single cells in the mouse brain |
| title_full_unstemmed | Alternative TSSs are co‐regulated in single cells in the mouse brain |
| title_short | Alternative TSSs are co‐regulated in single cells in the mouse brain |
| title_sort | alternative tsss are co regulated in single cells in the mouse brain |
| topic | alternative TSS usage neurons single‐cell RNA sequencing transcription UMI |
| url | https://doi.org/10.15252/msb.20167374 |
| work_keys_str_mv | AT kasperkarlsson alternativetsssarecoregulatedinsinglecellsinthemousebrain AT peterlonnerberg alternativetsssarecoregulatedinsinglecellsinthemousebrain AT stenlinnarsson alternativetsssarecoregulatedinsinglecellsinthemousebrain |