Alternative TSSs are co-regulated in single cells in the mouse brain.

Kasper Karlsson, Peter Lönnerberg, Sten Linnarsson

Molecular systems biology 2017 May 11

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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. © 2017 The Authors. Published under the terms of the CC BY 4.0 license.

Citation

Kasper Karlsson, Peter Lönnerberg, Sten Linnarsson. Alternative TSSs are co-regulated in single cells in the mouse brain. Molecular systems biology. 2017 May 11;13(5):930