Fig. 3: scUTRquant analysis of diverse cell types demonstrates that changes in gene expression and 3′UTR length are independent gene regulatory events.
From: Quantifying 3′UTR length from scRNA-seq data reveals changes independent of gene expression
a scUTRquant pipeline schematic. Inputs are scRNA-seq raw data and a truncated CS annotation file. The txcutr tool generates truncated UTRomes for any genome. Outputs are quality control parameters and count matrices for gene and 3′UTR expression. The 3′UTR count output can be used as input for scUTRboot to identify significant differences across known cell types. b Fraction of all multi-UTR genes with dominant isoform switch in at least one cell type across 234 human and 82 mouse cell types. c Heatmap showing DGE for single- and multi-UTR genes between mouse HSC and Ery. DGE was tested with Welch t-test ( | FC | > 1.5, q-value < 0.05), with 1059 genes increasing and 252 genes decreasing expression between Ery and HSC. HSC, hematopoietic stem cell, Prog1, progenitor cell type 1, Prog2, progenitor cell type 2, MEP, myeloid-erythroid progenitor, ProE, pro-erythroblast, Baso1, basophilic erythroblast 1, Baso2, basophilic erythroblast 2, Ery, polychromatic erythroblast. d As in (c), but shown is DUL for multi-UTR genes, calculated with scUTRboot’s WUI bootstrap test (difference in WUI > 0.10, q-value < 0.05). Across the differentiation trajectory, 3′UTR lengthening and shortening is observed in 362 and 1275 genes, respectively. e Example gene (mouse Rac1) with significant DUL, but not significant DGE. Box shows median and IQR; whiskers are 95% confidence intervals for TPM (left) and WUI (right). Numbers of cells expressing the gene are indicated. f As in (e), but example gene (mouse Pim1) with significant DGE, but not significant DUL. g, As in (c) and (d), but pair-wise cell type comparisons were performed. Shown is significant DGE of single- and multi-UTR genes. For multi-UTR genes, DUL only or DUL and DGE is also shown. MEF, mouse embryonic fibroblast; ODC, oligodendrocyte; MG, microglia; OPC, oligodendrocyte precursor; epi, epithelial cell; mes, mesenchymal cell; imm, immature; lum, luminal cell; mamm, mammary; neuroendo, neuroendocrine. h As in (g), but the fraction of DUL genes relative to the number of expressed multi-UTR genes is shown, when using two different CS annotations as input for scUTRquant.
