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. 2018 Jan 24;15(3):359–368. doi: 10.1080/15476286.2017.1384120

Figure 5.

Figure 5.

RNA binding of YBX1. (A) Spatial RNA binding of YBX1. The YBX1-bound reads of the two fusion clones were separated according to specific mapping to either the human (PC12f-Y1hum and PC12f-Y2hum) or the rat genome (PC12f-Y1rat and PC12f-Y2rat). In all analyzed cell lines YBX1 binds its targets mainly in the 3‘-UTR and the coding region. The main difference in human/rat reads bound by YBX1 in the fusion cells is due to the lower annotation of the rat genome leading to the identification of not annotated reads in the condition of PC12f-Y1rat and PC12f-Y2rat. (B) MEME binding sequence analysis. YBX1 binds to the UCUUUNNCAUC-sequence in all three cell lines. (C+D) YBX1 consists of the arginine/proline- (A/P) rich domain, the cold-shock domain (CSD) and the C-terminal domain (CTD) and is highly conserved among species. The conservation is depicted by a grey heatmap and were analyzed by the program PRALINE. Human and rat YBX1 share 97% of the protein sequence with an identical sequence of the RNA-binding CSD.