Alternative polyadenylation sites in rats

A total of 83 WTTS-seq (whole transcriptome termini site sequencing) libraries were constructed individually using total RNA samples derived from several brain tissues of rats. Library sequencing produced a total of 312,092,803 raw reads, but the mapped reads were 240,225,046 (76.97%) on Rnor6.0, while 251,188,567 (80.49%) on mRatBN7.2, respectively. Using 25 reads per clustered site as a cutoff, we identified 173,124 APA sites mapped to the new reference genome, while 167,136 APA sites were assigned to the old reference genome. For Rnor6.0, only 127,460 (76.26%) APA sites were assigned to the genome regions with 18,177 annotated genes. In contrast, 141,399 (81.67%) APA sites were mapped to the 20,102 annotated genes on mRatBN7.2. In brief, our results provide evidence that mRatBN7.2 has improved qualities of both genome assembly and gene annotation in rat. 

Zhou, X., Li, R., Michal, J.J., Wu, X.-L., Liu, Z., Zhao, H., Xia, Y., Du, W., Wildung, M.R., Pouchnik, D.J., et al. (2016). Accurate Profiling of Gene Expression and Alternative Polyadenylation with Whole Transcriptome Termini Site Sequencing (WTTS-Seq). Genetics 203, 683–697.

This work was supported by the National Institute of Food and Agriculture, United States Department of Agriculture under Award Numbers 2016-67015-24470/2020-67015-31733/2022-51300-38058/2023-67015-39566/2023-67015-40080 to ZJ.