Fig. 7

Expression analysis of novel transcripts and genes. a The log₂ expression fold changes of MAML2 and ESYT2 novel and canonical transcripts following etoposide or imatinib treatment compared to the DMSO-treated control (left and middle). (Right) Red and blue arrows indicate the RT-qPCR primers designed for novel and canonical transcript respectively. b The log₂ expression fold change of InSETGs under etoposide or imatinib treatment. c Comparison of the log₂ relative expression levels of canonical transcripts, InSETTs and InSETGs following the treatments with etoposide or DMSO control. d The log₂ expression fold changes of canonical transcripts, InSETTs and InSETGs under etoposide treatment compared to the DMSO-treated control. e The distribution of log₂ relative expression level of canonical transcripts, InSETTs and InSETGs before and after etoposide treatment. f Illustration of the hypothetical model proposed in this study to explain expression level and functionality of transcripts containing novel functional exons. Under normal growth condition, the expression level of novel transcripts is below the detection limit explaining why they remain unannotated. With stress, their expression level increases significantly, presumably to improve cell fitness and survivability. Thus, these transcripts represent a hidden layer of elements required for cellular fitness in response to stress. For a, b, error bars indicate the SE of a total of 6 technical replicates corresponding to 2 biological replicates. Asterisks indicate significant differences under two-sided paired Student’s t test (p value < 0.05). Panels c–e are based on RT-qPCR experiments (a total of 6 technical replicates corresponding to 2 biological replicates, each dot represents a technical replicate) of all novel transcripts and genes and known genes profiled in this study. For InSETTs, only the ones with connection to known genes were included. In the boxplots, center lines indicate median; box limits indicate upper and lower quartiles; whiskers extend from the box limits no more than 1.5× interquartile range. Two-sided Welch’s t test was performed with the p values shown in the figures. Source data are provided in Additional file 2: Tables S18 and S19