Extended Data Fig. 10: An A-rich element in 5’UTR promotes translation-independent decay.
From: Decoding mRNA translatability and stability from the 5′ UTR
a, HEK293-Kb cells were transfected with 10A or 10C mRNA reporters capped with m7G (right) or ApppG (left), followed by RT-qPCR at indicated time points. (n = 3 biological replicates; t test). Error bars indicate SEM. b, The left panel shows the distribution of in vitro half-lives of mRNA reporters. The most stable (top 10%) sequences are highlighted in red, and the most unstable sequences are highlighted in light blue. The right panel shows the heat map of base frequency at different positions of random sequences. c, A violin plot shows half-life of mRNAs groups with different number of continuous As in random sequences. d, A heat map shows the effect of A-cluster length and position on the in vitro half-life of mRNA reporters. e, The in vitro decay of mRNA reporters (10A, 5A, and 4A) in the lysates of HEK293-Kb cells was determined by RT-qPCR at indicated time points. (n = 3 biological replicates; t test). Error bars indicate SEM. f, The in vitro decay of 10A mRNA reporters in the lysates of HEK293-Kb cells with or without UPF1 knockdown was determined by RT-qPCR at indicated time points (left). For the in vivo stability, HEK293-Kb cells with or without UPF1 knockdown were transfected with 10A mRNA reporters followed by RT-qPCR at indicated time points (right). (n = 3 biological replicates; t test). Error bars indicate SEM. g, The in vitro stability of mRNA reporters (10A, M1, and P1) in the lysates of HEK293-Kb cells with CNOT1, PARN, or PAN3 knockdown was determined by RT-qPCR at indicated time points. (n = 3 biological replicates; t test). Error bars indicate SEM. ** P < 0.01.
