LAUSR

3‐Methyladenine (3‐MA) is a chemical additive that enhances the specific productivity (q p) in recombinant Chinese hamster ovary (rCHO) cell lines. Different from its widely known function of inhibiting autophagy, 3‐MA has instead shown to increase autophagic flux in various rCHO cell lines. Thus, the mechanism by which 3‐MA enhances the qp requires investigation. To evaluate the effect of 3‐MA on transcriptome dynamics in rCHO cells, RNA‐seq was performed with Fc‐fusion protein–producing rCHO cells treated with 3‐MA. By analyzing genes that were differentially expressed following the addition of 3‐MA during culture, the role of 3‐MA in the biological processes of rCHO cells was identified. One pathway markedly influenced by the addition of 3‐MA was the unfolded protein response (UPR). Having a close relationship with autophagy, the UPR reestablishes protein‐folding homeostasis under endoplasmic reticulum (ER) stress. The addition of 3‐MA increased the expression of key regulators of the UPR, such as Atf4, Ddit3, and Creb3l3, further supporting the idea that the enhancement of ER capacity acts as a key in increasing the qp. Consequently, the downstream effectors of UPR, which include autophagy‐promoting genes, were upregulated as well. Hence, the role of 3‐MA in increasing UPR pathway could have made a salient contribution to the increased autophagic flux in rCHO cells. Taken together, transcriptome analysis improved the understanding of the role of 3‐MA in gene expression dynamics in rCHO cells and its mechanism in enhancing the qp.