Fig. 3: Cyclin Y and CDK16 are required for efficient induction of autophagy.

a NIH3T3 cells were transfected with siRNA against Cdk16, Cyclin Y or a control for 72 h and grown in EBSS for 2 h. Proteins were detected as indicated (n = 3). b Representative confocal images of the NIH3T3 treated as in panel a. Endogenous LC3 was stained with the 4E12 antibody to monitor autophagy. Scale bar: 50 µm. c Quantification of the LC3 dots shown in panel b. Statistical significance was measured via unpaired and two-tailed Student’s t-tests and is presented as follows: ***p < 0.001. All error bars indicate SD (n = 3; 100 cells counted for each replicate; siControl vs. siCdk16: t = 10.09, df = 4; siControl vs. siCyclin Y: t = 9.866, df = 4). d NIH3T3 cells were transfected with siControl or siCyclin Y, treated with 200 nM Bafilomycin A1 (Baf. A1) or 3-MA for 2 h, and grown in EBSS for additional 2 h as indicated. Lysates were immunoblotted with the indicated antibodies (n = 2). e Immortalized Cdk16^+/+ and Cdk16^−/− MEFs were treated with 200 nM Baf. A1 for 4 h prior to growth in EBSS for additional 2 h. Proteins were measured by immunoblotting (n = 3). f Representative confocal images of the Cdk16^+/+ and Cdk16^−/− MEFs treated as in panel e. Endogenous LC3 was stained (antibody 4E12) to monitor autophagy. Scale bar: 50 µm. g Quantification of the LC3 dots shown in panel f. Statistical significance was measured via unpaired and two-tailed Student’s t-tests and is presented as follows: *p < 0.05 and ***p < 0.001. All error bars indicate SD (n = 3; 100 cells counted for each replicate; EBSS: t = 10.850, df = 4; Baf. A1: t = 4.58, df = 4; EBSS/Baf. A1: t = 3.978, df = 4). h Human CDK16 was stably expressed in immortalized Cdk16^−/− MEFs ( + CDK16). Control cells were infected with an empty virus. Cells were treated with 200 nM Baf. A1 and grown in EBSS. Proteins were detected as indicated (n = 2). n biological independent replicate. SD standard deviation. Source data are provided as a Source Data file.