GSE126736
ribosome profiling of cell line models of human breast cancer
We performed ribosome profiling in cell line models of human breast cancer. We profiled 2 representative estrogen receptor-positive (T47D and ZR75-1) and 2 representative triple negative (SUM159PT and MDA-MB-231) cell lines. Translational profiles of a nonmalignant (Human Mammary Epithelial Cells, HMECs) and a nontumorigenic (MCF10A cells) counterparts were also analyzed. We analyzed and compared translational efficiencies, variances of the translational efficiencies, differential gene and transcript expression between malignant and non-malignant cell lines. We performed discriminative motif analysis of the 5'untranslated regions of the transcripts that are commonly transcribed in nonmalignant and malignant cells but preferentially translated in malignant cells and identified common motifs. Some of these motifs are highly similar to the RNA binding motifs of a small list of RNA interacting proteins. This approach led us to identify SRSF1 as an RNA binding protein commonly expressed among all analyzed cell lines that has a pervasive impact on the translational landscape of a representative estrogen receptor-positive and -negative cell line Overall design: Ribosome profiling of 6 different cell lines in at least 2 biological replicates