GSE110014
Global analysis of the actively translating portion of the transcriptome of control and YBX1 depleted proliferating epidermal cells by high-resolution RNA-seq analysis
To investigate the mechanisms underlying the effects of YBX1 depletion on epidermal progenitors, we performed deep RNA-seq analysis of control versus YBX1-depleted proliferating epidermal cells. Since YBX1 can affect both transcription and translation, we analyzed both total mRNA and polysomaly associated mRNAs using sucrose density gradient sedimentation. Deep RNA-seq analysis based on duplicate samples showed that 57 genes were significantly modulated in YBX1 siRNA treated cells at the level of total mRNA as compared to control siRNA cells, while 115 genes exhibited changes in polysomal mRNA, respectively. Considering the predominantly cytosolic localization of YBX1 in the epidermis, we hypothesized that most of the observed transcriptional changes are secondary to changes in YBX1 mediated translational regulation of specific mRNA subsets. To identify such translational targets of YBX1, we analyzed transcripts that were equally expressed within total RNA populations of control and YBX1 siRNA cells but were selectively modulated in the polysomal mRNA fractions of YBX1 depleted cells. Further examination revealed that out of the 96 affected polysomaly associated mRNAs, 39 were most discriminatory in expression in polysomal versus total mRNA. Overall design: Analysis of total mRNA and polysomaly associated mRNAs from epidermal cells transfected with either control or YBX1 siRNAs using sucrose density gradient sedimentation and deep RNA-sequencing.