Alternative polyadenylation is a minor feature of primary human muscle differentiation

Alternative polyadenylation has been explored in multiple native and disease transitions. The prevailing hypothesis being that differentiated cells use longer 3’UTRs with more scope for regulation, whereas undifferentiated cells use shorter, less regulated 3’UTRs. Here we describe gene-expression and alternative polyadenylation of human primary myocytes over a time course differentiation. Contrary to expectation, only minor changes to 3’-end choice were detected. To reconcile this finding with published differentiation data in the immortalized C2C12 myocyte cell line, a systematic comparison was undertaken. Less than half the genes differentially expressed in the immortalized model were recapitulated in primary cells, and of these, important metabolic states were either absent, underrepresented or regulated in the opposite direction. A new bioinformatic approach, developed to quantitate the degree of alternative polyadenylation between unrelated experiments demonstrated that alternative polyadenylation was reduced by ~50% with less than 1/10 of the genes that underwent alternative polyadenylation in C2C12 differentiation showing alternative processing in primary muscle differentiation. A possible explanation for this difference was a less pronounced down regulation of the cleavage and polyadenylation factors in the differentiation primary cell. In sum, the data promote the use of primary human myocytes to model muscle biogenesis over immortalized models that may not fully recapitulate human muscle development. Two primary human skeletal muscle cell lines were cultivated in Hams F-10 with 20% Fetal Bovine Serum and basic Fibroblast Growth Factor (bFGF) at 37˚C until 80% confluent. Samples T1 was collected 24h post seeding and T2 was collected at 80% confluence. Cells were differentiating in high glucose Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 2% horse serum. Samples T3, T4, T5 and T6, were collected 1, 3, 5 and 7 days post differentiation respectively. Samples were analyzed via Quant-seq 3'UTR focused deep-sequencing in replicate using the Illumina Hiseq 3000 platform.