The reprogramming of somatic cells into induced pluripotent stem cells (iPSCs) is a major challenge for medical applications such as regenerative medicine since iPSCs can be used to generate different types of functional differentiated cells. Up to now, strategies aiming at reprogramming somatic cells have been mainly conducted toward the targeting of factors modifying gene expression at the transcriptional level. However, gene expression is a multistep process involving epigenetic and transcriptional regulators, as well as RNA binding proteins and miRNAs regulating mRNA splicing, stability or translation. The different steps of the gene expression process are physically, spatially and temporally interconnected, and each factor involved in this process may itself be controlled by other regulators within that chain of molecular mechanisms. Therefore, understanding the interplay between the different gene expression layers during cell differentiation and cell reprogramming is expected to improve strategies aiming at producing both pluripotent stem cell and differentiated cells.