LncRNA HOTAIR in adipogenesis: transcriptomic and functional characterization

Abstract

Human adipose tissue depots are physiologically different, with distinct metabolic properties and contributions to disease. The underlying mechanisms for these differences are yet to be uncovered. Large-scale transcriptomic studies of human adipose tissues have identified HOX genes, particularly the lncRNA HOTAIR, as the most differentially expressed gene between upper and lower body adipose depots. However, the role of HOTAIR and its regulation during adipogenesis are not fully elucidated. To gain a deeper understanding of HOTAIR regulation during adipogenic differentiation of adipose stem cells (ASCs), we have performed a de novo annotation of HOTAIR transcripts. Using long-read PacBio sequencing, we uncover a tightly regulated shift in isoform composition upon induction of adipogenesis. Our results highlight the complexity and cell type-specificity of HOTAIR isoforms and open perspectives on the functional implications of these variants and their balance to key cellular processes. We further explored the function of HOTAIR during adipogenesis by performing stable knockdown. We find that upon adipogenic commitment, HOTAIR regulates protein synthesis and cytoskeleton remodeling pathways, later impacting mature adipocyte lipid storage capacity. Our results support novel and important functions of HOTAIR in the physiological context of adipogenesis. The emerging link between translation regulation and cytoskeleton prompted us to investigate the nucleolar dynamics during adipogenesis, a system where cytoskeletal remodeling is crucial. Altogether, our results point to nucleolar remodeling as an active, mechano-regulated mechanism during adipogenic differentiation and demonstrate a key role of the actin cytoskeleton in defining nuclear and nucleolar architecture in differentiating ASCs. This thesis includes three research articles, two of which are dedicated to lncRNA HOTAIR and one to nucleolar dynamics during differentiation. Although primarily relevant in an adipose tissue context, the results presented in this thesis will be of interest to researchers working with other cellular models where cells transit from state to state.