Profiling temporal lncRNA dynamics in keratinocyte differentiation

Rationale: The epidermis is the first barrier protecting the body from the external environment, and its development and mainten- ance are tightly regulated by epigenetic mechanisms controlling the temporal dynamics of gene expression. Long non-coding RNAs (lncRNAs) have emerged as key epigenetic modulators of epidermal homeostasis and keratinocyte differentiation. However, a comprehensive temporal characterization of lncRNA expression during keratinocyte differentiation has not yet been conducted. Methods: For this purpose, we utilized an in vitro calcium- induced keratinocyte differentiation model using HaCaT cell line to profile lncRNA expression across stem cell-like, early, and late differentiation stages. Following RNA-sequencing, differentially expressed genes (DEGs) at early and late differentiation stages compared to the stem cell-like stage were identified using DESeq2. Annotation and filtering were performed based on Ensembl (GRCh38.p14), genomic location and structural features of lncRNAs were analyzed using BioMart.