Long non-coding RNAs (lncRNAs) have been identified as key regulators of gene expression and participate in many vital physiological processes. Chromatin remodeling, being an important epigenetic modification, has been identified in many biological activities as well. However, the regulatory mechanism of lncRNA in chromatin remodeling remains unclear. In order to characterize the genome-wide lncRNA expression and their potential interacting factors during this process in , we investigated the expression pattern of lncRNAs and mRNAs based on the transcriptome analyses and found significant differences between lncRNAs and mRNAs. Then, we performed TSA-FISH experiments of candidate lncRNAs and their potential interactors that have different functions in embryos to determine their expression pattern. In addition, we also analyzed the expression of transposable elements (TEs) and their interactors to explore their expression in mutants. Our results provide a new perspective for understanding the possible regulatory mechanism of lncRNAs and TEs as well as their targets in chromatin remodeling.