Genome-Wide Identification of Long Noncoding RNA and Their Potential Interactors in ISWI Mutants

Abstract

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 Drosophila, 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 Drosophila 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 ISWI 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.

Characteristics and expression of lncRNA and transposable elements in Drosophila aneuploidy

“…According to genomic positions, lncRNAs were divided into four types: long intergenic noncoding RNA (lincRNA, 56.4%), intronic-lncRNA (17.1%), sense-lncRNA (4.3%), and antisense-lncRNA (22.2%) ( Figure 1 A). Among them, lincRNA has the highest proportion, accounting for approximately half of all lncRNAs, which is consistent with previous studies 65 , 66 Benefiting from the strand-specific sequencing, which can retain the directional information of transcripts, the proportion of lncRNAs from antisense strands also accounts for more than 20%. The number of mRNA transcripts on each chromosome is much greater than that of lncRNAs, and the number of transcripts is approximately related to chromosome length (Pearson correlation coefficients: lncRNA = 0.932, mRNA = 0.992; p values: lncRNA = 2.20e-3, mRNA = 1.16e-5) ( Figure 1 B).…”

Dynamics and Regulatory Roles of RNA m6A Methylation in Unbalanced Genomes

“…Differential alternative splicing events were identified by rMATS (version 4.2.0) program (Shen et al, 2014) (with the parameters of -t paired --readLength 150 --cstat 0.0001 --libType fr-firststrand). The method of generating the ratio distributions of gene expression changes was as described previously (Zhang et al, 2022). The plots were generated using ggplot2 (version 3. pathway data was obtained from the network (https://www.kegg.jp/).…”