Fig. 6

Profile of the distribution of repeat elements in zebrafish brain tissue transcripts and the relationship with RNA methylation of m1A, m5C, m6A and m7G. A RE expression levels in brain (human brain organoid) tissues of different species as determined by analyzing the corresponding RNA-seq data (RNA-seq data of human brain organoids and mouse brain tissue were downloaded from the GEO database with GSE171719 and GSE39911, respectively); purple and blue represent REs and ERV family members, respectively. B We analyzed the RE expression level (based on count) of RNA-seq data of zebrafish brain tissue (normoxia and hypoxia group) using featureCounts. After removing REs with counts less than 10 and setting 1.5 times the threshold, the differentially expressed REs were calculated and counted. C The distribution of all REs and differentially expressed REs on mRNA. The location information of REs and differentially expressed REs was extracted from the results of featureCounts, and the distribution curve was plotted based on the R package Guitar. D Correlation analysis between REs and miRNA targets of REs predicted by TargetScan. The distribution status of sites of REs and miRNA targets of REs in the 3’UTR was plotted through GuitarPlot. E Analysis of the expression level of methylation-modified REs. Four methylation (m1A, m5C, m6A and m7G) MeRIP-seq datasets were used to calculate the counts of REs using featureCounts software. After removing the REs with counts < 10 and normalizing the results to the logarithm of the expression of all REs, a plot of those four methylated REs was generated