Transcriptome analysis reveals negative correlation between transcripts of mitochondrial genes and L1HS, and positive correlation between KRAB-ZFPs and older LINE elements in normal somatic tissue

Despite the long-held assumption that transposons are normally only expressed in the germ-line, recent evidence shows that transcripts of LINE sequences are frequently found in the somatic cells. However, the extent of variation in LINE transcript levels across different tissues and different individuals, and the genes and pathways that are co-expressed with LINEs are unknown. Here we report the variation in LINE transcript levels across tissues and between individuals observed in the normal tissues collected for The Cancer Genome Atlas. Mitochondrial genes and ribosomal protein genes were enriched among the genes that showed negative correlation with L1HS in transcript level. We hypothesize that oxidative stress is the factor that leads to both repressed mitochondrial transcription and LINE over-expression. KRAB zinc finger proteins (KZFPs) were enriched among the transcripts positively correlated with older LINE families. The correlation between transcripts of individual LINE loci and individual KZFPs showed highly tissue-specific patterns. There was also a significant enrichment of the corresponding KZFPs binding motif in the sequences of the correlated LINE loci, among KZFP-LINE locus pairs that showed co-expression. These results support the KZFP-LINE interactions previously identified through ChIP-seq, and provide information on the in vivo tissue context of the interaction.