Positive Feedback Between GC-Gradient Of Genes and Acquisition By Pack-MULEs In Grasses

The availability of genomic sequences provided new opportunities to decipher how plant genomes evolve. One recent discovery about plant genomes is the abundance of Pack-MULEs, a special group of transposable elements that duplicate, amplify, and recombine gene fragments in many species at a very large scale. Despite the widespread occurrence of Pack-MULEs, their function remains an enigma. Our analysis using maize, rice, and Arabidopsis genomic sequences indicates that the acquisition of genic sequences by Pack-MULEs is not random. Pack-MULEs in grasses specifically acquire and amplify GC-rich gene fragments and preferentially insert into the 5’ end of genes. The resulting GC-rich elements have the ability to form independent transcripts with negative GC gradient, which refers to the decline of GC content along the orientation of transcription of genes. In other cases, Pack-MULEs insert near the 5’ region of “normal” genes, and consequently form additional 5’ exons or replace the original 5’ exon of genes. In this manner, Pack-MULEs raise the GC content of the 5’ termini of genes, modify the gene structure, and contribute to the increased number of genes with negative GC gradient in grasses. Due to the short life span of transposons, the 5’ ends of some normal genes may represent ancient, degenerate Pack-MULEs. As such, the combination of the acquisition bias with the insertion preference of Pack-MULEs would be expected to form a self-perpetuating cycle that would maintain and enhance the negative GC gradient of genes.