Pack- Mutator –like transposable elements (Pack-MULEs) induce directional modification of genes through biased insertion and DNA acquisition

Abstract

In monocots, many genes demonstrate a significant negative GC gradient, meaning that the GC content declines along the orientation of transcription. Such a gradient is not observed in the genes of the dicot plant Arabidopsis. In addition, a lack of homology is often observed when comparing the 5′ end of the coding region of orthologous genes in rice and Arabidopsis. The reasons for these differences have been enigmatic. The presence of GC-rich sequences at the 5′ end of genes may influence the conformation of chromatin, the expression level of genes, as well as the recombination rate. Here we show that Pack-Mutator-like transposable elements (PackMULEs) that carry gene fragments specifically acquire GC-rich fragments and preferentially insert into the 5′ end of genes. The resulting Pack-MULEs form independent, GC-rich transcripts with a negative GC gradient. Alternatively, the Pack-MULEs evolve into additional exons at the 5′ end of existing genes, thus altering the GC content in those regions. We demonstrate that Pack-MULEs modify the 5′ end of genes and are at least partially responsible for the negative GC gradient of genes in grasses. Such a unique and global impact on gene composition and gene structure has not been observed for any other transposable elements.gene duplication | gene modification

Transposition of a Rice Mutator-Like Element in the Yeast Saccharomyces cerevisiae

“…In addition, fewer reinsertions occurred in repetitive regions, including telomeres and long terminal repeat retrotransposons, which is consistent with the target specificity of MULEs in plants for low copy sequences (Raizada et al, 2001;Liu et al, 2009). Previous studies showed that MULEs or PackMULEs prefer to insert into the 59 region of genes, with decreasing frequencies toward the 39 region (Dietrich et al, 2002;Liu et al, 2009;Jiang et al, 2011). Among cv Nipponbare's four copies of Os3378, only one of them is located in proximity to a gene (in the 59 region) (Gao, 2012), which is insufficient to determine whether this preference is similar to other MULEs.…”

Mutator and MULE Transposons

“…Pack-MULEs have a propensity to transduplicate GC regions of genes and they tend to insert into the 5′ ends of genes. In some cases, PackMULEs end up constituting the 5′ end of genes, presumably because after insertion, transcript initiates from within the element, a phenomenon that has been documented in both maize and rice (135,138). This raises the intriguing possibility that the observed GC gradient in monocots is at least in part a consequence of millions of years of sequence capture and deposition of GC-rich sequences by Pack-MULEs into the 5′ end of genes.…”

Evolution of Gene Duplication in Plants

“…There are approximately 3,000 rice Pack-MULEs that collectively contain approximately 1,000 fragmented or whole-gene sequences (Jiang et al, 2004). There are a similar number of Helitrons (approximately 2,800) in maize (Zea mays; Du et al, 2009) but only 46 PackMULEs in Arabidopsis (Jiang et al, 2011). This difference potentially reflects the historical difference in TE activity.…”