The distribution of transposable elements (TEs) in the promoter regions of moso bamboo genes and its influence on downstream genes

Abstract

Transposable elements are abundant in the promoter regions of moso bamboo genome and influence the expression of downstream genes. As important components of animal and plant genomes, transposable elements (TEs) can shape host genomes and regulate gene expression. In the present study, TEs distributed in the promoter regions of moso bamboo genome were systematically investigated with stringy parameters using RepeatMasker. Approximately 85.7% of the promoter regions were anchored into the TE sequences. Among TE families, three types of TEs are preferentially inserted into the promoter regions: hAT-like transposons, miniature inverted-repeat elements (MITEs), and short interspersed elements (SINEs). The TE insertion sites in promoter regions were amplified by PCR. One site (TE-20) exhibited insertion polymorphism. The expression of downstream gene PH01003704G0280 was three to five times higher with the absence of TE-20 than with the presence of it. On the basis of previous studies it was hypothesized that TEs distributed in the promoter regions of four homologs of floral pathway integrators (FPIs) might be responsible for the observed low expression level. To test the hypothesis, four promoter sequences with TE insertions and TE deletions were inserted upstream of the open reading frame of the β-glucuronidase (GUS) gene and green fluorescent protein (GFP) reporter genes. The expression level of downstream genes was higher with TE deletions than with TE insertions. These results show that the TEs are abundant in the promoter regions and influence the expression of downstream genes in moso bamboo genome.