Extensive amplification of the E2F transcription factor binding sites by transposons during evolution of Brassica species.
Transposable elements (TEs) are major players in genome evolution. The effects of their movement vary from gene knockouts to more subtle effects such as changes in gene expression. It has recently been shown that TEs may contain transcription factor binding sites (TFBSs), and it has been proposed that they may rewire new genes into existing transcriptional networks. However, little is known about the dynamics of this process and its effect on transcription factor binding. Here we show that TEs have extensively amplified the number of sequences that match the E2F TFBS during Brassica speciation, and, as a result, as many as 85% of the sequences that fit the E2F TFBS consensus are within TEs in some Brassica species. We show that these sequences found within TEs bind E2Fa in vivo, which indicates a direct effect of these TEs on E2F-mediated gene regulation. Our results suggest that the TEs located close to genes may directly participate in gene promoters, whereas those located far from genes may have an indirect effect by diluting the effective amount of E2F protein able to bind to its cognate promoters. These results illustrate an extreme case of the effect of TEs in TFBS evolution, and suggest a singular way by which they affect host genes by modulating essential transcriptional networks.
Center for Research in Agricultural Genomics, Consejo Superior de Investigaciones Científicas-Institut de Recerca i Tecnologia Agroalimentàries-Universitat Autònoma de Barcelona-Universitat de Barcelona, Campus Universitat Autònoma de Barcelona, Bellaterra - Cerdanyola del Vallès, 08193, Barcelona, Spain.
Elizabeth
E
Hénaff
Cristina
C
Vives
Bénédicte
B
Desvoyes
Ankita
A
Chaurasia
Jordi
J
Payet
Crisanto
C
Gutierrez
Josep M
JM
Casacuberta
D001483:Base Sequence; D001665:Binding Sites; D001937:Brassica / Q000235:genetics*; D004251:DNA Transposable Elements / Q000235:genetics*; D050684:E2F Transcription Factors / Q000235:genetics*; D019143:Evolution, Molecular; D005784:Gene Amplification; D018506:Gene Expression Regulation, Plant; D049810:Genetic Speciation; D018745:Genome, Plant / Q000235:genetics*; D055029:Inverted Repeat Sequences / Q000235:genetics; D008969:Molecular Sequence Data; D010940:Plant Proteins / Q000235:genetics; D011401:Promoter Regions, Genetic / Q000235:genetics
D004251:DNA Transposable Elements; D050684:E2F Transcription Factors; D010940:Plant Proteins
Arabidopsis lyrata; Arabidopsis thaliana; Brassica rapa; Capsela rubella; MITE; Thelungella halopila; evolution; transcription factor binding site; transcriptional network; transposon