RT Journal
A1 Zhang, Yuyun
A1 Li, Zijuan
A1 Zhang, Yu'e
A1 Lin, Kande
A1 Peng, Yuan
A1 Ye, Luhuan
A1 Zhuang, Yili
A1 Wang, Meiyue
A1 Xie, Yilin
A1 Guo, Jingyu
A1 Teng, Wan
A1 Tong, Yiping
A1 Zhang, Wenli
A1 Xue, Yongbiao
A1 Lang, Zhaobo
A1 Zhang, Yijing
T1 Evolutionary rewiring of the wheat transcriptional regulatory network by lineage-specific transposable elements
JF Genome Research 
JO Genome Research 
YR 2021 
FD December 01 
VO 31 
IS 12 
SP 2276 
OP 2289 
DO 10.1101/gr.275658.121 
UL http://genome.cshlp.org/content/31/12/2276.abstract 
AB More than 80% of the wheat genome consists of transposable elements (TEs), which act as major drivers of wheat genome evolution. However, their contributions to the regulatory evolution of wheat adaptations remain largely unclear. Here, we created genome-binding maps for 53 transcription factors (TFs) underlying environmental responses by leveraging DAP-seq in Triticum urartu, together with epigenomic profiles. Most TF binding sites (TFBSs) located distally from genes are embedded in TEs, whose functional relevance is supported by purifying selection and active epigenomic features. About 24% of the non-TE TFBSs share significantly high sequence similarity with TE-embedded TFBSs. These non-TE TFBSs have almost no homologous sequences in non-Triticeae species and are potentially derived from Triticeae-specific TEs. The expansion of TE-derived TFBS linked to wheat-specific gene responses, suggesting TEs are an important driving force for regulatory innovations. Altogether, TEs have been significantly and continuously shaping regulatory networks related to wheat genome evolution and adaptation.