TY  - JOUR
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
Y1  - 2021/12/01 
JF  - Genome Research 
JO  - Genome Research 
SP  - 2276 
EP  - 2289 
DO  - 10.1101/gr.275658.121 
VL  - 31 
IS  - 12 
UR  - http://genome.cshlp.org/content/31/12/2276.abstract 
N2  - 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. 
ER  -