Journal Article

Specificity landscapes of 40 R2R3‐MYBs reveal how paralogs target different cis‐elements by homodimeric binding

Jiang, Dingkun, Guan, Yuefeng, Lin, Juncheng, Li, Hao, Wu, Jiacheng, Guo, Honghong, Chen, Piaojuan, Zhang, Jilin, Li, Tian, Su, Jiaqing, Zhang, Xinfeng, Liu, Qing, Zhu, Fangjie, Ma, Nana, Chen, Hao, Zhu, Xiaoyue, Wang, Qin

2025

Overview

Paralogous transcription factors (TFs) frequently recognize highly similar DNA motifs. Homodimerization can help distinguish them according to their different dimeric configurations. Here, by studying R2R3‐MYB TFs, we show that homodimerization can also directly change the recognized DNA motifs to distinguish between similar TFs. By high‐throughput SELEX, we profiled the specificity landscape for 40 R2R3‐MYBs of subfamily VIII and curated 833 motif models. The dimeric models show that homodimeric binding has evoked specificity changes for AtMYBs. Focusing on AtMYB2 as an example, we show that homodimerization has modified its specificity and allowed it to recognize additional cis‐regulatory sequences that are different from the closely related CCWAA‐box AtMYBs and are unique among all AtMYBs. Genomic sites described by the modified dimeric specificities of AtMYB2 are conserved in evolution and involved in AtMYB2‐specific transcriptional activation. Collectively, this study provides rich data on sequence preferences of VIII R2R3‐MYBs and suggests an alternative mechanism that guides closely related TFs to respective cis‐regulatory sites. Closely related transcription factor (TF) paralogs are facing the “specificity paradox”—they share similar binding motifs, but their cis‐regulatory targets and physiological roles can be different. By applying high‐throughput SELEX to 40 R2R3‐MYB TFs, this study currently generates the largest data set illustrating the homodimeric specificities of plant TFs, while also reveals a yet unrecognized mechanism to solve the “specificity paradox”—a TF's binding specificity can change drastically upon homodimerization, and become unique across the whole family. Highlights A homodimerization‐based mechanism enables eukaryotes to distinguish paralogous transcription factors. The largest plant SELEX data set illustrates the sequence preferences of 40 VIII R2R3‐MYBs. The high specificity AtMYBs were discovered and named CCWAA‐box.

• Publisher: John Wiley & Sons, Inc,John Wiley and Sons Inc,Wiley
• Subject: Binding sites / cis‐elements / Datasets / DNA binding specificity / Genomes / homodimerization / Ligands / MYB family transcription factors / paralogs / Physiology / Preferences / regulatory noncoding genome / transcriptional regulation