Many roads lead to a plant cistrome: mapping and interpreting transcription factor binding in plants

Ammari M.*, Choudhary A*. and Zander M.

Waksman Institute of Microbiology, Department of Plant Biology, Rutgers State University of New Jersey, Piscataway, NJ, United States

* equal contribution

Elucidating transcription factor (TF) function is essential for advancing our understanding and manipulation of the mechanisms that orchestrate gene expression programs underlying plant growth, development, and resilience. Defining the genomic binding sites of a TF—its cistrome—is particularly critical, as it reveals where TF activity can occur and, when integrated with gene expression and chromatin landscape data, delineates the full scope of TF function. In this review, we highlight the biological factors that shape plant cistromes and, importantly, the potential alterations in cistrome composition that may arise during experimental mapping. We further emphasize recent methodological advances now available to the plant science community and outline future directions for the emerging field of plant cistromics.

https://link.springer.com/article/10.1186/s13059-026-03979-2