iCREPCP:A deep learning-based web server for identifying base-resolution cis-regulatory elements within plant core promoters

Dear Editor,A central question of plant biology is how to specify the temporal and spatial patterns as well as the quantitative levels of gene expression,which are significantly associated with important agronomic traits.There has been a growing consensus in the past decade that the two key factors determining gene expression level are cis-regulatory modules(CRMs)and trans-acting factors(TAFs)(Schmitz et al.,2022).Common CRMs include gene-proximal promoters and distal enhancers,which are both considered to be complex assemblies of cis-regulatory elements(CREs).It is the binding or interaction between CREs and TAFs(often transcription factors[TFs])in a ubiquitous or cell-specific manner that determines in which cell,at what time,and at what level a gene is expressed.Therefore,the identification of plant CRMs or critical CREs will not only help us understand transcriptional regulatory mechanisms in plants but also serve as an essential prerequisite for plant breeding 4.0—breeding by genome editing(Gao,2021).