# Plant Synthetic Promoters
## 2 Sections of Plant Promoters
### Core Promoter
The analysis of promoters revealed the sequence Wnt/aC/tA/cw (\(-\)4 to +2) in 217 unrelated dicot plants, and aN-nCA (\(-\)2 to +3) in 70 unrelated monocots [95]. Similarly, 171 TATA-box promoters showed T/cCAnM, while 130 TATA-less promoters indicated T/a/cYA/ca/c/tt/a/g (\(-\)2 to +3), where W=A or T, N=any nucleotide of A, C, T, or G, Y=C or T, and M=A or C [95]. A general rule of TSS in _A. thaliana_ and rice is the localization of Y (C or T) at \(-\)1 and R (A or G) at +1 [96]. Besides the TATA-box, an important constituent required for plant transcription initiation is the Inr of the PyTCANTPPy consensus sequence, usually overlapping the TSS (Figure 1) [90; 91]. In plant photosynthesis nuclear genes, the TATA-box is frequently lacking, and its role is played by Inr interacting with the TFIID trans-factor [90; 96]. This interaction is supported by the evolution-conserved downstream promoter element (DPE) A/GGA/TCGTG (_Drosophila melanogaster_) interacting with subunits of TFIID in the form of the heterotetramer dTAFII60-dtAFII40 [97]. Another regulatory sequence found in plant promoters is the Y patch, built from repeated pyrimidine CT or TC dimers, which may alternatively exist as a Y-patch-related motif (TTTCTTCTC) (Figure 1) [96].The fraction of Y patches in plant promoters with distribution peaks around TSS is directionally oriented and methylation sensitive [96]. Moreover, plant promoters with Y-patch and Inr sequences are also generally stronger than those lacking them, suggesting their putative function in a proper organization of an RNA polymerase II preinitiation complex [85]. Some elements of core promoters observed in humans and _D. melanogaster_ were not found in _A. thaliana_, such as the Sp1-binding sites or CpG and BRE elements, referring to the putative specificity of DNA-protein interactions between plants and animals [96; 98]. The analysis of both core promoter types, TATA-box- and TATA-less-containing Inr, suggests that TATA and Inr are not swappable and regulate light-responsive gene expression in a different way. Moreover, the TATA-box core promoters are enriched in AC/CA motifs, conserved around the TSS and immediately downstream in the 5\({}^{\prime}\)-UTR region. However, TATA-less promoters showed a higher percentage of pyrimidine-rich TC/CT motifs around the TSS and immediately downstream in the 5\({}^{\prime}\)-UTR region [99].The putative functional role of these differences in DNA sequences could be explained by X-ray crystallography studies providing details of DNA-protein interactions in both types of core promoters. In _A. thaliana_, three types of core promoters were identified: TATA, GA, and Coreless (Figure 1). An analysis of 10,285 gene promoters indicated that the TATA-containing promoters are relatively long and a short distance from the TSS or CDS [100]. Moreover, their expression profile is high and regulated. In contrast, the Coreless promoters do not contain any elements such as TATA, Y patch, GA, or CA, are relatively short, and are found a long distance from the TSS or CDS. The expression level of these promoters is low, and they are constitutive in nature [100]. Putatively, the transcription initiation in these promoters is controlled by specific and abundant cis-regulatory elements as well as the open nucleosomal status. Another GA type of plant core promoter regulates the expression of constitutive genes and is characterized by a short distance from TSS or CDS [100]. By combining the cap-trapper and massively parallel signature sequencing methods (CT-MPSS), it was possible to identify 158,237 _Arabidopsis_ transcription start site (TSS) tags corresponding to 38,311 TSS loci [101]. The TATA-type promoters (25.1%) are enriched in the Y patch and the Inr motif, and cause high gene expression with sharp-peak TSS clusters. By contrast, the GA type, representing 21.6% of _A. thaliana_ core promoters, is not associated with Y patch or Inr, and contains broad-type TSS clusters [101].