Arabidopsis DREB1-type genes DREB1A, DREB1B and DREB1C were identified as transcription factors that bind to a cis-acting element, DRE/CRT.
CBF/DREB-type genes first identified from Arabidopsis encode AP2/ERF domains that bind to a cis-acting element, DRE/CRT with a core sequence A/GCCGAC (Yamaguchi-Shinozaki and Shinozaki 2005; Todaka et al. 2012).
Since LOV1 negatively regulates CO expression, an important question is whether LOV1 directly binds to a cis-acting element within the CO sequence.
KAP1 also binds to a cis-acting promoter element named fibroblast transcription site-1 (FTS-1) which exists in the promoters of genes that are known to modulate a broader EMT transcriptome, including FSP1, Twist, Snail, E-cadherin, β-catenin, vimentin, and α-smooth muscle actin [ 45].
After entering the nucleus, the HIV-1 Rev protein binds to a specific cis-acting element, termed the Rev-responsive element (RRE), within the viral pre-mRNA [10], [11], multimerizes [12], [13] and then facilitates nuclear export of incompletely spliced viral mRNA via the Crm1 nuclear export pathway [14], [15].
This was speculated to be due to a cis-acting element in A1 ensuring lifelong activation by the SOX trio.
In rice and alfalfa (Medicago sativa), two group D MAPK genes (OsBMWK1 and MsTDY1) are induced transcriptionally by pathogen challenge and wounding, respectively [ 36, 46] Activated OsBMWK1 (now annotated as OsMPK17-1 [ 39]) has also been shown to phosphorylate a transcription factor that binds a cis-acting element in the promoter of defence-related genes [ 47].
According to this hypothesis in the dormant gene negative regulators bind to the corresponding cis-acting elements in the promoter and form a "repressosome," this diminishes the binding or transactivating activities of positive regulators to the promoter, thereby preventing Amy32b transcription.
Other regulatory factors could selectively bind to long-range cis-acting elements (such as enhancers, silencers) to regulate transcription of target gene (Dean, 2011; de Laat and Duboule, 2013).
These transcription factors might interact with each other and/or bind to the same cis-acting regulatory elements in the promoter region of target genes.
Previous studies showed that most WRKY proteins can bind to the cognate cis-acting element "C/TTGACT/C" in the promoter or the 5' untranslated regions of target genes [ 21].
