Table 1.
Information of different transcription factors (TFs) in uni- and bi-directional promoters.
| TATA-Less or TATA-Containing Promoters | TF Name | Location | Sequence (5′–3′) | Bidirectional Promoter | Unidirectional Promoter | Mechanism |
|---|---|---|---|---|---|---|
| TATA-box lacking promoters | INR | −3–+5 | YYANWYY | 25.30% [7,59] | 30.80% [7,59] | It can function independently, and together with the TATA box or DPE [7,44,45,59]. |
| BRE | −37–−32 | SSRCGCC | 16.50% [7,59] | 11.10% [7,59] | TFIIB–BRE interaction may play a dominant role in the assembly of the pre-initiation complex and transcription initiation [7,58,59]. | |
| CCAAT | −75–−80 | GGCCAATCT | 12.9% [7,59] | 6.90% [7,59] | Enhances the transcriptional rate [7]. | |
| DPE | +28–+32 | DSWYVY(T) | 46.65% [7,59] | 50.60% [7,59] | It can be recognized by TBP-associated factors (TAFs), such as TAF6 and TAF9 [58,59]. | |
| TATA-box containing promoters | Sp1 | Ubiquitously located near the TSS [66] | GGGGCGG | / | / | Sp1 acts through its zinc finger domain at the carboxyl end to interact with GC rich sequences of downstream target genes [56,57,67]. It binds to the GC-rich box and recruits TFIID to regulate the bidirectional promoter HIV-1 LTR [66,68]. Recognizes the core sequence 5-GGGGCGGG-3 of the target promoter. |
| NF-κB | / | / | / | / | It binds to the DNA sequence: 5-GGGRNYYY-3 [68,69,70]. | |
| TATA | −25–−30 | TATAAA | 9% [59] | 29% [59] | TATA box and INR interact synergistically when they are separated by 25–30 bp [7,44,59,64]. | |
| CpGI | 5′-regions of housekeeping genes and many tissues-specific genes [66] | size: 0.5–2 kb in length | 77% [7,71], enriched binding sites of many transcription factors: Sp1, GABPA, MYC, E2F1, E2F4, Nrf1, YY1, NF-Y [42,72,73]; 86.37% [72]. | 56% [43]; 38%, compared with a bidirectional promoter, more lack GC-pairs [7,71]; 28.48% [72]. | Hypermethylation of a CpGI in the promoter region usually suppresses gene expression [74,75,76], and the promoters of some tumor suppressor genes are hypermethylated in cancer [7,71,77]. Bi-directional genes tend to relate to housekeeping functions in metabolism pathways and nuclear processes [66,72]. |
Information derived from Orekhova and Rubtsov (2013) [7], Lepoivre et al. (2013) [42], Hildebrandt et al. (1992) [43], Silverman et al. (1992) [44], Duart-Garcia and Braunschweig (2014) [45], Gazon et al. (2012) [56], Yoshida et al. (2008) [57], Xie et al. (2007) [58], Yang and Elnitski (2008) [59], Abe and Gemmell (2014) [64], Wierstra (2008) [66], Zanotto et al. (2008) [67], Arpin-André et al. (2014) [68], Bentley et al. (2004) [69], Kobayashi-Ishihara et al. (2012) [70], Tufarelli et al. (2013) [71], Liu et al. (2011) [72], Lin et al. (2007) [73], Li et al. (2011) [74], Weber et al. (2010) [75], Rao et al. (2013) [76] and Shu et al. (2006) [77]. (DNA fragment no less than 500 bp with a GC-content ≥55% and Obs/Exp value ≥0.60). R, N, and Y denote for any purine, any pyrimidine, and any nucleotide, respectively.