CGCG box gene transcriptions
A. thaliana is a popular model organism in plant biology and genetics. For a complex multicellular eukaryote, A. thaliana has a relatively small genome of approximately 135 megabase pairs (Mbp).
"The minimum DNA-binding elements are 6-bp CGCG box, (A/C/G)CGCG(C/G/T)."
"AtSR1  targets the nucleus and specifically recognizes a novel 6-bp CGCG box (A/C/G)CGCG(G/T/C). The multiple CGCG cis-elements are found in promoters of genes such as those involved in ethylene signaling, abscisic acid signaling, and light signal perception. The DNA-binding domain in AtSR1 is located on the N-terminal 146 bp where all AtSR1-related proteins share high similarity but have no similarity to other known DNA-binding proteins. The calmodulin-binding nuclear proteins isolated from wounded leaves exhibit specific CGCG box DNA binding activities. These results suggest that the AtSR gene family encodes a family of calmodulin-binding/DNA-binding proteins involved in multiple signal transduction pathways in plants."
"Ca2+-mediated signaling is involved in the transduction of physical signals such as temperature, wind, touch, light, and gravity; oxidative signals such as those arising from pathogen attacks; and hormone signals such as ethylene, abscisic acid (ABA),1 gibberellins, and auxin (2-7). All these signals have been shown to trigger changes in amplitude or oscillation in cytosolic free Ca2+ level. Recently, the signal-induced nuclear free calcium changes were also observed (8). Free Ca2+ changes are sensed by a number of Ca2+-binding proteins that usually contain a common structural motif, the EF-hand, a helix-loop-helix structure (9). One of the best characterized Ca2+-binding proteins is calmodulin (CaM), a highly conserved and multifunctional regulatory protein in eukaryotes. Its regulatory activities are triggered by its ability to modulate the activity of a certain set of CaM-binding proteins after binding to Ca2+, and thereby generating physiological responses to various stimuli (10-15)."
"The CaM-regulated basic helix-loop-helix family of transcription factors was reported in mammals, where CaM inhibits the protein-DNA interaction by competing with the DNA-binding domain in certain proteins (16)."
"cis-acting elements ACGCGG/CCGCGT were present in the promoter regions of about 130 genes (more than two copies) in Arabidopsis genome."
"The promoter regions are assumed to be within 1 kb upstream of the starting transcription site (for the known genes) or the first ATG (for the predicted genes). These genes are related to ethylene signaling (EIN3) and ABA signaling (a putative ABA responsive protein), light perception (phytochrome A, phyA), stress responsive such as the DNA repairing protein, heat shock protein, touch protein (TCH 4), and CaM-regulated ion channel. CaM genes (CaM2 andCaM3) and AtSR6 also contains CGCGcis-elements in their promoter regions."

# CGCG box samplings
For the Basic programs (starting with SuccessablesCGCG.bas) written to compare nucleotide sequences with the sequences on either the template strand (-), or coding strand (+), of the DNA, in the negative direction (-), or the positive direction (+), the programs are, are looking for (A/C/G)CGCG(C/G/T), and found:
- Negative strand, negative direction: 2, CCGCGC at 1761, GCGCGT at 161.
- Negative strand, positive direction: 9, CCGCGC at 1650, CCGCGG at 1437, CCGCGG at 1337, GCGCGT at 1215, ACGCGG at 971, ACGCGG at 871, GCGCGC at 683, CCGCGC at 681, GCGCGT at 543.
- Positive strand, negative direction: 1, GCGCGG at 1762.
- Positive strand, positive direction: 23, CCGCGG at 1769, ACGCGG at 1656, CCGCGT at 1550, ACGCGT at 1523, ACGCGG at 1498, ACGCGG at 1454, ACGCGT at 1414, ACGCGG at 1398, ACGCGG at 1354, ACGCGT at 1314, CCGCGT at 1298, ACGCGG at 1246, CCGCGC at 1214, ACGCGG at 1162, ACGCGG at 1078, CCGCGT at 1046, CCGCGT at 976, CCGCGT at 876, GCGCGT at 684, GCGCGC at 682, CCGCGC at 542, ACGCGG at 452, CCGCGC at 161.
The inverse complements are the same as the directs.

## CGCG negative direction (2596-1) distal promoters
- Negative strand, negative direction: CCGCGC at 1761, GCGCGT at 161.
- Positive strand, negative direction: GCGCGG at 1762.

## CGCG positive direction (4050-1) distal promoters
- Negative strand, positive direction: CCGCGC at 1650, CCGCGG at 1437, CCGCGG at 1337, GCGCGT at 1215, ACGCGG at 971, ACGCGG at 871, GCGCGC at 683, CCGCGC at 681, GCGCGT at 543.
- Positive strand, positive direction: CCGCGG at 1769, ACGCGG at 1656, CCGCGT at 1550, ACGCGT at 1523, ACGCGG at 1498, ACGCGG at 1454, ACGCGT at 1414, ACGCGG at 1398, ACGCGG at 1354, ACGCGT at 1314, CCGCGT at 1298, ACGCGG at 1246, CCGCGC at 1214, ACGCGG at 1162, ACGCGG at 1078, CCGCGT at 1046, CCGCGT at 976, CCGCGT at 876, GCGCGT at 684, GCGCGC at 682, CCGCGC at 542, ACGCGG at 452, CCGCGC at 161.

# CGCG box random dataset samplings
- CGCGr0: 5, GCGCGC at 3885, GCGCGC at 3238, GCGCGG at 3116, GCGCGG at 2069, CCGCGG at 1893.
- CGCGr1: 3, CCGCGG at 3800, GCGCGG at 2791, ACGCGG at 1299.
- CGCGr2: 13, CCGCGG at 3874, CCGCGG at 3564, CCGCGG at 3370, ACGCGT at 3086, CCGCGT at 2847, GCGCGT at 2588, ACGCGC at 2214, ACGCGG at 1931, CCGCGC at 1818, CCGCGT at 1807, CCGCGC at 1535, GCGCGC at 1151, CCGCGT at 418.
- CGCGr3: 8, ACGCGG at 3721, CCGCGC at 2377, ACGCGT at 2218, ACGCGT at 2211, ACGCGG at 1763, GCGCGC at 650, ACGCGT at 588, GCGCGG at 8.
- CGCGr4: 7, ACGCGT at 4517, ACGCGT at 4441, ACGCGG at 4018, CCGCGG at 2117, ACGCGC at 1939, ACGCGG at 565, CCGCGC at 18.
- CGCGr5: 7, CCGCGC at 4412, ACGCGT at 4313, CCGCGT at 3325, CCGCGC at 598, CCGCGG at 400, ACGCGG at 206, ACGCGG at 105.
- CGCGr6: 8, GCGCGG at 4386, ACGCGC at 4305, CCGCGC at 4275, GCGCGC at 2071, GCGCGG at 1968, CCGCGC at 1281, ACGCGC at 979, GCGCGG at 319.
- CGCGr7: 6, CCGCGC at 4215, CCGCGC at 3956, ACGCGT at 3560, CCGCGC at 2991, CCGCGG at 2747, ACGCGG at 985.
- CGCGr8: 2, ACGCGG at 4216, CCGCGT at 1573.
- CGCGr9: 9, ACGCGG at 3892, CCGCGG at 3885, CCGCGT at 3382, ACGCGG at 2881, ACGCGT at 2118, CCGCGC at 1954, GCGCGT at 1769, GCGCGC at 1767, ACGCGC at 683.

## CGCGr arbitrary (evens) (4560-2846) UTRs
- CGCGr0: GCGCGC at 3885, GCGCGC at 3238, GCGCGG at 3116.
- CGCGr2: CCGCGG at 3874, CCGCGG at 3564, CCGCGG at 3370, ACGCGT at 3086, CCGCGT at 2847.
- CGCGr4: ACGCGT at 4517, ACGCGT at 4441, ACGCGG at 4018.
- CGCGr6: GCGCGG at 4386, ACGCGC at 4305, CCGCGC at 4275.
- CGCGr8: ACGCGG at 4216.

## CGCGr alternate (odds) (4560-2846) UTRs
- CGCGr1: CCGCGG at 3800.
- CGCGr3: ACGCGG at 3721.
- CGCGr5: CCGCGC at 4412, ACGCGT at 4313, CCGCGT at 3325.
- CGCGr7: CCGCGC at 4215, CCGCGC at 3956, ACGCGT at 3560, CCGCGC at 2991.
- CGCGr9: ACGCGG at 3892, CCGCGG at 3885, CCGCGT at 3382, ACGCGG at 2881.

## CGCGr arbitrary positive direction (odds) (4445-4265) core promoters
- CGCGr5: CCGCGC at 4412, ACGCGT at 4313.

## CGCGr alternate positive direction (evens) (4445-4265) core promoters
- CGCGr4: ACGCGT at 4441.
- CGCGr6: GCGCGG at 4386, ACGCGC at 4305, CCGCGC at 4275.

## CGCGr alternate negative direction (odds) (2811-2596) proximal promoters
- CGCGr1: GCGCGG at 2791.
- CGCGr7: CCGCGG at 2747.

## CGCGr arbitrary positive direction (odds) (4265-4050) proximal promoters
- CGCGr7: CCGCGC at 4215.

## CGCGr alternate positive direction (evens) (4265-4050) proximal promoters
- CGCGr8: ACGCGG at 4216.

## CGCGr arbitrary negative direction (evens) (2596-1) distal promoters
- CGCGr0: GCGCGG at 2069, CCGCGG at 1893.
- CGCGr2: GCGCGT at 2588, ACGCGC at 2214, ACGCGG at 1931, CCGCGC at 1818, CCGCGT at 1807, CCGCGC at 1535, GCGCGC at 1151, CCGCGT at 418.
- CGCGr4: CCGCGG at 2117, ACGCGC at 1939, ACGCGG at 565, CCGCGC at 18.
- CGCGr6: GCGCGC at 2071, GCGCGG at 1968, CCGCGC at 1281, ACGCGC at 979, GCGCGG at 319.
- CGCGr8: CCGCGT at 1573.

## CGCGr alternate negative direction (odds) (2596-1) distal promoters
- CGCGr1: ACGCGG at 1299.
- CGCGr3: CCGCGC at 2377, ACGCGT at 2218, ACGCGT at 2211, ACGCGG at 1763, GCGCGC at 650, ACGCGT at 588, GCGCGG at 8.
- CGCGr5: CCGCGC at 598, CCGCGG at 400, ACGCGG at 206, ACGCGG at 105.
- CGCGr7: ACGCGG at 985.
- CGCGr9: ACGCGT at 2118, CCGCGC at 1954, GCGCGT at 1769, GCGCGC at 1767, ACGCGC at 683.

## CGCGr arbitrary positive direction (odds) (4050-1) distal promoters
- CGCGr1: CCGCGG at 3800, GCGCGG at 2791, ACGCGG at 1299.
- CGCGr3: ACGCGG at 3721, CCGCGC at 2377, ACGCGT at 2218, ACGCGT at 2211, ACGCGG at 1763, GCGCGC at 650, ACGCGT at 588, GCGCGG at 8.
- CGCGr5: CCGCGT at 3325, CCGCGC at 598, CCGCGG at 400, ACGCGG at 206, ACGCGG at 105.
- CGCGr7: CCGCGC at 3956, ACGCGT at 3560, CCGCGC at 2991, CCGCGG at 2747, ACGCGG at 985.
- CGCGr9: ACGCGG at 3892, CCGCGG at 3885, CCGCGT at 3382, ACGCGG at 2881, ACGCGT at 2118, CCGCGC at 1954, GCGCGT at 1769, GCGCGC at 1767, ACGCGC at 683.

## CGCGr alternate positive direction (evens) (4050-1) distal promoters
- CGCGr0: GCGCGC at 3885, GCGCGC at 3238, GCGCGG at 3116, GCGCGG at 2069, CCGCGG at 1893.
- CGCGr2: CCGCGG at 3874, CCGCGG at 3564, CCGCGG at 3370, ACGCGT at 3086, CCGCGT at 2847, GCGCGT at 2588, ACGCGC at 2214, ACGCGG at 1931, CCGCGC at 1818, CCGCGT at 1807, CCGCGC at 1535, GCGCGC at 1151, CCGCGT at 418.
- CGCGr4: ACGCGG at 4018, CCGCGG at 2117, ACGCGC at 1939, ACGCGG at 565, CCGCGC at 18.
- CGCGr6: GCGCGC at 2071, GCGCGG at 1968, CCGCGC at 1281, ACGCGC at 979, GCGCGG at 319.
- CGCGr8: CCGCGT at 1573.

# CGCG box analysis and results
All of the real CGCG boxes found are more closely associated with ZSCAN22 or ZNF497 than A1BG.
The real promoters only have three CGCG boxes closer to ZSCAN22 (for an occurrence of 1.5) or thirty-two closer to ZNF497 than A1BG (for an occurrence of 16.0).
The random datasets had fifteen CGCG boxes in the A1BG UTR on the ZSCAN22 side for an occurrence of 3.0.
The random datasets had two CGCG boxes in the core promoter (arbitrary positive direction) for an occurrences of 0.2.
In the proximal promoters the random datasets had one (positive direction) for an occurrence of 0.1.
The distal promoters had twenty sequences in the arbitrary negative direction some closer to A1BG some to ZSCAN22 for an occurrence of 4.0. There were thirty sequences in the arbitrary positive direction some closer to A1BG than to ZNF497 for an occurrence of 6.0.
The disparity between the real consensus sequences regarding their occurrences closer to the zinc fingers than A1BG and between the values of occurrences in the distal promoters 1.5 in the negative direction vs 4.0 and 16.0 vs 6.0 in the positive direction suggests that the real consensus sequences are likely active or activable probably for the respective zinc fingers.
"The minimum DNA-binding elements are 6-bp CGCG box, (A/C/G)CGCG(C/G/T)."
Comparison:
The occurrences of real CGCG negative distals are less than the randoms and the positive distals are greater than the randoms. This suggests that the real CGCGs are likely active or activable.

# Acknowledgements
The content on this page was first contributed by: Henry A. Hoff.
Initial content for this page in some instances came from Wikiversity.