Coupling element gene transcriptions

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Associate Editor(s)-in-Chief: Henry A. Hoff

"In Arabidopsis, the CE3 element is practically absent; thus, Arabidopsis relies on paired ABREs to form ABRCs (Gomez‐Porras et al. 2007) or on the coupling of a DRE (TACCGACAT) with ABRE (Narusaka et al. 2003; Nakashima et al. 2006)."[1]

"To identify potential cis-regulatory elements in the promoter sequences of ZmGRXCC genes, the 1500 bp sequences of each [maize CC-type glutaredoxin (GRX)] ZmGRXCC gene upstream of the ATG start codon were selected from the maize genome as the promoter, and the promoter sequence was screened using PlantCARE [32]. The elements searched included Skn-1_motif (-GGGCGG-), CCGTCC-box (-CCGTCC-box-), CAT-box (-GCCACT-), and RY-element (-CATGCATG-) for development and metabolism; TGACG-motif (-TGACG-) and CGTCA-motif (-CGTCA-) for jasmonic acid responsiveness; GARE-motif (-AAACAGA- or -TCTGTTG-) for gibberellin responsiveness; TGA-element (-AACGAC-) for auxin responsiveness; ABRE (ABA-responsive element, -CACGTG- or -TACGTG-) and CE3 (coupling element 3, -CACGCG-) for ABA responsiveness; ERE (ethylene-responsive element, -ATTTCAAA-) for ethylene responsiveness; GC-motif (-CCCCCG-), LTR (-CCGAAA-) and box S (-AGCCACC-) for stress responsiveness; and MBS (MYB-binding site, -CAACTG- or -TAACTG-), DRE (dehydration-responsive element, -GCCGAC- or -ACCGAC-), T/G Box (-CACGTT-), EE (evening element, -AATATC-), MYCR (MYC-binding site, -CACATG-), and NACR (binding site of drought-inducible NAC TFs, -CACGCA-) for drought/dehydration responsiveness [33–37]."[2]

Consensus sequences

Main article: Consensus sequence gene transcriptions

"In barley, the combination of an ABRE and one of two known coupling elements CE1 (TGCCACCGG) and CE3 (GCGTGTC) constitutes an ABA responsive complex (ABRC) in the regulation of the ABA‐inducible genes HVA1 and HVA22 (Shen and Ho 1995; Shen et al. 1996)."[1]

"The EM gene of rice has a CE (CE3) of GACGCGTGTC (Hobo et al., 1999); maize RAB28 has CE3 of ACGCGCCTCCTC (Busk et al., 1997), and barley HVA1 has CE3 of ACGCGTGTCCTC and HVA22 has CE1 of TGCCACCGG (Shen and Ho, 1997)."[3]

Promoter occurrences

Hypotheses

Main article: Hypotheses
  1. A1BG has no coupling elements in either promoter.
  2. A1BG is not transcribed by a coupling element.
  3. A coupling element does not participate in the transcription of A1BG.

CE1 (Watanabe) samplings

Main article: Model samplings

Copying a responsive elements consensus sequence 5'-TGCCACCGG-3' and putting the sequence in "⌘F" finds none between ZNF497 and A1BG or none between ZSCAN22 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence 5'-TGCCACCGG-3' (starting with SuccessablesCE1.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, and found:

  1. negative strand, negative direction, looking for 5'-TGCCACCGG-3', 0.
  2. negative strand, positive direction, looking for 5'-TGCCACCGG-3', 0.
  3. positive strand, negative direction, looking for 5'-TGCCACCGG-3', 0.
  4. positive strand, positive direction, looking for 5'-TGCCACCGG-3', 0.
  5. complement, negative strand, negative direction, looking for 5'-ACGGTGGCC-3', 0.
  6. complement, negative strand, positive direction, looking for 5'-ACGGTGGCC-3', 0.
  7. complement, positive strand, negative direction, looking for 5'-ACGGTGGCC-3', 0.
  8. complement, positive strand, positive direction, looking for 5'-ACGGTGGCC-3', 0.
  9. inverse complement, negative strand, negative direction, looking for 5'-CCGGTGGCA-3', 0.
  10. inverse complement, negative strand, positive direction, looking for 5'-CCGGTGGCA-3', 0.
  11. inverse complement, positive strand, negative direction, looking for 5'-CCGGTGGCA-3', 0.
  12. inverse complement, positive strand, positive direction, looking for 5'-CCGGTGGCA-3', 0.
  13. inverse negative strand, negative direction, looking for 5'-GGCCACCGT-3', 0.
  14. inverse negative strand, positive direction, looking for 5'-GGCCACCGT-3', 0.
  15. inverse positive strand, negative direction, looking for 5'-GGCCACCGT-3', 0.
  16. inverse positive strand, positive direction, looking for 5'-GGCCACCGT-3', 0.

CE3 (Watanabe) samplings

Copying a responsive elements consensus sequence 5'-GCGTGTC-3' and putting the sequence in "⌘F" finds none between ZNF497 and A1BG or none between ZSCAN22 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence 5'-GCGTGTC-3' (starting with SuccessablesCE3W.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, and found:

  1. negative strand, negative direction, looking for 5'-GCGTGTC-3', 0.
  2. negative strand, positive direction, looking for 5'-GCGTGTC-3', 0.
  3. positive strand, negative direction, looking for 5'-GCGTGTC-3', 0.
  4. positive strand, positive direction, looking for 5'-GCGTGTC-3', 1, 5'-GCGTGTC-3' at 1053.
  5. complement, negative strand, negative direction, looking for 5'-CGCACAG-3', 0.
  6. complement, negative strand, positive direction, looking for 5'-CGCACAG-3', 1, 5'-CGCACAG-3' at 1053.
  7. complement, positive strand, negative direction, looking for 5'-CGCACAG-3', 0.
  8. complement, positive strand, positive direction, looking for 5'-CGCACAG-3', 0.
  9. inverse complement, negative strand, negative direction, looking for 5'-GACACGC-3', 0.
  10. inverse complement, negative strand, positive direction, looking for 5'-GACACGC-3', 0.
  11. inverse complement, positive strand, negative direction, looking for 5'-GACACGC-3', 0.
  12. inverse complement, positive strand, positive direction, looking for 5'-GACACGC-3', 0.
  13. inverse negative strand, negative direction, looking for 5'-CTGTGCG-3', 0.
  14. inverse negative strand, positive direction, looking for 5'-CTGTGCG-3', 0.
  15. inverse positive strand, negative direction, looking for 5'-CTGTGCG-3', 0.
  16. inverse positive strand, positive direction, looking for 5'-CTGTGCG-3', 0.

CE3W positive direction (4050-1) distal promoters

  1. Positive strand, positive direction: GCGTGTC at 1053.

CE3 (Watanabe) random dataset samplings

  1. CE3Wr0: 1, GCGTGTC at 3282.
  2. CE3Wr1: 0.
  3. CE3Wr2: 1, GCGTGTC at 593.
  4. CE3Wr3: 0.
  5. CE3Wr4: 0.
  6. CE3Wr5: 0.
  7. CE3Wr6: 1, GCGTGTC at 1337.
  8. CE3Wr7: 0.
  9. CE3Wr8: 0.
  10. CE3Wr9: 0.
  11. CE3Wr0ci: 0.
  12. CE3Wr1ci: 0.
  13. CE3Wr2ci: 0.
  14. CE3Wr3ci: 0.
  15. CE3Wr4ci: 0.
  16. CE3Wr5ci: 0.
  17. CE3Wr6ci: 0.
  18. CE3Wr7ci: 0.
  19. CE3Wr8ci: 0.
  20. CE3Wr9ci: 0.

CE3W arbitrary (evens) (4560-2846) UTRs

  1. CE3Wr0: GCGTGTC at 3282.

CE3Wr arbitrary negative direction (evens) (2596-1) distal promoters

  1. CE3Wr2: GCGTGTC at 593.
  2. CE3Wr6: GCGTGTC at 1337.

CE3Wr alternate positive direction (evens) (4050-1) distal promoters

  1. CE3Wr0: GCGTGTC at 3282.
  2. CE3Wr2: GCGTGTC at 593.
  3. CE3Wr6: GCGTGTC at 1337.

CE3W analysis and results

Main article: Complex locus A1BG and ZNF497 § CE3Ws

The consensus sequence for coupling element 3 (Watanabe) has only one occurrence in the promoters for A1BG: GCGTGTC at 1053 on the positive strand in the positive direction in the distal promoter. For the positive direction, this is an occurrence of 0.5.

The random datasets had one in the UTR between ZSCAN22 and A1BG: GCGTGTC at 3282, for an occurrence of 0.1. There were two consensus sequences in the distal promoters: GCGTGTC at 1337 and GCGTGTC at 593, both in the negative direction for an overall occurrence of 0.2. These occurrences in the arbitrary negative direction distal promoters are much lower than the real suggesting that the one real occurrence is likely active or activable.

"In barley, the combination of an ABRE and one of two known coupling elements CE1 (TGCCACCGG) and CE3 (GCGTGTC) constitutes an ABA responsive complex (ABRC) in the regulation of the ABA‐inducible genes HVA1 and HVA22 (Shen and Ho 1995; Shen et al. 1996)."[1]

Reals or randoms Promoters direction Numbers Strands Occurrences Averages (± 0.1)
Reals UTR negative 0 2 0 0
Randoms UTR arbitrary negative 1 10 0.1 0.05
Randoms UTR alternate negative 0 10 0 0.05
Reals Core negative 0 2 0 0
Randoms Core arbitrary negative 0 10 0 0
Randoms Core alternate negative 0 10 0 0
Reals Core positive 0 2 0 0
Randoms Core arbitrary positive 0 10 0 0
Randoms Core alternate positive 0 10 0 0
Reals Proximal negative 0 2 0 0
Randoms Proximal arbitrary negative 0 10 0 0
Randoms Proximal alternate negative 0 10 0 0
Reals Proximal positive 0 2 0 0
Randoms Proximal arbitrary positive 0 10 0 0
Randoms Proximal alternate positive 0 10 0 0
Reals Distal negative 0 2 0 0
Randoms Distal arbitrary negative 2 10 0.2 0.1
Randoms Distal alternate negative 0 10 0 0.1
Reals Distal positive 1 2 0.5 0.5
Randoms Distal arbitrary positive 0 10 0 0.15
Randoms Distal alternate positive 3 10 0.3 0.15

Comparison:

The occurrences of real CE3Ws are greater than the randoms. This suggests that the real CE3Ws are likely active or activable.

CE3 (Ding) samplings

Copying a responsive elements consensus sequence 5'-CACGCG-3' and putting the sequence in "⌘F" finds none between ZNF497 and A1BG or none between ZSCAN22 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence 5'-CACGCG-3' (starting with SuccessablesCE3D.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, and found:

  1. negative strand, negative direction, looking for 5'-CACGCG-3', 0.
  2. negative strand, positive direction, looking for 5'-CACGCG-3', 2, 5'-CACGCG-3' at 970, 5'-CACGCG-3' at 870, and complements.
  3. positive strand, negative direction, looking for 5'-CACGCG-3', 0.
  4. positive strand, positive direction, looking for 5'-CACGCG-3', 4, 5'-CACGCG-3' at 1726, 5'-CACGCG-3' at 1522, 5'-CACGCG-3' at 1245, 5'-CACGCG-3' at 1161, and complements.
  5. complement, negative strand, negative direction, looking for 5'-GTGCGC-3', 0.
  6. complement, negative strand, positive direction, looking for 5'-GTGCGC-3', 4, 5'-GTGCGC-3' at 1726, 5'-GTGCGC-3' at 1522, 5'-GTGCGC-3' at 1245, 5'-GTGCGC-3' at 1161.
  7. complement, positive strand, negative direction, looking for 5'-GTGCGC-3', 0.
  8. complement, positive strand, positive direction, looking for 5'-GTGCGC-3', 2, 5'-GTGCGC-3' at 970, 5'-GTGCGC-3' at 870.
  9. inverse complement, negative strand, negative direction, looking for 5'-CGCGTG-3', 0.
  10. inverse complement, negative strand, positive direction, looking for 5'-CGCGTG-3', 2, 5'-CGCGTG-3' at 1216, 5'-CGCGTG-3' at 544, and complements.
  11. inverse complement, positive strand, negative direction, looking for 5'-CGCGTG-3', 0.
  12. inverse complement, positive strand, positive direction, looking for 5'-CGCGTG-3', 7, 5'-CGCGTG-3' at 1551, 5'-CGCGTG-3' at 1299, 5'-CGCGTG-3' at 1131, 5'-CGCGTG-3' at 1047, 5'-CGCGTG-3' at 977, 5'-CGCGTG-3' at 877, 5'-CGCGTG-3' at 685, and complements.
  13. inverse negative strand, negative direction, looking for 5'-GCGCAC-3', 0.
  14. inverse negative strand, positive direction, looking for 5'-GCGCAC-3', 7, 5'-GCGCAC-3' at 1551, 5'-GCGCAC-3' at 1299, 5'-GCGCAC-3' at 1131, 5'-GCGCAC-3' at 1047, 5'-GCGCAC-3' at 977, 5'-GCGCAC-3' at 877, 5'-GCGCAC-3' at 685.
  15. inverse positive strand, negative direction, looking for 5'-GCGCAC-3', 0.
  16. inverse positive strand, positive direction, looking for 5'-GCGCAC-3', 2, 5'-GCGCAC-3' at 1216, 5'-GCGCAC-3' at 544.

CE3D positive direction (4050-1) distal promoters

  1. Negative strand, positive direction: CACGCG at 970, CACGCG at 870.
  2. inverse complement, negative strand, positive direction: CGCGTG at 1216, CGCGTG at 544.
  3. Positive strand, positive direction: CACGCG at 1726, CACGCG at 1522, CACGCG at 1245, CACGCG at 1161.
  4. inverse complement, positive strand, positive direction: CGCGTG at 1551, CGCGTG at 1299, CGCGTG at 1131, CGCGTG at 1047, CGCGTG at 977, CGCGTG at 877, CGCGTG at 685.

CE3 (Ding) random dataset samplings

  1. CE3Dr0: 0.
  2. CE3Dr1: 0.
  3. CE3Dr2: 1, CACGCG at 1930.
  4. CE3Dr3: 1, CACGCG at 587.
  5. CE3Dr4: 0.
  6. CE3Dr5: 1, CACGCG at 2700.
  7. CE3Dr6: 0.
  8. CE3Dr7: 0.
  9. CE3Dr8: 1, CACGCG at 15.
  10. CE3Dr9: 1, CACGCG at 2117.
  11. CE3Dr0ci: 0.
  12. CE3Dr1ci: 0.
  13. CE3Dr2ci: 2, CGCGTG at 3087, CGCGTG at 591.
  14. CE3Dr3ci: 0.
  15. CE3Dr4ci: 0.
  16. CE3Dr5ci: 1, CGCGTG at 4314.
  17. CE3Dr6ci: 0.
  18. CE3Dr7ci: 1, CGCGTG at 3561.
  19. CE3Dr8ci: 0.
  20. CE3Dr9ci: 0.

CE3Dr arbitrary (evens) (4560-2846) UTRs

  1. CE3Dr2ci: CGCGTG at 3087.

CE3Dr alternate (odds) (4560-2846) UTRs

  1. CE3Dr5ci: CGCGTG at 4314.

CE3Dr arbitrary positive direction (odds) (4445-4265) core promoters

  1. CE3Dr5ci: CGCGTG at 4314.

CE3Dr alternate negative direction (odds) (2811-2596) proximal promoters

  1. CE3Dr5: CACGCG at 2700.

CE3Dr arbitrary negative direction (evens) (2596-1) distal promoters

  1. CE3Dr2: CACGCG at 1930.
  2. CE3Dr8: CACGCG at 15.
  3. CE3Dr2ci: CGCGTG at 591.

CE3Dr alternate negative direction (odds) (2596-1) distal promoters

  1. CE3Dr3: CACGCG at 587.
  2. CE3Dr5: CACGCG at 2700.
  3. CE3Dr9: CACGCG at 2117.

CE3Dr arbitrary positive direction (odds) (4050-1) distal promoters

  1. CE3Dr5: CACGCG at 2700.
  2. CE3Dr9: CACGCG at 2117.
  3. CE3Dr7ci: CGCGTG at 3561.

CE3Dr alternate positive direction (evens) (4050-1) distal promoters

  1. CE3Dr8: CACGCG at 15.
  2. CE3Dr2ci: CGCGTG at 3087, CGCGTG at 591.

CE3D analysis and results

Main article: Complex locus A1BG and ZNF497 § CE3Ds

"The elements searched included [...] CE3 (coupling element 3, -CACGCG-) [...]."[2]

Reals or randoms Promoters direction Numbers Strands Occurrences Averages (± 0.1)
Reals UTR negative 0 2 0 0
Randoms UTR arbitrary negative 1 10 0.1 0.1
Randoms UTR alternate negative 1 10 0.1 0.1
Reals Core negative 0 2 0 0
Randoms Core arbitrary negative 0 10 0 0
Randoms Core alternate negative 0 10 0 0
Reals Core positive 0 2 0 0
Randoms Core arbitrary positive 1 10 0.1 0.05
Randoms Core alternate positive 0 10 0 0.05
Reals Proximal negative 0 2 0 0
Randoms Proximal arbitrary negative 0 10 0 0.05
Randoms Proximal alternate negative 1 10 0.1 0.05
Reals Proximal positive 0 2 0 0
Randoms Proximal arbitrary positive 0 10 0 0
Randoms Proximal alternate positive 0 10 0 0
Reals Distal negative 0 2 0 0
Randoms Distal arbitrary negative 3 10 0.3 0.3
Randoms Distal alternate negative 3 10 0.3 0.3
Reals Distal positive 15 2 7.5 7.5
Randoms Distal arbitrary positive 3 10 0.3 0.3
Randoms Distal alternate positive 3 10 0.3 0.3

Comparison:

The occurrences of real CE3Ds are greater than the randoms. This suggests that the real CE3Ds are likely active or activable.

Acknowledgements

The content on this page was first contributed by: Henry A. Hoff.

See also

References

  1. ↑ 1.0 1.1 1.2 Kenneth A. Watanabe; Arielle Homayouni; Lingkun Gu; Kuan‐Ying Huang; Tuan‐Hua David Ho; Qingxi J. Shen (18 June 2017). "Transcriptomic analysis of rice aleurone cells identified a novel abscisic acid response element". Plant, Cell & Environment. 40 (9): 2004–2016. doi:10.1111/pce.13006. Retrieved 5 October 2020.
  2. ↑ 2.0 2.1 Shuangcheng Ding, Fengyu He, Wenlin Tang, Hewei Du and Hongwei Wang (12 August 2019). "Identification of Maize CC-Type Glutaredoxins That Are Associated with Response to Drought Stress". Genes. 10 (610): 1–15. doi:10.3390/genes10080610. Retrieved 30 November 2020.
  3. ↑ Weixiong Zhang, Jianhua Ruan, Tuan-hua David Ho, Youngsook You, Taotao Yu, Ralph S. Quatrano (2005). "Cis-regulatory element based targeted gene finding: genome-wide identification of abscisic acid- and abiotic stress-responsive genes in Arabidopsis thaliana". Bioinformatics. 21 (14): 307493081. doi:10.1093/bioinformatics/bti490. Retrieved 1 December 2020.

External links


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