Antioxidant-electrophile responsive element gene transcriptions

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

The "perfect ARE sequence [GCTGAGTCA] is strongly conserved across mammals [...]."[1]

Consensus sequences

5'-GTGAGGTCGC-3'[2]

5'-GCTGAGT-3', 5'-GCAGGCT-3' of 5'-GC(A/C/T)(A/G/T)(A/G/T)(C/G/T)T(A/C)A-3'[1], an antioxidant response element (ARE).

Hypotheses

Main article: Hypotheses
  1. A1BG has no Antioxidant-electrophile responsive element in either promoter.
  2. A1BG is not transcribed by an Antioxidant-electrophile responsive element.
  3. Antioxidant-electrophile responsive element does not participate in the transcription of A1BG.

AERE (Otsuki) samplings

Copying an antioxidant-electrophile responsive elements consensus sequence 5'-GTGAGGTCGC-3' and putting the sequence in "⌘F" finds no location between ZNF497 and A1BG or none locations between ZSCAN22 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence 5'-GTGAGGTCGC-3' (starting with SuccessablesAERE.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'-GTGAGGTCGC-3', 0.
  2. negative strand, positive direction, looking for 5'-GTGAGGTCGC-3', 0.
  3. positive strand, negative direction, looking for 5'-GTGAGGTCGC-3', 0.
  4. positive strand, positive direction, looking for 5'-GTGAGGTCGC-3', 0.
  5. complement, negative strand, negative direction, looking for 5'-CACTCCAGCG-3', 0.
  6. complement, negative strand, positive direction, looking for 5'-CACTCCAGCG-3', 0.
  7. complement, positive strand, negative direction, looking for 5'-CACTCCAGCG-3', 0.
  8. complement, positive strand, positive direction, looking for 5'-CACTCCAGCG-3', 0.
  9. inverse complement, negative strand, negative direction, looking for 5'-GCGACCTCAC-3', 0.
  10. inverse complement, negative strand, positive direction, looking for 5'-GCGACCTCAC-3', 0.
  11. inverse complement, positive strand, negative direction, looking for 5'-GCGACCTCAC-3', 0.
  12. inverse complement, positive strand, positive direction, looking for 5'-GCGACCTCAC-3', 0.
  13. inverse negative strand, negative direction, looking for 5'-CGCTGGAGTG-3', 0.
  14. inverse negative strand, positive direction, looking for 5'-CGCTGGAGTG-3', 0.
  15. inverse positive strand, negative direction, looking for 5'-CGCTGGAGTG-3', 0.
  16. inverse positive strand, positive direction, looking for 5'-CGCTGGAGTG-3', 0.

AERE (Lacher) samplings

Copying 5'-GCTGAGT-3', 5'-GCAGGCT-3' of 5'-GC(A/C/T)(A/G/T)(A/G/T)(C/G/T)T(A/C)A-3' and putting the sequence in "⌘F" finds no location between ZNF497 and A1BG or none locations between ZSCAN22 and A1BG as can be found by the computer programs. The predominant consensus sequence for Human, Chimp, Gorilla, Rhesus, Mouse, and Rat is TGCTGAGTCAT.[1]

For the Basic programs testing consensus sequence 5'-GC(A/C/T)(A/G/T)(A/G/T)(C/G/T)T(A/C)A-3' (starting with SuccessablesAERE.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 GC(A/C/T)(A/G/T)(A/G/T)(C/G/T)T(A/C)A, 0.
  2. negative strand, positive direction, looking for GC(A/C/T)(A/G/T)(A/G/T)(C/G/T)T(A/C)A, 0.
  3. positive strand, negative direction, looking for GC(A/C/T)(A/G/T)(A/G/T)(C/G/T)T(A/C)A, 2, GCAGTGTAA at 2087, GCATTTTAA at 192.
  4. positive strand, positive direction, looking for GC(A/C/T)(A/G/T)(A/G/T)(C/G/T)T(A/C)A, 0.
  5. inverse complement, negative strand, negative direction, looking for T(G/T)A(A/C/G)(A/C/T)(A/C/T)(A/G/T)GC, 2, TGACTATGC at 3546, TTAATCGGC at 1237.
  6. inverse complement, negative strand, positive direction, looking for T(G/T)A(A/C/G)(A/C/T)(A/C/T)(A/G/T)GC, 1, TGACCAGGC at 2877.
  7. inverse complement, positive strand, negative direction, looking for T(G/T)A(A/C/G)(A/C/T)(A/C/T)(A/G/T)GC, 3, TGAGTTGGC at 4098, TTAAAAGGC at 3442, TTAGCCAGC at 504.
  8. inverse complement, positive strand, positive direction, looking for T(G/T)A(A/C/G)(A/C/T)(A/C/T)(A/G/T)GC, 1, TGAAAAAGC at 1750.

AERE (Lacher) (4560-2846) UTRs

  1. Negative strand, negative direction: TGACTATGC at 3546.
  2. Positive strand, negative direction: TGAGTTGGC at 4098, TTAAAAGGC at 3442.

AERE (Lacher) negative direction (2596-1) distal promoters

  1. Negative strand, negative direction: TTAATCGGC at 1237.
  2. Positive strand, negative direction: GCAGTGTAA at 2087, TTAGCCAGC at 504, GCATTTTAA at 192.

AERE (Lacher) positive direction (4050-1) distal promoters

  1. Negative strand, positive direction: TGACCAGGC at 2877.
  2. Positive strand, positive direction: TGAAAAAGC at 1750.

AERE (Lacher) random dataset samplings

  1. AEREr0: 2, GCATATTCA at 3451, GCCATTTAA at 2392.
  2. AEREr1: 4, GCTTACTAA at 4451, GCCAATTAA at 2602, GCTTTTTCA at 2198, GCCTTCTCA at 1531.
  3. AEREr2: 2, GCTAAGTCA at 4374, GCTGAGTAA at 3017.
  4. AEREr3: 2, GCAGTTTAA at 2152, GCAGAGTCA at 477.
  5. AEREr4: 5, GCAAGCTCA at 4407, GCAAAGTCA at 3239, GCTTGTTAA at 3189, GCCATTTAA at 3028, GCCTATTAA at 2934.
  6. AEREr5: 2, GCCTACTAA at 1804, GCTTAGTCA at 1354.
  7. AEREr6: 1, GCAAGTTAA at 4441.
  8. AEREr7: 1, GCAAGTTCA at 3748.
  9. AEREr8: 3, GCCAACTCA at 3817, GCTTTGTAA at 2945, GCCAGTTCA at 2794.
  10. AEREr9: 5, GCTTATTAA at 3503, GCTATCTAA at 2819, GCTTTTTCA at 2687, GCATACTCA at 1195, GCCTACTAA at 986.
  11. AEREr0ci: 3, TTAACAGGC at 3997, TTAACCTGC at 3980, TTAGCCTGC at 3331.
  12. AEREr1ci: 3, TGACATAGC at 4503, TGAGCAAGC at 2219, TTAAATTGC at 1672.
  13. AEREr2ci: 1, TTAGCAAGC at 3890.
  14. AEREr3ci: 1, TGAGATAGC at 1777.
  15. AEREr4ci: 2, TTAATTGGC at 709, TGAGACAGC at 76.
  16. AEREr5ci: 1, TGAACAGGC at 2615.
  17. AEREr6ci: 3, TGAACCGGC at 2428, TTACATGGC at 1894, TGAATTGGC at 1327.
  18. AEREr7ci: 2, TTAATTTGC at 2255, TTAGATAGC at 1551.
  19. AEREr8ci: 3, TGAATAAGC at 3890, TTAACCTGC at 3055, TTACTCGGC at 834.
  20. AEREr9ci: 4, TGACTCTGC at 3525, TTAACAGGC at 1254, TTAATTAGC at 1004, TTACAAGGC at 211.

AEREr arbitrary (evens) (4560-2846) UTRs

  1. AEREr0: GCATATTCA at 3451.
  2. AEREr2: GCTAAGTCA at 4374, GCTGAGTAA at 3017.
  3. AEREr4: GCAAGCTCA at 4407, GCAAAGTCA at 3239, GCTTGTTAA at 3189, GCCATTTAA at 3028, GCCTATTAA at 2934.
  4. AEREr6: GCAAGTTAA at 4441.
  5. AEREr8: GCCAACTCA at 3817, GCTTTGTAA at 2945.
  6. AEREr0ci: TTAACAGGC at 3997, TTAACCTGC at 3980, TTAGCCTGC at 3331.
  7. AEREr2ci: TTAGCAAGC at 3890.
  8. AEREr8ci: TGAATAAGC at 3890, TTAACCTGC at 3055.

AEREr alternate (odds) (4560-2846) UTRs

  1. AEREr1: GCTTACTAA at 4451.
  2. AEREr7: GCAAGTTCA at 3748.
  3. AEREr9: GCTTATTAA at 3503.
  4. AEREr1ci: TGACATAGC at 4503.
  5. AEREr9ci: TGACTCTGC at 3525.

AEREr alternate negative direction (odds) (2846-2811) core promoters

  1. AEREr9: GCTATCTAA at 2819.

AEREr alternate positive direction (evens) (4445-4265) core promoters

  1. AEREr2: GCTAAGTCA at 4374.
  2. AEREr4: GCAAGCTCA at 4407.
  3. AEREr6: GCAAGTTAA at 4441.

AEREr arbitrary negative direction (evens) (2811-2596) proximal promoters

  1. AEREr8: GCCAGTTCA at 2794.

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

  1. AEREr1: GCCAATTAA at 2602.
  2. AEREr9: GCTTTTTCA at 2687.
  3. AEREr5ci: TGAACAGGC at 2615.

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

  1. AEREr0: GCCATTTAA at 2392.
  2. AEREr4ci: TTAATTGGC at 709, TGAGACAGC at 76.
  3. AEREr6ci: TGAACCGGC at 2428, TTACATGGC at 1894, TGAATTGGC at 1327.
  4. AEREr8ci: TTACTCGGC at 834.

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

  1. AEREr1: GCTTTTTCA at 2198, GCCTTCTCA at 1531.
  2. AEREr3: GCAGTTTAA at 2152, GCAGAGTCA at 477.
  3. AEREr5: GCCTACTAA at 1804, GCTTAGTCA at 1354.
  4. AEREr9: GCATACTCA at 1195, GCCTACTAA at 986.
  5. AEREr1ci: TGAGCAAGC at 2219, TTAAATTGC at 1672.
  6. AEREr3ci: TGAGATAGC at 1777.
  7. AEREr7ci: TTAATTTGC at 2255, TTAGATAGC at 1551.
  8. AEREr9ci: TTAACAGGC at 1254, TTAATTAGC at 1004, TTACAAGGC at 211.

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

  1. AEREr1: GCCAATTAA at 2602, GCTTTTTCA at 2198, GCCTTCTCA at 1531.
  2. AEREr3: GCAGTTTAA at 2152, GCAGAGTCA at 477.
  3. AEREr5: GCCTACTAA at 1804, GCTTAGTCA at 1354.
  4. AEREr7: GCAAGTTCA at 3748.
  5. AEREr9: GCTTATTAA at 3503, GCTATCTAA at 2819, GCTTTTTCA at 2687, GCATACTCA at 1195, GCCTACTAA at 986.
  6. AEREr1ci: TGAGCAAGC at 2219, TTAAATTGC at 1672.
  7. AEREr3ci: TGAGATAGC at 1777.
  8. AEREr5ci: TGAACAGGC at 2615.
  9. AEREr7ci: TTAATTTGC at 2255, TTAGATAGC at 1551.
  10. AEREr9ci: TGACTCTGC at 3525, TTAACAGGC at 1254, TTAATTAGC at 1004, TTACAAGGC at 211.

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

  1. AEREr0: GCATATTCA at 3451, GCCATTTAA at 2392.
  2. AEREr2: GCTGAGTAA at 3017.
  3. AEREr4: GCAAAGTCA at 3239, GCTTGTTAA at 3189, GCCATTTAA at 3028, GCCTATTAA at 2934.
  4. AEREr8: GCCAACTCA at 3817, GCTTTGTAA at 2945, GCCAGTTCA at 2794.
  5. AEREr0ci: TTAACAGGC at 3997, TTAACCTGC at 3980, TTAGCCTGC at 3331.
  6. AEREr2ci: TTAGCAAGC at 3890.
  7. AEREr4ci: TTAATTGGC at 709, TGAGACAGC at 76.
  8. AEREr6ci: TGAACCGGC at 2428, TTACATGGC at 1894, TGAATTGGC at 1327.
  9. AEREr8ci: TGAATAAGC at 3890, TTAACCTGC at 3055, TTACTCGGC at 834.

AERE analysis and results

Main article: Complex locus A1BG and ZNF497 § AEREs

GCTGAGT, GCAGGCT of GC(A/C/T)(A/G/T)(A/G/T)(C/G/T)T(A/C)A[1]

Reals or randoms Promoters direction Numbers Strands Occurrences Averages (± 0.1)
Reals UTR negative 3 2 1.5 1.5
Randoms UTR arbitrary negative 17 10 1.7 1.1
Randoms UTR alternate negative 5 10 0.5 1.1
Reals Core negative 0 2 0 0
Randoms Core arbitrary negative 0 10 0 0.05
Randoms Core alternate negative 1 10 0.1 0.05
Reals Core positive 0 2 0 0
Randoms Core arbitrary positive 0 10 0 0.15
Randoms Core alternate positive 3 10 0.3 0.15
Reals Proximal negative 0 2 0 0
Randoms Proximal arbitrary negative 1 10 0.1 0.2
Randoms Proximal alternate negative 3 10 0.3 0.2
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 4 2 2 2 ± 1 (--1,+-3)
Randoms Distal arbitrary negative 7 10 0.7 1.15
Randoms Distal alternate negative 16 10 1.6 1.15
Reals Distal positive 2 2 1 1
Randoms Distal arbitrary positive 23 10 2.3 2.25
Randoms Distal alternate positive 22 10 2.2 2.25

Comparison:

The occurrences of real AERE UTRs and negative direction distals overlap the upper occurrences of the randoms and the positive direction distals are less than the randoms. This suggests that the real AEREs are likely active or activable.

Predominant AERE

The predominant consensus sequence for Human, Chimp, Gorilla, Rhesus, Mouse, and Rat is TGCTGAGTCAT.[1]

For the Basic programs testing consensus sequence TGCTGAGTCAT (starting with SuccessablesPAERE.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 TGCTGAGTCAT, 0.
  2. positive strand, negative direction, looking for TGCTGAGTCAT, 0.
  3. positive strand, positive direction, looking for TGCTGAGTCAT, 0.
  4. negative strand, positive direction, looking for TGCTGAGTCAT, 0.
  5. inverse complement, negative strand, negative direction, looking for ATGACTCAGCA, 0.
  6. inverse complement, positive strand, negative direction, looking for ATGACTCAGCA, 0.
  7. inverse complement, positive strand, positive direction, looking for ATGACTCAGCA, 0.
  8. inverse complement, negative strand, positive direction, looking for ATGACTCAGCA, 0.

See also

References

  1. ↑ 1.0 1.1 1.2 1.3 1.4 Sarah E. Lacher, Daniel C. Levings, Samuel Freeman, Matthew Slattery (October 2018). "Identification of a functional antioxidant response element at the HIF1A locus". Redox Biology. 19: 401–411. doi:10.1016/j.redox.2018.08.014. Retrieved 6 October 2020.
  2. ↑ Akihito Otsuki, Mikiko Suzuki, Fumiki Katsuoka, Kouhei Tsuchida, Hiromi Suda, Masanobu Morita, Ritsuko Shimizu, Masayuki Yamamoto (February 2016). "Unique cistrome defined as CsMBE is strictly required for Nrf2-sMaf heterodimer function in cytoprotection". Free Radical Biology and Medicine. 91: 45–57. doi:10.1016/j.freeradbiomed.2015.12.005. PMID 26677805. Retrieved 21 August 2020.

Acknowledgements

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

External links

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