B box gene transcriptions

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

"The mP2 EB fragment used for binding was the 118 nucleotide fragment extending from the Dde I site at position -140 to the Dde I site at position -23 [...]. This fragment contains the GC, E, B, CAAT, and TATA boxes."[1]

Consensus sequences

Main article: Consensus sequence gene transcriptions

TGGGCA is a B-box.[1]

"The human [Transforming growth factor b1] TGFB1 promoter region contains two binding sequences for [Activator protein-1] AP-1, designated AP-1 box A (TGACTCT) and box B (TGTCTCA), which mediate the upregulation of promoter activity via a PKC-dependent pathway after exposure of cells to a high-glucose environment (Refs 37, 38)."[2]

Hypotheses

  1. A1BG has neither a B-box (TGGGCA) nor a box B (or B1 box) (TGTCTCA) in either promoter.
  2. A1BG is not transcribed by either B box.
  3. Neither B box participates in the transcription of A1BG.

B box (Johnson) samplings

Copying the above consensus B box and putting the sequences in "⌘F" locates any consensus sequences in any nucleotide positions as may be found by the computer programs.

One 3'-TGGGCA-5' shows up at about -600 nucleotides from the TSS between ZSCAN22 and A1BG as A1BG is approached from ZSCAN22 on the positive strand. This warrants testing with the computer programs.

  1. Negative strand, negative direction: 0.
  2. Positive strand, negative direction: 9, TGGGCA at 4191, TGGGCA at 4040, TGGGCA at 3301, TGGGCA at 2773, TGGGCA at 2438, TGGGCA at 1359, TGGGCA at 1114, TGGGCA at 902, TGGGCA at 462.
  3. Negative strand, positive direction: 4, TGGGCA at 4180, TGGGCA at 2894, TGGGCA at 1945, TGGGCA at 27.
  4. Positive strand, positive direction: 0.
  5. Inverse complement, negative strand, negative direction: 0.
  6. Inverse complement, positive strand, negative direction: 4, TGCCCA at 4251, TGCCCA at 3883, TGCCCA at 3854, TGCCCA at 1458.
  7. Inverse complement, negative strand, positive direction: 2, TGCCCA at 3377, TGCCCA at 3237.
  8. Inverse complement, positive strand, positive direction: 1, TGCCCA at 3750.

Bbox (4560-2846) UTRs

  1. Positive strand, negative direction: TGCCCA at 4251, TGGGCA at 4191, TGGGCA at 4040, TGCCCA at 3883, TGCCCA at 3854, TGGGCA at 3301.

Bbox negative direction (2811-2596) proximal promoters

  1. Positive strand, negative direction: TGGGCA at 2773.

Bbox positive direction (4265-4050) proximal promoters

  1. Negative strand, positive direction: TGGGCA at 4180.

Bbox negative direction (2596-1) distal promoters

  1. Positive strand, negative direction: TGGGCA at 2438, TGCCCA at 1458, TGGGCA at 1359, TGGGCA at 1114, TGGGCA at 902, TGGGCA at 462.

Bbox positive direction (4050-1) distal promoters

  1. Negative strand, positive direction: TGCCCA at 3377, TGCCCA at 3237, TGGGCA at 2894, TGGGCA at 1945, TGGGCA at 27.
  2. Positive strand, positive direction: TGCCCA at 3750.

B box (Johnson) random dataset samplings

  1. Bboxr0: 1, TGGGCA at 1253.
  2. Bboxr1: 2, TGGGCA at 3675, TGGGCA at 2650.
  3. Bboxr2: 0.
  4. Bboxr3: 3, TGGGCA at 3857, TGGGCA at 3329, TGGGCA at 2535.
  5. Bboxr4: 1, TGGGCA at 4228.
  6. Bboxr5: 0.
  7. Bboxr6: 0.
  8. Bboxr7: 1, TGGGCA at 2615.
  9. Bboxr8: 2, TGGGCA at 2952, TGGGCA at 1018.
  10. Bboxr9: 1, TGGGCA at 3599.
  11. Bboxr0ci: 2, TGCCCA at 1080, TGCCCA at 245.
  12. Bboxr1ci: 0.
  13. Bboxr2ci: 0.
  14. Bboxr3ci: 5, TGCCCA at 4519, TGCCCA at 2177, TGCCCA at 1577, TGCCCA at 1423, TGCCCA at 136.
  15. Bboxr4ci: 0.
  16. Bboxr5ci: 1, TGCCCA at 2606.
  17. Bboxr6ci: 1, TGCCCA at 956.
  18. Bboxr7ci: 4, TGCCCA at 4059, TGCCCA at 3010, TGCCCA at 1406, TGCCCA at 1338.
  19. Bboxr8ci: 3, TGCCCA at 4140, TGCCCA at 1901, TGCCCA at 1380.
  20. Bboxr9ci: 2, TGCCCA at 1672, TGCCCA at 732.

Bboxr arbitrary (evens) (4560-2846) UTRs

  1. Bboxr4: TGGGCA at 4228.
  2. Bboxr8: TGGGCA at 2952.
  3. Bboxr8ci: TGCCCA at 4140.

Bboxr alternate (odds) (4560-2846) UTRs

  1. Bboxr1: TGGGCA at 3675.
  2. Bboxr3: TGGGCA at 3857, TGGGCA at 3329.
  3. Bboxr9: TGGGCA at 3599.
  4. Bboxr3ci: TGCCCA at 4519.
  5. Bboxr7ci: TGCCCA at 4059, TGCCCA at 3010.

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

  1. Bboxr1: TGGGCA at 2650.
  2. Bboxr7: TGGGCA at 2615.
  3. Bboxr5ci: TGCCCA at 2606.

Bboxr arbitrary positive direction (odds) (4265-4050) proximal promoters

  1. Bboxr7ci: TGCCCA at 4059.

Bboxr alternate positive direction (evens) (4265-4050) proximal promoters

  1. Bboxr4: TGGGCA at 4228.
  2. Bboxr8ci: TGCCCA at 4140.

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

  1. Bboxr0: TGGGCA at 1253.
  2. Bboxr8: TGGGCA at 1018.
  3. Bboxr0ci: TGCCCA at 1080, TGCCCA at 245.
  4. Bboxr6ci: TGCCCA at 956.
  5. Bboxr8ci: TGCCCA at 1901, TGCCCA at 1380.

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

  1. Bboxr3: TGGGCA at 2535.
  2. Bboxr7: TGGGCA at 2615.
  3. Bboxr3ci: TGCCCA at 2177, TGCCCA at 1577, TGCCCA at 1423, TGCCCA at 136.
  4. Bboxr7ci: TGCCCA at 1406, TGCCCA at 1338.
  5. Bboxr9ci: TGCCCA at 1672, TGCCCA at 732.

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

  1. Bboxr1: TGGGCA at 3675, TGGGCA at 2650.
  2. Bboxr3: TGGGCA at 3857, TGGGCA at 3329, TGGGCA at 2535.
  3. Bboxr7: TGGGCA at 2615.
  4. Bboxr9: TGGGCA at 3599.
  5. Bboxr3ci: TGCCCA at 2177, TGCCCA at 1577, TGCCCA at 1423, TGCCCA at 136.
  6. Bboxr5ci: TGCCCA at 2606.
  7. Bboxr7ci: TGCCCA at 3010, TGCCCA at 1406, TGCCCA at 1338.
  8. Bboxr9ci: TGCCCA at 1672, TGCCCA at 732.

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

  1. Bboxr0: TGGGCA at 1253.
  2. Bboxr8: TGGGCA at 2952, TGGGCA at 1018.
  3. Bboxr0ci: TGCCCA at 1080, TGCCCA at 245.
  4. Bboxr6ci: TGCCCA at 956.
  5. Bboxr8ci: TGCCCA at 1901, TGCCCA at 1380.

B-box analysis and results

Main article: Complex locus A1BG and ZNF497 § B-boxes

TGGGCA is a B-box.[1]

Reals or randoms Promoters direction Numbers Strands Occurrences Averages (± 0.1)
Reals UTR negative 6 2 3 3 ± 3 (--0,+-6)
Randoms UTR arbitrary negative 3 10 0.3 0.5
Randoms UTR alternate negative 7 10 0.7 0.5
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 1 2 0.5 0.5 ± 0.5 (--0,+-1)
Randoms Proximal arbitrary negative 0 10 0 0.15
Randoms Proximal alternate negative 3 10 0.3 0.15
Reals Proximal positive 1 2 0.5 0.5 ± 0.5 (-+1,++0)
Randoms Proximal arbitrary positive 1 10 0.1 0.15
Randoms Proximal alternate positive 2 10 0.2 0.15
Reals Distal negative 6 2 3 3 ± 3 (--0,+-6)
Randoms Distal arbitrary negative 7 10 0.7 0.85
Randoms Distal alternate negative 10 10 1 0.85
Reals Distal positive 6 2 3 3 ± 2 (-+5,++1)
Randoms Distal arbitrary positive 17 10 1.7 1.25
Randoms Distal alternate positive 8 10 0.8 1.25

Comparison:

The occurrences of real B-boxes UTRs, proximals and negative direction distals are greater than the randoms, positive direction distals are greater than or equal to the randoms. This suggests that the real B-boxes are likely active or activable.

B1 box (Sanchez) samplings

  1. Negative strand, negative direction: 2, TGTCTCA at 2445, TGTCTCA at 1075.
  2. Positive strand, negative direction: 5, TGTCTCA at 4373, TGTCTCA at 3323, TGTCTCA at 2033, TGTCTCA at 1089, TGTCTCA at 923.
  3. Negative strand, positive direction: 2, TGTCTCA at 2468, TGTCTCA at 2174.
  4. Positive strand, positive direction: 0.
  5. Negative strand, negative direction, inverse complement: 3, TGAGACA at 2029, TGAGACA at 1085, TGAGACA at 919.
  6. Positive strand, negative direction, inverse complement: 0.
  7. Positive strand, positive direction, inverse complement: 1, TGAGACA at 2308.
  8. Negative strand, positive direction, inverse complement: 0.

B1 (4560-2846) UTRs

  1. Positive strand, negative direction: TGTCTCA at 4373, TGTCTCA at 3323.

B1 negative direction (2811-2596) proximal promoters

  1. Negative strand, negative direction: TGTCTCA at 2445.

B1 negative direction (2596-1) distal promoters

  1. Negative strand, negative direction: TGTCTCA at 2445, TGAGACA at 2029, TGAGACA at 1085, TGTCTCA at 1075, TGAGACA at 919.
  2. Positive strand, negative direction: TGTCTCA at 2033, TGTCTCA at 1089, TGTCTCA at 923.

B1 positive direction (4050-1) distal promoters

  1. Negative strand, positive direction: TGTCTCA at 2468, TGTCTCA at 2174.
  2. Positive strand, positive direction: TGAGACA at 2308.

B1 box (Sanchez) random dataset samplings

  1. B1boxr0: 0.
  2. B1boxr1: 0.
  3. B1boxr2: 0.
  4. B1boxr3: 0.
  5. B1boxr4: 0.
  6. B1boxr5: 0.
  7. B1boxr6: 0.
  8. B1boxr7: 0.
  9. B1boxr8: 0.
  10. B1boxr9: 0.
  11. B1boxr0ci: 1, TGAGACA at 4234.
  12. B1boxr1ci: 0.
  13. B1boxr2ci: 0.
  14. B1boxr3ci: 0.
  15. B1boxr4ci: 1, TGAGACA at 74.
  16. B1boxr5ci: 0.
  17. B1boxr6ci: 0.
  18. B1boxr7ci: 0.
  19. B1boxr8ci: 0.
  20. B1boxr9ci: 0.

B1r arbitrary (evens) (4560-2846) UTRs

  1. B1boxr0ci: TGAGACA at 4234.

B1r alternate positive direction (evens) (4265-4050) proximal promoters

  1. B1boxr0ci: TGAGACA at 4234.

B1r arbitrary negative direction (evens) (2596-1) distal promoters

  1. B1boxr4ci: TGAGACA at 74.

B1r alternate positive direction (evens) (4050-1) distal promoters

  1. B1boxr4ci: TGAGACA at 74.

Box B (B1box) analysis and results

Main article: Complex locus A1BG and ZNF497 § Box Bs

And "box B (TGTCTCA) [mediates] the upregulation of promoter activity via a PKC-dependent pathway after exposure of cells to a high-glucose environment (Refs 37, 38)."[2]

Reals or randoms Promoters direction Numbers Strands Occurrences Averages (± 0.1)
Reals UTR negative 2 2 1 1
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 1 2 0.5 0.5
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 0.05
Randoms Proximal alternate positive 1 10 0.1 0.05
Reals Distal negative 8 2 4 4 ± 1 (--5,+-3)
Randoms Distal arbitrary negative 1 10 0.1 0.05
Randoms Distal alternate negative 0 10 0 0.05
Reals Distal positive 3 2 1.5 1.5
Randoms Distal arbitrary positive 0 10 0 0.05
Randoms Distal alternate positive 1 10 0.1 0.05

Comparison:

The occurrences of real box Bs are greater than the randoms. This suggests that the real box Bs 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.

See also

References

  1. ↑ 1.0 1.1 1.2 PA Johnson, D Bunick, NB Hecht (1991). "Protein Binding Regions in the Mouse and Rat Protamine-2 Genes" (PDF). Biology of Reproduction. 44 (1): 127–134. Retrieved 6 April 2019.
  2. ↑ 2.0 2.1 Amber Paratore Sanchez and Kumar Sharma (July 2009). "Transcription factors in the pathogenesis of diabetic nephropathy". Expert Reviews in Molecular Medicine. 11: e13. doi:10.1017/S1462399409001057. Retrieved 1 October 2018.

External links


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