Pollen1 element gene transcriptions

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

"Electrophoretic mobility shift assays identified a pollen-specific cis-acting element POLLEN1 (AGAAA) mapped at AtACBP4 (−157/−153) which interacted with nuclear proteins from flower and this was substantiated by DNase I footprinting."[1]

"POLLEN1 and the TCCACCATA element are co-dependent regulatory elements responsible for pollen-specific activation of tomato LAT52 (Bate and Twell 1998)."[1]

Human genes

Consensus sequences

"Given that AtACBP4pro::GUS (−156/−67) could drive promoter activity for pollen expression, [electrophoretic mobility shift assays] EMSAs were carried out to investigate the role of the putative POLLEN1 cis-element, AGAAA (−150/−146), and its adjacent co-dependent regulatory element TCCACCATA (–141/–133)."[1]

Pollen1 samplings

Main article: Model samplings

Copying the consensus for POLLEN1: 3'-AGAAA-5' and putting the sequence in "⌘F" finds many locations for this sequence in the A1BG directions as can be found by the computer programs.

For the Basic programs testing consensus sequence AGAAA (starting with SuccessablesPOL.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 AGAAA, 5, AGAAA at 1733, AGAAA at 1418, AGAAA at 347, AGAAA at 47, AGAAA at 25.
  2. positive strand, negative direction, looking for AGAAA, 23, AGAAA at 4394, AGAAA at 4389, AGAAA at 4382, AGAAA at 4085, AGAAA at 4081, AGAAA at 3591, AGAAA at 3376, AGAAA at 3342, AGAAA at 2838, AGAAA at 2831, AGAAA at 2821, AGAAA at 2814, AGAAA at 2804, AGAAA at 2800, AGAAA at 2505, AGAAA at 2055, AGAAA at 1630, AGAAA at 357, AGAAA at 303, AGAAA at 226, AGAAA at 135, AGAAA at 102, AGAAA at 52.
  3. negative strand, positive direction, looking for AGAAA, 2, AGAAA at 3918, AGAAA at 2629.
  4. positive strand, positive direction, looking for AGAAA, 6, AGAAA at 4382, AGAAA at 3397, AGAAA at 2585, AGAAA at 2278, AGAAA at 1981, AGAAA at 110.
  5. inverse complement, negative strand, negative direction, looking for TTTCT, 22, TTTCT at 4505, TTTCT at 4392, TTTCT at 4387, TTTCT at 4380, TTTCT at 4083, TTTCT at 3924, TTTCT at 3665, TTTCT at 3378, TTTCT at 2892, TTTCT at 2836, TTTCT at 2824, TTTCT at 2819, TTTCT at 2807, TTTCT at 2802, TTTCT at 2798, TTTCT at 2175, TTTCT at 2053, TTTCT at 1628, TTTCT at 1549, TTTCT at 1400, TTTCT at 224, TTTCT at 55.
  6. inverse complement, positive strand, negative direction, looking for TTTCT, 2, TTTCT at 1604, TTTCT at 23.
  7. inverse complement, negative strand, positive direction, looking for TTTCT, 5, TTTCT at 4384, TTTCT at 2276, TTTCT at 2165, TTTCT at 1979, TTTCT at 137.
  8. inverse complement, positive strand, positive direction, looking for TTTCT, 2, TTTCT at 3929, TTTCT at 3065.

POL (4560-2846) UTRs

  1. Negative strand, negative direction: TTTCT at 4505, TTTCT at 4392, TTTCT at 4387, TTTCT at 4380, TTTCT at 4083, TTTCT at 3924, TTTCT at 3665, TTTCT at 3378, TTTCT at 2892.
  2. Positive strand, negative direction: AGAAA at 4394, AGAAA at 4389, AGAAA at 4382, AGAAA at 4085, AGAAA at 4081, AGAAA at 3591, AGAAA at 3376, AGAAA at 3342.

POL negative direction (2846-2811) core promoters

  1. Negative strand, negative direction: TTTCT at 2836, TTTCT at 2824, TTTCT at 2819.
  2. Positive strand, negative direction: AGAAA at 2838, AGAAA at 2831, AGAAA at 2821, AGAAA at 2814.

POL positive direction (4445-4265) core promoters

  1. Negative strand, positive direction: TTTCT at 4384.
  2. Positive strand, positive direction: AGAAA at 4382.

POL negative direction (2811-2596) proximal promoters

  1. Negative strand, negative direction: TTTCT at 2807, TTTCT at 2802, TTTCT at 2798.
  2. Positive strand, negative direction: AGAAA at 2804, AGAAA at 2800.

POL negative direction (2596-1) distal promoters

  1. Negative strand, negative direction: AGAAA at 1733, AGAAA at 1418, AGAAA at 347, AGAAA at 47, AGAAA at 25.
  2. Negative strand, negative direction: TTTCT at 2175, TTTCT at 2053, TTTCT at 1628, TTTCT at 1549, TTTCT at 1400, TTTCT at 224, TTTCT at 55.
  3. Positive strand, negative direction: AGAAA at 2505, AGAAA at 2055, AGAAA at 1630, AGAAA at 357, AGAAA at 303, AGAAA at 226, AGAAA at 135, AGAAA at 102, AGAAA at 52.
  4. Positive strand, negative direction: TTTCT at 1604, TTTCT at 23.

POL positive direction (4050-1) distal promoters

  1. Negative strand, positive direction: AGAAA at 3918, AGAAA at 2629.
  2. Negative strand, positive direction: TTTCT at 2276, TTTCT at 2165, TTTCT at 1979, TTTCT at 137.
  3. Positive strand, positive direction: AGAAA at 3397, AGAAA at 2585, AGAAA at 2278, AGAAA at 1981, AGAAA at 110.
  4. Positive strand, positive direction: TTTCT at 3929, TTTCT at 3065.

Response element random dataset samplings

  1. RDr0: 0.
  2. RDr1: 0.
  3. RDr2: 0.
  4. RDr3: 0.
  5. RDr4: 0.
  6. RDr5: 0.
  7. RDr6: 0.
  8. RDr7: 0.
  9. RDr8: 0.
  10. RDr9: 0.
  11. RDr0ci: 0.
  12. RDr1ci: 0.
  13. RDr2ci: 0.
  14. RDr3ci: 0.
  15. RDr4ci: 0.
  16. RDr5ci: 0.
  17. RDr6ci: 0.
  18. RDr7ci: 0.
  19. RDr8ci: 0.
  20. RDr9ci: 0.

RDr arbitrary (evens) (4560-2846) UTRs

RDr alternate (odds) (4560-2846) UTRs

RDr arbitrary negative direction (evens) (2846-2811) core promoters

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

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

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

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

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

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

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

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

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

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

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

Pollen1 analysis and results

Main article: Complex locus A1BG and ZNF497 § Pollen1s

"Electrophoretic mobility shift assays identified a pollen-specific cis-acting element POLLEN1 (AGAAA) mapped at AtACBP4 (−157/−153) which interacted with nuclear proteins from flower and this was substantiated by DNase I footprinting."[1]

Reals or randoms Promoters direction Numbers Strands Occurrences Averages (± 0.1)
Reals UTR negative 17 2 8.5 8.5 ± 0.5 (--9,+-8)
Randoms UTR arbitrary negative 0 10 0 0
Randoms UTR alternate negative 0 10 0 0
Reals Core negative 7 2 3.5 3.5
Randoms Core arbitrary negative 0 10 0 0
Randoms Core alternate negative 0 10 0 0
Reals Core positive 2 2 1 1
Randoms Core arbitrary positive 0 10 0 0
Randoms Core alternate positive 0 10 0 0
Reals Proximal negative 5 2 2.5 2.5
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
Randoms Proximal alternate positive 0 10 0 0
Reals Distal negative 23 2 11.5 11.5 ± 0.5 (--12,+-11)
Randoms Distal arbitrary negative 0 10 0 0
Randoms Distal alternate negative 0 10 0 0
Reals Distal positive 13 2 6.5 6.5 ± 0.5 (-+6,++7)
Randoms Distal arbitrary positive 0 10 0 0
Randoms Distal alternate positive 0 10 0 0

Comparison:

The occurrences of real Pollen1s are greater than the randoms. This suggests that the real Pollen1s are likely active or activable.

Pollen and TCC regulatory element samplings

Copying the consensus for POLLEN1: 3'-AGAAA-5' and putting the sequence in "⌘F" finds many locations for this sequence in the A1BG directions as can be found by the computer programs. POLLEN1, AGAAA (−150/−146), has adjacent co-dependent regulatory element TCCACCATA (–141/–133), so that a combined consensus sequence expected would have AGAAANNNNTCCACCATA.

For the Basic programs testing consensus sequence AGAAANNNNTCCACCATA (starting with SuccessablesPol.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 AGAAANNNNTCCACCATA, 0.
  2. positive strand, negative direction, looking for AGAAANNNNTCCACCATA, 0.
  3. positive strand, positive direction, looking for AGAAANNNNTCCACCATA, 0.
  4. negative strand, positive direction, looking for AGAAANNNNTCCACCATA, 0.
  5. complement, negative strand, negative direction, looking for TCTTTNNNNAGGTGGTAT, 0.
  6. complement, positive strand, negative direction, looking for TCTTTNNNNAGGTGGTAT, 0.
  7. complement, positive strand, positive direction, looking for TCTTTNNNNAGGTGGTAT, 0.
  8. complement, negative strand, positive direction, looking for TCTTTNNNNAGGTGGTAT, 0.
  9. inverse complement, negative strand, negative direction, looking for TATGGTGGANNNNTTTCT, 0.
  10. inverse complement, positive strand, negative direction, looking for TATGGTGGANNNNTTTCT, 0.
  11. inverse complement, positive strand, positive direction, looking for TATGGTGGANNNNTTTCT, 0.
  12. inverse complement, negative strand, positive direction, looking for TATGGTGGANNNNTTTCT, 0.
  13. inverse negative strand, negative direction, looking for ATACCACCTNNNNAAAGA, 0.
  14. inverse positive strand, negative direction, looking for ATACCACCTNNNNAAAGA, 0.
  15. inverse positive strand, positive direction, looking for ATACCACCTNNNNAAAGA, 0.
  16. inverse negative strand, positive direction, looking for ATACCACCTNNNNAAAGA, 0.

TCCACCATA regulatory element samplings

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

See also

References

  1. ↑ 1.0 1.1 1.2 1.3 Zi-Wei Ye, Jie Xu, Jianxin Shi, Dabing Zhang and Mee-Len Chye (January 2017). "Kelch-motif containing acyl-CoA binding proteins AtACBP4 and AtACBP5 are differentially expressed and function in floral lipid metabolism" (PDF). Plant Molecular Biology. 93: 209–225. doi:10.1007/s11103-016-0557-5. PMID 27826761. Retrieved 7 May 2020.

External links

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