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.

Pollen1 random dataset samplings

  1. Polr0: 8, AGAAA at 3656, AGAAA at 3365, AGAAA at 3344, AGAAA at 2199, AGAAA at 748, AGAAA at 633, AGAAA at 543, AGAAA at 215.
  2. Polr1: 5, AGAAA at 4353, AGAAA at 3872, AGAAA at 3268, AGAAA at 2797, AGAAA at 2422.
  3. Polr2: 8, AGAAA at 2338, AGAAA at 1848, AGAAA at 1843, AGAAA at 1331, AGAAA at 945, AGAAA at 578, AGAAA at 471, AGAAA at 367.
  4. Polr3: 6, AGAAA at 4420, AGAAA at 4340, AGAAA at 2917, AGAAA at 2083, AGAAA at 1833, AGAAA at 568.
  5. Polr4: 7, AGAAA at 3414, AGAAA at 2511, AGAAA at 2491, AGAAA at 2336, AGAAA at 2178, AGAAA at 1658, AGAAA at 1611.
  6. Polr5: 3, AGAAA at 2765, AGAAA at 2258, AGAAA at 2103.
  7. Polr6: 4, AGAAA at 4248, AGAAA at 1103, AGAAA at 68, AGAAA at 7.
  8. Polr7: 7, AGAAA at 4397, AGAAA at 3524, AGAAA at 2855, AGAAA at 2281, AGAAA at 2092, AGAAA at 1129, AGAAA at 140.
  9. Polr8: 8, AGAAA at 4269, AGAAA at 4247, AGAAA at 4108, AGAAA at 3875, AGAAA at 1687, AGAAA at 418, AGAAA at 313, AGAAA at 281.
  10. Polr9: 10, AGAAA at 4498, AGAAA at 4315, AGAAA at 3852, AGAAA at 3203, AGAAA at 3191, AGAAA at 3018, AGAAA at 1930, AGAAA at 1864, AGAAA at 585, AGAAA at 401.
  11. Polr0ci: 10, TTTCT at 4221, TTTCT at 3666, TTTCT at 3032, TTTCT at 2827, TTTCT at 2569, TTTCT at 1972, TTTCT at 1673, TTTCT at 1195, TTTCT at 1039, TTTCT at 131.
  12. Polr1ci: 11, TTTCT at 3953, TTTCT at 3690, TTTCT at 3586, TTTCT at 2204, TTTCT at 1293, TTTCT at 1276, TTTCT at 1102, TTTCT at 980, TTTCT at 944, TTTCT at 831, TTTCT at 201.
  13. Polr2ci: 5, TTTCT at 3343, TTTCT at 2464, TTTCT at 2350, TTTCT at 2288, TTTCT at 1511.
  14. Polr3ci: 7, TTTCT at 4400, TTTCT at 4095, TTTCT at 4006, TTTCT at 3690, TTTCT at 3250, TTTCT at 2020, TTTCT at 410.
  15. Polr4ci: 7, TTTCT at 3870, TTTCT at 2122, TTTCT at 1188, TTTCT at 541, TTTCT at 412, TTTCT at 363, TTTCT at 44.
  16. Polr5ci: 6, TTTCT at 4197, TTTCT at 3439, TTTCT at 3329, TTTCT at 3192, TTTCT at 1978, TTTCT at 146.
  17. Polr6ci: 4, TTTCT at 4481, TTTCT at 1880, TTTCT at 1353, TTTCT at 1319.
  18. Polr7ci: 5, TTTCT at 4270, TTTCT at 3202, TTTCT at 3095, TTTCT at 712, TTTCT at 25.
  19. Polr8ci: 4, TTTCT at 4356, TTTCT at 2384, TTTCT at 1481, TTTCT at 1159.
  20. Polr9ci: 7, TTTCT at 2900, TTTCT at 2784, TTTCT at 2345, TTTCT at 2310, TTTCT at 1736, TTTCT at 1353, TTTCT at 351.

Polr arbitrary (evens) (4560-2846) UTRs

  1. Polr0: AGAAA at 3656, AGAAA at 3365, AGAAA at 3344.
  2. Polr4: AGAAA at 3414.
  3. Polr6: AGAAA at 4248.
  4. Polr8: AGAAA at 4269, AGAAA at 4247, AGAAA at 4108, AGAAA at 3875.
  5. Polr0ci: TTTCT at 4221, TTTCT at 3666, TTTCT at 3032.
  6. Polr2ci: TTTCT at 3343.
  7. Polr4ci: TTTCT at 3870.
  8. Polr6ci: TTTCT at 4481.
  9. Polr8ci: TTTCT at 4356.

Polr alternate (odds) (4560-2846) UTRs

  1. Polr1: AGAAA at 4353, AGAAA at 3872, AGAAA at 3268.
  2. Polr3: AGAAA at 4420, AGAAA at 4340, AGAAA at 2917.
  3. Polr7: AGAAA at 4397, AGAAA at 3524, AGAAA at 2855.
  4. Polr9: AGAAA at 4498, AGAAA at 4315, AGAAA at 3852, AGAAA at 3203, AGAAA at 3191, AGAAA at 3018.
  5. Polr1ci: TTTCT at 3953, TTTCT at 3690, TTTCT at 3586.
  6. Polr3ci: TTTCT at 4400, TTTCT at 4095, TTTCT at 4006, TTTCT at 3690, TTTCT at 3250.
  7. Polr5ci: TTTCT at 4197, TTTCT at 3439, TTTCT at 3329, TTTCT at 3192.
  8. Polr7ci: TTTCT at 4270, TTTCT at 3202, TTTCT at 3095.
  9. Polr9ci: TTTCT at 2900.

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

  1. Polr0ci: TTTCT at 2827.

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

  1. Polr1: AGAAA at 4353.
  2. Polr3: AGAAA at 4420, AGAAA at 4340.
  3. Polr7: AGAAA at 4397.
  4. Polr9: AGAAA at 4315.
  5. Polr3ci: TTTCT at 4400.
  6. Polr7ci: TTTCT at 4270.

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

  1. Polr8: AGAAA at 4269.
  2. Polr8ci: TTTCT at 4356.

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

  1. Polr1: AGAAA at 2797.
  2. Polr5: AGAAA at 2765.
  3. Polr9ci: TTTCT at 2784.

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

  1. Polr3ci: TTTCT at 4400, TTTCT at 4095.
  2. Polr5ci: TTTCT at 4197.

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

  1. Polr6: AGAAA at 4248.
  2. Polr8: AGAAA at 4247, AGAAA at 4108.
  3. Polr0ci: TTTCT at 4221.

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

  1. Polr0: AGAAA at 2199, AGAAA at 748, AGAAA at 633, AGAAA at 543, AGAAA at 215.
  2. Polr2: AGAAA at 2338, AGAAA at 1848, AGAAA at 1843, AGAAA at 1331, AGAAA at 945, AGAAA at 578, AGAAA at 471, AGAAA at 367.
  3. Polr4: AGAAA at 2511, AGAAA at 2491, AGAAA at 2336, AGAAA at 2178, AGAAA at 1658, AGAAA at 1611.
  4. Polr6: AGAAA at 1103, AGAAA at 68, AGAAA at 7.
  5. Polr8: AGAAA at 1687, AGAAA at 418, AGAAA at 313, AGAAA at 281.
  6. Polr0ci: TTTCT at 2569, TTTCT at 1972, TTTCT at 1673, TTTCT at 1195, TTTCT at 1039, TTTCT at 131.
  7. Polr2ci: TTTCT at 2464, TTTCT at 2350, TTTCT at 2288, TTTCT at 1511.
  8. Polr4ci: TTTCT at 2122, TTTCT at 1188, TTTCT at 541, TTTCT at 412, TTTCT at 363, TTTCT at 44.
  9. Polr6ci: TTTCT at 1880, TTTCT at 1353, TTTCT at 1319.
  10. Polr8ci: TTTCT at 2384, TTTCT at 1481, TTTCT at 1159.

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

  1. Polr1: AGAAA at 2422.
  2. Polr3: AGAAA at 2083, AGAAA at 1833, AGAAA at 568.
  3. Polr5: AGAAA at 2258, AGAAA at 2103.
  4. Polr7: AGAAA at 2281, AGAAA at 2092, AGAAA at 1129, AGAAA at 140.
  5. Polr9: AGAAA at 1930, AGAAA at 1864, AGAAA at 585, AGAAA at 401.
  6. Polr1ci: TTTCT at 2204, TTTCT at 1293, TTTCT at 1276, TTTCT at 1102, TTTCT at 980, TTTCT at 944, TTTCT at 831, TTTCT at 201.
  7. Polr3ci: TTTCT at 2020, TTTCT at 410.
  8. Polr5ci: TTTCT at 1978, TTTCT at 146.
  9. Polr7ci: TTTCT at 712, TTTCT at 25.
  10. Polr9ci: TTTCT at 2345, TTTCT at 2310, TTTCT at 1736, TTTCT at 1353, TTTCT at 351.

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

  1. Polr1: AGAAA at 3872, AGAAA at 3268, AGAAA at 2797, AGAAA at 2422.
  2. Polr3: AGAAA at AGAAA at 2917, AGAAA at 2083, AGAAA at 1833, AGAAA at 568.
  3. Polr5: AGAAA at 2765, AGAAA at 2258, AGAAA at 2103.
  4. Polr7: AGAAA at 3524, AGAAA at 2855, AGAAA at 2281, AGAAA at 2092, AGAAA at 1129, AGAAA at 140.
  5. Polr9: AGAAA at 3852, AGAAA at 3203, AGAAA at 3191, AGAAA at 3018, AGAAA at 1930, AGAAA at 1864, AGAAA at 585, AGAAA at 401.
  6. Polr1ci: TTTCT at 3953, TTTCT at 3690, TTTCT at 3586, TTTCT at 2204, TTTCT at 1293, TTTCT at 1276, TTTCT at 1102, TTTCT at 980, TTTCT at 944, TTTCT at 831, TTTCT at 201.
  7. Polr3ci: TTTCT at 4006, TTTCT at 3690, TTTCT at 3250, TTTCT at 2020, TTTCT at 410.
  8. Polr5ci: TTTCT at 3439, TTTCT at 3329, TTTCT at 3192, TTTCT at 1978, TTTCT at 146.
  9. Polr7ci: TTTCT at 3202, TTTCT at 3095, TTTCT at 712, TTTCT at 25.
  10. Polr9ci: TTTCT at 2900, TTTCT at 2784, TTTCT at 2345, TTTCT at 2310, TTTCT at 1736, TTTCT at 1353, TTTCT at 351.

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

  1. Polr0: AGAAA at 3656, AGAAA at 3365, AGAAA at 3344, AGAAA at 2199, AGAAA at 748, AGAAA at 633, AGAAA at 543, AGAAA at 215.
  2. Polr2: AGAAA at 2338, AGAAA at 1848, AGAAA at 1843, AGAAA at 1331, AGAAA at 945, AGAAA at 578, AGAAA at 471, AGAAA at 367.
  3. Polr4: AGAAA at 3414, AGAAA at 2511, AGAAA at 2491, AGAAA at 2336, AGAAA at 2178, AGAAA at 1658, AGAAA at 1611.
  4. Polr6: AGAAA at 1103, AGAAA at 68, AGAAA at 7.
  5. Polr8: AGAAA at 3875, AGAAA at 1687, AGAAA at 418, AGAAA at 313, AGAAA at 281.
  6. Polr0ci: TTTCT at 3666, TTTCT at 3032, TTTCT at 2827, TTTCT at 2569, TTTCT at 1972, TTTCT at 1673, TTTCT at 1195, TTTCT at 1039, TTTCT at 131.
  7. Polr2ci: TTTCT at 3343, TTTCT at 2464, TTTCT at 2350, TTTCT at 2288, TTTCT at 1511.
  8. Polr4ci: TTTCT at 3870, TTTCT at 2122, TTTCT at 1188, TTTCT at 541, TTTCT at 412, TTTCT at 363, TTTCT at 44.
  9. Polr6ci: TTTCT at 1880, TTTCT at 1353, TTTCT at 1319.
  10. Polr8ci: TTTCT at 2384, TTTCT at 1481, TTTCT at 1159.

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 16 10 1.6 2.35
Randoms UTR alternate negative 31 10 3.1 2.35
Reals Core negative 7 2 3.5 3.5 ± 0.5 (--3.+-4)
Randoms Core arbitrary negative 1 10 0.1 0.05
Randoms Core alternate negative 0 10 0 0.05
Reals Core positive 2 2 1 1 ± 0 (-+1,++1)
Randoms Core arbitrary positive 7 10 0.7 0.45
Randoms Core alternate positive 2 10 0.2 0.45
Reals Proximal negative 5 2 2.5 2.5 ± 0.5 (--3,+-2)
Randoms Proximal arbitrary negative 0 10 0 0.15
Randoms Proximal alternate negative 3 10 0.3 0.15
Reals Proximal positive 0 2 0 0
Randoms Proximal arbitrary positive 3 10 0.3 0.35
Randoms Proximal alternate positive 4 10 0.4 0.35
Reals Distal negative 23 2 11.5 11.5 ± 0.5 (--12,+-11)
Randoms Distal arbitrary negative 48 10 4.8 4.05
Randoms Distal alternate negative 33 10 3.3 4.05
Reals Distal positive 13 2 6.5 6.5 ± 0.5 (-+6,++7)
Randoms Distal arbitrary positive 58 10 5.8 5.8
Randoms Distal alternate positive 58 10 5.8 5.8

Comparison:

The occurrences of real Pollen1 UTRs, cores, proximals and distals 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: 0.
  2. positive strand, negative direction: 0.
  3. positive strand, positive direction: 0.
  4. negative strand, positive direction: 0.
  5. inverse complement, negative strand, negative direction: 0.
  6. inverse complement, positive strand, negative direction: 0.
  7. inverse complement, positive strand, positive direction: 0.
  8. inverse complement, negative strand, positive direction: 0.
  1. No TCCACCATAs were found nor their ci's.

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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