Endoplasmic reticulum stress response element gene transcriptions

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

Human genes

Consensus sequences

"The released aminoterminal of ATF6 (ATF6-N) then migrates to the nucleus and binds to the ER stress response element (ERSE) containing the consensus sequence CCAAT-N9-CCACG to activate genes encoding ER chaperones, ERAD components, and XBP1 (Chen et al., 2010; Yamamoto et al., 2004; Yoshida et al., 2001)."[1]

CCAAT samplings

Copying an apparent consensus sequence of CCAAT and putting it in "⌘F" finds none located between ZSCAN22 and A1BG on the negative strand and finds one on the positive strand but CCAAT-1A-2T-3T-4T5T-6A-7A-8A-9GT finds none and CCAAT occurs once between ZNF497 and A1BG but CCAAT-1G-2G-3G-4C-5T-6G-7A-8A-9AC finds none between ZNF497 and A1BG on the negative strand and CCAAT occurs once between ZNF497 and A1BG but CCAAT-1A-2C-3T-4G-5A-6A-7G-8T-9CCG finds none on the positive strand as can be found by the computer programs.

For the Basic programs testing consensus sequence CCAAT (starting with SuccessablesERSE.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: 1, CCAAT at 2848.
  3. negative strand, positive direction: 1, CCAAT at 2908.
  4. positive strand, positive direction, looking for CCAAT, 1, CCAAT at 3024.
  5. inverse complement, negative strand, negative direction: 1, ATTGG at 614.
  6. inverse complement, positive strand, negative direction: 3, ATTGG at 3529, ATTGG at 1045, ATTGG at 643.
  7. inverse complement, negative strand, positive direction: 1, ATTGG at 24.
  8. inverse complement, positive strand, positive direction: 0.

ERSE (4560-2846) UTRs

  1. Positive strand, negative direction: CCAAT at 2848.
  2. Positive strand, negative direction: ATTGG at 3529.

ERSE negative direction (2596-1) distal promoters

  1. Negative strand, negative direction: ATTGG at 614.
  2. Positive strand, negative direction: ATTGG at 1045, ATTGG at 643.

ERSE positive direction (4050-1) distal promoters

  1. Negative strand, positive direction: CCAAT at 2908.
  2. Negative strand, positive direction: ATTGG at 24.
  3. Positive strand, positive direction: CCAAT at 3024.

ERSE random dataset samplings

  1. ERSEr0: 7, CCAAT at 4457, CCAAT at 3878, CCAAT at 3351, CCAAT at 2733, CCAAT at 2614, CCAAT at 2492, CCAAT at 2231.
  2. ERSEr1: 5, CCAAT at 3303, CCAAT at 2599, CCAAT at 2563, CCAAT at 786, CCAAT at 296.
  3. ERSEr2: 7, CCAAT at 4397, CCAAT at 3960, CCAAT at 3882, CCAAT at 2975, CCAAT at 1612, CCAAT at 1461, CCAAT at 1354.
  4. ERSEr3: 9, CCAAT at 4252, CCAAT at 3740, CCAAT at 3367, CCAAT at 3043, CCAAT at 1728, CCAAT at 1670, CCAAT at 1277, CCAAT at 830, CCAAT at 236.
  5. ERSEr4: 7, CCAAT at 4145, CCAAT at 2480, CCAAT at 2325, CCAAT at 2107, CCAAT at 1784, CCAAT at 1761, CCAAT at 717.
  6. ERSEr5: 8, CCAAT at 4474, CCAAT at 4156, CCAAT at 2635, CCAAT at 2225, CCAAT at 1869, CCAAT at 1463, CCAAT at 911, CCAAT at 192.
  7. ERSEr6: 10, CCAAT at 4188, CCAAT at 3103, CCAAT at 3037, CCAAT at 2486, CCAAT at 2228, CCAAT at 1955, CCAAT at 1646, CCAAT at 1626, CCAAT at 740, CCAAT at 692.
  8. ERSEr7: 8, CCAAT at 4452, CCAAT at 4262, CCAAT at 3779, CCAAT at 3386, CCAAT at 2924, CCAAT at 2355, CCAAT at 1561, CCAAT at 952.
  9. ERSEr8: 11, CCAAT at 3938, CCAAT at 3898, CCAAT at 3047, CCAAT at 2713, CCAAT at 2420, CCAAT at 2219, CCAAT at 1451, CCAAT at 1420, CCAAT at 1266, CCAAT at 1129, CCAAT at 604.
  10. ERSEr9: 3, CCAAT at 3562, CCAAT at 3429, CCAAT at 1526.
  11. ERSEr0ci: 5, ATTGG at 3851, ATTGG at 3203, ATTGG at 1776, ATTGG at 379, ATTGG at 81.
  12. ERSEr1ci: 3, ATTGG at 3814, ATTGG at 2647, ATTGG at 314.
  13. ERSEr2ci: 4, ATTGG at 3592, ATTGG at 1415, ATTGG at 1335, ATTGG at 755.
  14. ERSEr3ci: 11, ATTGG at 2942, ATTGG at 2842, ATTGG at 2826, ATTGG at 2389, ATTGG at 2353, ATTGG at 2050, ATTGG at 1231, ATTGG at 1163, ATTGG at 1048, ATTGG at 666, ATTGG at 182.
  15. ERSEr4ci: 4, ATTGG at 3576, ATTGG at 3097, ATTGG at 708, ATTGG at 651.
  16. ERSEr5ci: 3, ATTGG at 3810, ATTGG at 3172, ATTGG at 1888.
  17. ERSEr6ci: 10, ATTGG at 4430, ATTGG at 4099, ATTGG at 3233, ATTGG at 2516, ATTGG at 2495, ATTGG at 2489, ATTGG at 1389, ATTGG at 1326, ATTGG at 1026, ATTGG at 604.
  18. ERSEr7ci: 3, ATTGG at 4180, ATTGG at 3162, ATTGG at 2457.
  19. ERSEr8ci: 7, ATTGG at 4023, ATTGG at 4007, ATTGG at 3239, ATTGG at 3117, ATTGG at 1977, ATTGG at 855, ATTGG at 204.
  20. ERSEr9ci: 7, ATTGG at 4435, ATTGG at 3992, ATTGG at 3722, ATTGG at 2889, ATTGG at 2851, ATTGG at 2329, ATTGG at 1804.

ERSEr arbitrary (evens) (4560-2846) UTRs

  1. ERSEr0: CCAAT at 4457, CCAAT at 3878, CCAAT at 3351.
  2. ERSEr2: CCAAT at 4397, CCAAT at 3960, CCAAT at 3882, CCAAT at 2975.
  3. ERSEr4: CCAAT at 4145, CCAAT at 2480, CCAAT at 2325, CCAAT at 2107, CCAAT at 1784, CCAAT at 1761, CCAAT at 717.
  4. ERSEr6: CCAAT at 4188, CCAAT at 3103, CCAAT at 3037.
  5. ERSEr8: CCAAT at 3938, CCAAT at 3898, CCAAT at 3047.
  6. ERSEr0ci: ATTGG at 3851, ATTGG at 3203.
  7. ERSEr2ci: ATTGG at 3592.
  8. ERSEr4ci: ATTGG at 3576, ATTGG at 3097.
  9. ERSEr6ci: ATTGG at 4430, ATTGG at 4099, ATTGG at 3233.
  10. ERSEr8ci: ATTGG at 4023, ATTGG at 4007, ATTGG at 3239, ATTGG at 3117.

ERSEr alternate (odds) (4560-2846) UTRs

  1. ERSEr1: CCAAT at 3303, CCAAT at 2599, CCAAT at 2563, CCAAT at 786, CCAAT at 296.
  2. ERSEr3: CCAAT at 4252, CCAAT at 3740, CCAAT at 3367, CCAAT at 3043.
  3. ERSEr5: CCAAT at 4474, CCAAT at 4156.
  4. ERSEr7: CCAAT at 4452, CCAAT at 4262, CCAAT at 3779, CCAAT at 3386, CCAAT at 2924.
  5. ERSEr9: CCAAT at 3562, CCAAT at 3429.
  6. ERSEr1ci: ATTGG at 3814.
  7. ERSEr3ci: ATTGG at 2942.
  8. ERSEr5ci: ATTGG at 3810, ATTGG at 3172.
  9. ERSEr7ci: ATTGG at 4180, ATTGG at 3162, ATTGG at 2457.
  10. ERSEr9ci: ATTGG at 4435, ATTGG at 3992, ATTGG at 3722, ATTGG at 2889, ATTGG at 2851.

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

  1. ERSEr3ci: ATTGG at 2842, ATTGG at 2826.

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

  1. ERSEr9ci: ATTGG at 4435.

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

  1. ERSEr2: CCAAT at 4397.
  2. ERSEr4: CCAAT at 4145.
  3. ERSEr6ci: ATTGG at 4430.

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

  1. ERSEr0: CCAAT at 2733, CCAAT at 2614.
  2. ERSEr8: CCAAT at 2713.

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

  1. ERSEr5: CCAAT at 2635.
  2. ERSEr1ci: ATTGG at 2647.

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

  1. ERSEr3: CCAAT at 4252.
  2. ERSEr5: CCAAT at 4156.
  3. ERSEr7: CCAAT at 4262.
  4. ERSEr7ci: ATTGG at 4180.

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

  1. ERSEr4: CCAAT at 4145.
  2. ERSEr6: CCAAT at 4188.
  3. ERSEr6ci: ATTGG at 4099.

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

  1. ERSEr0: CCAAT at 2492, CCAAT at 2231.
  2. ERSEr2: CCAAT at 1612, CCAAT at 1461, CCAAT at 1354.
  3. ERSEr4: CCAAT at 2480, CCAAT at 2325, CCAAT at 2107, CCAAT at 1784, CCAAT at 1761, CCAAT at 717.
  4. ERSEr6: CCAAT at 2486, CCAAT at 2228, CCAAT at 1955, CCAAT at 1646, CCAAT at 1626, CCAAT at 740, CCAAT at 692.
  5. ERSEr8: CCAAT at 2420, CCAAT at 2219, CCAAT at 1451, CCAAT at 1420, CCAAT at 1266, CCAAT at 1129, CCAAT at 604.
  6. ERSEr0ci: ATTGG at 1776, ATTGG at 379, ATTGG at 81.
  7. ERSEr2ci: ATTGG at 1415, ATTGG at 1335, ATTGG at 755.
  8. ERSEr4ci: ATTGG at 708, ATTGG at 651.
  9. ERSEr6ci: ATTGG at 2516, ATTGG at 2495, ATTGG at 2489, ATTGG at 1389, ATTGG at 1326, ATTGG at 1026, ATTGG at 604.
  10. ERSEr8ci: ATTGG at 1977, ATTGG at 855, ATTGG at 204.

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

  1. ERSEr1: CCAAT at 2563, CCAAT at 786, CCAAT at 296.
  2. ERSEr3: CCAAT at 1728, CCAAT at 1670, CCAAT at 1277, CCAAT at 830, CCAAT at 236.
  3. ERSEr5: CCAAT at 2225, CCAAT at 1869, CCAAT at 1463, CCAAT at 911, CCAAT at 192.
  4. ERSEr7: CCAAT at 4452, CCAAT at 4262, CCAAT at 3779, CCAAT at 3386, CCAAT at 2924, CCAAT at 2355, CCAAT at 1561, CCAAT at 952.
  5. ERSEr9: CCAAT at 1526.
  6. ERSEr1ci: ATTGG at 314.
  7. ERSEr3ci: ATTGG at 2389, ATTGG at 2353, ATTGG at 2050, ATTGG at 1231, ATTGG at 1163, ATTGG at 1048, ATTGG at 666, ATTGG at 182.
  8. ERSEr5ci: ATTGG at 1888.
  9. ERSEr7ci: ATTGG at 2457.
  10. ERSEr9ci: ATTGG at 2329, ATTGG at 1804.

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

  1. ERSEr1: CCAAT at 3303, CCAAT at 2599, CCAAT at 2563, CCAAT at 786, CCAAT at 296.
  2. ERSEr3: CCAAT at 3740, CCAAT at 3367, CCAAT at 3043, CCAAT at 1728, CCAAT at 1670, CCAAT at 1277, CCAAT at 830, CCAAT at 236.
  3. ERSEr5: CCAAT at 2635, CCAAT at 2225, CCAAT at 1869, CCAAT at 1463, CCAAT at 911, CCAAT at 192.
  4. ERSEr7: CCAAT at 3779, CCAAT at 3386, CCAAT at 2924, CCAAT at 2355, CCAAT at 1561, CCAAT at 952.
  5. ERSEr9: CCAAT at 3562, CCAAT at 3429, CCAAT at 1526.
  6. ERSEr1ci: ATTGG at 3814, ATTGG at 2647, ATTGG at 314.
  7. ERSEr3ci: ATTGG at 2942, ATTGG at 2842, ATTGG at 2826, ATTGG at 2389, ATTGG at 2353, ATTGG at 2050, ATTGG at 1231, ATTGG at 1163, ATTGG at 1048, ATTGG at 666, ATTGG at 182.
  8. ERSEr5ci: ATTGG at 3810, ATTGG at 3172, ATTGG at 1888.
  9. ERSEr7ci: ATTGG at 3162, ATTGG at 2457.
  10. ERSEr9ci: ATTGG at 3992, ATTGG at 3722, ATTGG at 2889, ATTGG at 2851, ATTGG at 2329, ATTGG at 1804.

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

  1. ERSEr0: CCAAT at 3878, CCAAT at 3351, CCAAT at 2733, CCAAT at 2614, CCAAT at 2492, CCAAT at 2231.
  2. ERSEr2: CCAAT at 3960, CCAAT at 3882, CCAAT at 2975, CCAAT at 1612, CCAAT at 1461, CCAAT at 1354.
  3. ERSEr4: CCAAT at 2480, CCAAT at 2325, CCAAT at 2107, CCAAT at 1784, CCAAT at 1761, CCAAT at 717.
  4. ERSEr6: CCAAT at 3103, CCAAT at 3037, CCAAT at 2486, CCAAT at 2228, CCAAT at 1955, CCAAT at 1646, CCAAT at 1626, CCAAT at 740, CCAAT at 692.
  5. ERSEr8: CCAAT at 3938, CCAAT at 3898, CCAAT at 3047, CCAAT at 2713, CCAAT at 2420, CCAAT at 2219, CCAAT at 1451, CCAAT at 1420, CCAAT at 1266, CCAAT at 1129, CCAAT at 604.
  6. ERSEr0ci: ATTGG at 3851, ATTGG at 3203, ATTGG at 1776, ATTGG at 379, ATTGG at 81.
  7. ERSEr2ci: ATTGG at 3592, ATTGG at 1415, ATTGG at 1335, ATTGG at 755.
  8. ERSEr4ci: ATTGG at 3576, ATTGG at 3097, ATTGG at 708, ATTGG at 651.
  9. ERSEr6ci: ATTGG at 3233, ATTGG at 2516, ATTGG at 2495, ATTGG at 2489, ATTGG at 1389, ATTGG at 1326, ATTGG at 1026, ATTGG at 604.
  10. ERSEr8ci: ATTGG at 4023, ATTGG at 4007, ATTGG at 3239, ATTGG at 3117, ATTGG at 1977, ATTGG at 855, ATTGG at 204.

Endoplasmic reticulum stress response element first part analysis and results

Main article: Complex locus A1BG and ZNF497 § CCAAT

"The released aminoterminal of ATF6 (ATF6-N) then migrates to the nucleus and binds to the ER stress response element (ERSE) containing the consensus sequence CCAAT-N9-CCACG to activate genes encoding ER chaperones, ERAD components, and XBP1 (Chen et al., 2010; Yamamoto et al., 2004; Yoshida et al., 2001)."[1]

Reals or randoms Promoters direction Numbers Strands Occurrences Averages (± 0.1)
Reals UTR negative 2 2 1 1 ± 1 (--0,+-2)
Randoms UTR arbitrary negative 32 10 3.2 3.1
Randoms UTR alternate negative 30 10 3.0 3.1
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 1 10 0.1 0.2
Randoms Core alternate positive 3 10 0.3 0.2
Reals Proximal negative 0 2 0 0
Randoms Proximal arbitrary negative 3 10 0.3 0.25
Randoms Proximal alternate negative 2 10 0.2 0.25
Reals Proximal positive 0 2 0 0
Randoms Proximal arbitrary positive 4 10 0.4 0.35
Randoms Proximal alternate positive 3 10 0.3 0.35
Reals Distal negative 3 2 1.5 1.5 ± 0.5 (--1,+-2)
Randoms Distal arbitrary negative 43 10 4.3 3.9 ± 0.4
Randoms Distal alternate negative 35 10 3.5 3.9 ± 0.4
Reals Distal positive 3 2 1.5 1.5 ± 0.5(-+2,++1)
Randoms Distal arbitrary positive 53 10 5.3 5.95 ± 0.65
Randoms Distal alternate positive 66 10 6.6 5.95 ± 0.65

Comparison: The real ERSE UTRs and distals are lower than the randoms. The reals are likely active or activable.

The results here for part one are in agreement with those for the heme-activated protein (Hap).

CCACG samplings

Copying an apparent consensus sequence of CCACG and putting it in "⌘F" finds eight located between ZSCAN22 and A1BG on the negative strand and none on the positive strand and six on the negative strand between ZNF497 and eight on the positive strand and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence CCACG (starting with SuccessablesERSE2.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 CCACG, 8, CCACG at 3954, CCACG at 3880, CCACG at 3196, CCACG at 2333, CCACG at 2195, CCACG at 2080, CCACG at 1254, CCACG at 378.
  2. positive strand, negative direction, looking for CCACG, 0.
  3. negative strand, positive direction, looking for CCACG, 6, CCACG at 3604, CCACG at 968, CCACG at 868, CCACG at 775, CCACG at 298, CCACG at 241.
  4. positive strand, positive direction, looking for CCACG, 8, CCACG at 3882, CCACG at 3150, CCACG at 487, CCACG at 782, CCACG at 1762, CCACG at 2088, CCACG at 2333, CCACG at 2799,
  5. inverse complement, negative strand, negative direction, looking for CGTGG, 2, CGTGG at 2761, CGTGG at 1339.
  6. inverse complement, positive strand, negative direction, looking for CGTGG, 5, CGTGG at 4238, CGTGG at 3047, CGTGG at 1897, CGTGG at 1244, CGTGG at 741.
  7. inverse complement, negative strand, positive direction, looking for CGTGG, 2, CGTGG at 4377, CGTGG at 3813.
  8. inverse complement, positive strand, positive direction, looking for CGTGG, 17, CGTGG at 4343, CGTGG at 3885, CGTGG at 3601, CGTGG at 3322, CGTGG at 3044, CGTGG at 2566, CGTGG at 1628, CGTGG at 1460, CGTGG at 1360, CGTGG at 1208, CGTGG at 1124, CGTGG at 1040, CGTGG at 956, CGTGG at 856, CGTGG at 788, CGTGG at 772, CGTGG at 620.

ERSE2 (4560-2846) UTRs

  1. Negative strand, negative direction: CCACG at 3954, CCACG at 3880, CCACG at 3196.
  2. Positive strand, negative direction: CGTGG at 4238, CGTGG at 3047.

ERSE2 positive direction (4445-4265) core promoters

  1. Negative strand, positive direction: CGTGG at 4377.
  2. Positive strand, positive direction: CGTGG at 4343.

ERSE2 negative direction (2811-2596) proximal promoters

  1. Negative strand, negative direction: CGTGG at 2761.

ERSE2 negative direction (2596-1) distal promoters

  1. Negative strand, negative direction: CCACG at 2333, CCACG at 2195, CCACG at 2080, CCACG at 1254, CCACG at 378.
  2. Negative strand, negative direction: CGTGG at 1339.
  3. Positive strand, negative direction: CGTGG at 1897, CGTGG at 1244, CGTGG at 741.

ERSE2 positive direction (4050-1) distal promoters

  1. Negative strand, positive direction: CCACG at 3604, CCACG at 968, CCACG at 868, CCACG at 775, CCACG at 298, CCACG at 241.
  2. Negative strand, positive direction: CGTGG at 3813.
  3. Positive strand, positive direction: CCACG at 3882, CCACG at 3150, CCACG at 2799, CCACG at 2333, CCACG at 2088, CCACG at 1762, CCACG at 782, CCACG at 487.
  4. Positive strand, positive direction: CGTGG at 3885, CGTGG at 3601, CGTGG at 3322, CGTGG at 3044, CGTGG at 2566, CGTGG at 1628, CGTGG at 1460, CGTGG at 1360, CGTGG at 1208, CGTGG at 1124, CGTGG at 1040, CGTGG at 956, CGTGG at 856, CGTGG at 788, CGTGG at 772, CGTGG at 620.

ERSE2 random dataset samplings

  1. ERSE2r0: 3, CCACG at 4341, CCACG at 2167, CCACG at 441.
  2. ERSE2r1: 5, CCACG at 3663, CCACG at 3297, CCACG at 1759, CCACG at 1227, CCACG at 190.
  3. ERSE2r2: 1, CCACG at 1928.
  4. ERSE2r3: 4, CCACG at 4079, CCACG at 1481, CCACG at 883, CCACG at 585.
  5. ERSE2r4: 2, CCACG at 3158, CCACG at 1283.
  6. ERSE2r5: 3, CCACG at 1787, CCACG at 801, CCACG at 72.
  7. ERSE2r6: 2, CCACG at 3432, CCACG at 2903.
  8. ERSE2r7: 3, CCACG at 3250, CCACG at 1939, CCACG at 1239.
  9. ERSE2r8: 3, CCACG at 2934, CCACG at 942, CCACG at 896.
  10. ERSE2r9: 3, CCACG at 4212, CCACG at 2964, CCACG at 873.
  11. ERSE2r0ci: 3, CGTGG at 2384, CGTGG at 1936, CGTGG at 842.
  12. ERSE2r1ci: 4, CGTGG at 4419, CGTGG at 2339, CGTGG at 660, CGTGG at 575.
  13. ERSE2r2ci: 2, CGTGG at 2459, CGTGG at 100.
  14. ERSE2r3ci: 3, CGTGG at 3322, CGTGG at 3115, CGTGG at 1438.
  15. ERSE2r4ci: 4, CGTGG at 4272, CGTGG at 3733, CGTGG at 2288, CGTGG at 958.
  16. ERSE2r5ci: 6, CGTGG at 4315, CGTGG at 3956, CGTGG at 1588, CGTGG at 731, CGTGG at 631, CGTGG at 371.
  17. ERSE2r6ci: 3, CGTGG at 1275, CGTGG at 659, CGTGG at 336.
  18. ERSE2r7ci: 6, CGTGG at 3592, CGTGG at 3535, CGTGG at 3316, CGTGG at 2297, CGTGG at 1790, CGTGG at 453.
  19. ERSE2r8ci: 6, CGTGG at 4087, CGTGG at 3665, CGTGG at 1535, CGTGG at 1406, CGTGG at 304, CGTGG at 184.
  20. ERSE2r9ci: 8, CGTGG at 4505, CGTGG at 3274, CGTGG at 2943, CGTGG at 2703, CGTGG at 1641, CGTGG at 1431, CGTGG at 798, CGTGG at 429.

ERSE2r arbitrary (evens) (4560-2846) UTRs

  1. ERSE2r0: CCACG at 4341.
  2. ERSE2r4: CCACG at 3158.
  3. ERSE2r6: CCACG at 3432, CCACG at 2903.
  4. ERSE2r8: CCACG at 2934.
  5. ERSE2r4ci: CGTGG at 4272, CGTGG at 3733.
  6. ERSE2r8ci: CGTGG at 4087, CGTGG at 3665.

ERSE2r alternate (odds) (4560-2846) UTRs

  1. ERSE2r1: CCACG at 3663, CCACG at 3297.
  2. ERSE2r3: CCACG at 4079.
  3. ERSE2r7: CCACG at 3250.
  4. ERSE2r9: CCACG at 4212, CCACG at 2964.
  5. ERSE2r1ci: CGTGG at 4419.
  6. ERSE2r3ci: CGTGG at 3322, CGTGG at 3115.
  7. ERSE2r5ci: CGTGG at 4315, CGTGG at 3956.
  8. ERSE2r7ci: CGTGG at 3592, CGTGG at 3535, CGTGG at 3316.
  9. ERSE2r9ci: CGTGG at 4505, CGTGG at 3274, CGTGG at 2943.

ERSE2r arbitrary positive direction (odds) (4445-4265) core promoters

  1. ERSE2r1ci: CGTGG at 4419.
  2. ERSE2r5ci: CGTGG at 4315.

ERSE2r alternate positive direction (evens) (4445-4265) core promoters

  1. ERSE2r0: CCACG at 4341.
  2. ERSE2r4ci: CGTGG at 4272.

ERSE2r alternate negative direction (odds) (2811-2596) proximal promoters

  1. ERSE2r9ci: CGTGG at 2703.

ERSE2r arbitrary positive direction (odds) (4265-4050) proximal promoters

  1. ERSE2r3: CCACG at 4079.
  2. ERSE2r9: CCACG at 4212.

ERSE2r alternate positive direction (evens) (4265-4050) proximal promoters

  1. ERSE2r8ci: CGTGG at 4087.

ERSE2r arbitrary negative direction (evens) (2596-1) distal promoters

  1. ERSE2r0: CCACG at 2167, CCACG at 441.
  2. ERSE2r2: CCACG at 1928.
  3. ERSE2r4: CCACG at 1283.
  4. ERSE2r8: CCACG at 942, CCACG at 896.
  5. ERSE2r0ci: CGTGG at 2384, CGTGG at 1936, CGTGG at 842.
  6. ERSE2r2ci: CGTGG at 2459, CGTGG at 100.
  7. ERSE2r4ci: CGTGG at 2288, CGTGG at 958.
  8. ERSE2r6ci: CGTGG at 1275, CGTGG at 659, CGTGG at 336.
  9. ERSE2r8ci: CGTGG at 1535, CGTGG at 1406, CGTGG at 304, CGTGG at 184.

ERSE2r alternate negative direction (odds) (2596-1) distal promoters

  1. ERSE2r1: CCACG at 1759, CCACG at 1227, CCACG at 190.
  2. ERSE2r3: CCACG at 1481, CCACG at 883, CCACG at 585.
  3. ERSE2r5: CCACG at 1787, CCACG at 801, CCACG at 72.
  4. ERSE2r7: CCACG at 1939, CCACG at 1239.
  5. ERSE2r9: CCACG at 873.
  6. ERSE2r1ci: CGTGG at 2339, CGTGG at 660, CGTGG at 575.
  7. ERSE2r3ci: CGTGG at 1438.
  8. ERSE2r5ci: CGTGG at 1588, CGTGG at 731, CGTGG at 631, CGTGG at 371.
  9. ERSE2r7ci: CGTGG at 2297, CGTGG at 1790, CGTGG at 453.
  10. ERSE2r9ci: CGTGG at 1641, CGTGG at 1431, CGTGG at 798, CGTGG at 429.

ERSE2r arbitrary positive direction (odds) (4050-1) distal promoters

  1. ERSE2r1: CCACG at 3663, CCACG at 3297, CCACG at 1759, CCACG at 1227, CCACG at 190.
  2. ERSE2r3: CCACG at 1481, CCACG at 883, CCACG at 585.
  3. ERSE2r5: CCACG at 1787, CCACG at 801, CCACG at 72.
  4. ERSE2r7: CCACG at 3250, CCACG at 1939, CCACG at 1239.
  5. ERSE2r9: CCACG at 2964, CCACG at 873.
  6. ERSE2r1ci: CGTGG at 2339, CGTGG at 660, CGTGG at 575.
  7. ERSE2r3ci: CGTGG at 3322, CGTGG at 3115, CGTGG at 1438.
  8. ERSE2r5ci: CGTGG at 3956, CGTGG at 1588, CGTGG at 731, CGTGG at 631, CGTGG at 371.
  9. ERSE2r7ci: CGTGG at 3592, CGTGG at 3535, CGTGG at 3316, CGTGG at 2297, CGTGG at 1790, CGTGG at 453.
  10. ERSE2r9ci: CGTGG at 3274, CGTGG at 2943, CGTGG at 2703, CGTGG at 1641, CGTGG at 1431, CGTGG at 798, CGTGG at 429.

ERSE2r alternate positive direction (evens) (4050-1) distal promoters

  1. ERSE2r0: CCACG at 2167, CCACG at 441.
  2. ERSE2r2: CCACG at 1928.
  3. ERSE2r4: CCACG at 3158, CCACG at 1283.
  4. ERSE2r6: CCACG at 3432, CCACG at 2903.
  5. ERSE2r8: CCACG at 2934, CCACG at 942, CCACG at 896.
  6. ERSE2r0ci: CGTGG at 2384, CGTGG at 1936, CGTGG at 842.
  7. ERSE2r2ci: CGTGG at 2459, CGTGG at 100.
  8. ERSE2r4ci: CGTGG at 3733, CGTGG at 2288, CGTGG at 958.
  9. ERSE2r6ci: CGTGG at 1275, CGTGG at 659, CGTGG at 336.
  10. ERSE2r8ci: CGTGG at 3665, CGTGG at 1535, CGTGG at 1406, CGTGG at 304, CGTGG at 184.

Endoplasmic reticulum stress response element second part analysis and results

Main article: Complex locus A1BG and ZNF497 § CCACG

"The released aminoterminal of ATF6 (ATF6-N) then migrates to the nucleus and binds to the ER stress response element (ERSE) containing the consensus sequence CCAAT-N9-CCACG to activate genes encoding ER chaperones, ERAD components, and XBP1 (Chen et al., 2010; Yamamoto et al., 2004; Yoshida et al., 2001)."[1]

The second part is CCACG.[1] This same nucleotide sequence occurs in the perfect palindrome G-boxes known as the G-box motif.[2] It also occurs within a second activating protein response element GCCCACGGG.[3]

Reals or randoms Promoters direction Numbers Strands Occurrences Averages (± 0.1)
Reals UTR negative 5 2 2.5 2.5 ± 0.5 (--3,+-2)
Randoms UTR arbitrary negative 9 10 0.9 1.3 ± 0.4
Randoms UTR alternate negative 17 10 1.7 1.3 ± 0.4
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 2 2 1 1
Randoms Core arbitrary positive 2 10 0.2 0.2
Randoms Core alternate positive 2 10 0.2 0.2
Reals Proximal negative 1 2 0.5 0.5
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 2 10 0.2 0.15
Randoms Proximal alternate positive 1 10 0.1 0.15
Reals Distal negative 9 2 4.5 4.5 ± 1.5 (--6,+-3)
Randoms Distal arbitrary negative 20 10 2.0 2.35 ± 0.35
Randoms Distal alternate negative 27 10 2.7 2.35 ± 0.35
Reals Distal positive 31 2 15.5 15.5 ± 8.5 (-+7,++24)
Randoms Distal arbitrary positive 40 10 4.0 3.3 ± 0.7
Randoms Distal alternate positive 26 10 2.6 3.3 ± 0.7

Comparison:

The occurrences of real ERSE2s are greater than the randoms. This suggests that the real responsive element consensus sequences are likely active or activable.

CCAAT-N9-CCACG Samplings

According to So (2018) the endoplasmic reticulum stress response element should be CCAAT-N9-CCACG. Samplings below demonstrate that the ideal CCAAT-N9-CCACG or its complement inverse do not occur on either side of A1BG or close to ZSCAN22 or ZNF497.

For the Basic programs testing consensus sequence CCAAT-N9-CCACG (starting with SuccessablesERSECo.bas), or CGTGG-N9-ATTGG (starting with SuccessablesERSECoci.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. Negative strand, positive direction: 0.
  4. Positive strand, positive direction: 0.
  5. inverse complement, negative strand, negative direction: 0.
  6. inverse complement, positive strand, negative direction: 0.
  7. inverse complement, negative strand, positive direction: 0.
  8. inverse complement, positive strand, positive direction: 0.

See also

References

  1. ↑ 1.0 1.1 1.2 1.3 Jae-Seon So (31 August 2018). "Roles of Endoplasmic Reticulum Stress in Immune Responses". Molecules and Cells. 41 (8): 705–16. doi:10.14348/molcells.2018.0241. PMID 30078231. Retrieved 5 September 2020.
  2. ↑ K Oeda, J Salinas, and N H Chua (July 1991). "A tobacco bZip transcription activator (TAF-1) binds to a G-box-like motif conserved in plant genes". The EMBO Journal. 10 (7): 1793–1802. PMID 2050116. Retrieved 2017-02-13.
  3. ↑ Takayuki Murata, Chieko Noda, Yohei Narita1, Takahiro Watanabe, Masahiro Yoshida, Keiji Ashio, Yoshitaka Sato, Fumi Goshima, Teru Kanda, Hironori Yoshiyama, Tatsuya Tsurumi, and Hiroshi Kimura (27 January 2016). "Induction of Epstein-Barr Virus Oncoprotein Latent Membrane Protein 1 (LMP1) by Transcription Factors Activating Protein 2 (AP-2) and Early B Cell Factor (EBF)" (PDF). Journal of Virology. doi:10.1128/JVI.03227-15. Retrieved 4 October 2020.

External links


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