Cold-responsive element gene transcriptions

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

A "putative cold-responsive element (CRE) [...] is specified by a conserved 5-bp core sequence (CCGAC) typical for C-repeat (CRT)/dehydration-responsive elements (DRE) that are recognized by cold-specific transcription factors (TFs) [16]."[1]

Consensus sequences

Main article: Consensus sequence gene transcriptions

A "conserved 5-bp core sequence (CCGAC) [is] typical for C-repeat (CRT)/dehydration-responsive elements (DRE)".[1]

Cold-responsive element samplings

Main article: Model samplings

Copying a responsive elements consensus sequence CCGAC and putting the sequence in "⌘F" finds none between ZNF497 and A1BG or none between ZSCAN22 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence CCGAC (starting with SuccessablesCold.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: 21, CCGAC at 4275, CCGAC at 4144, CCGAC at 3993, CCGAC at 3718, CCGAC at 3223, CCGAC at 3084, CCGAC at 3040, CCGAC at 2695, CCGAC at 2561, CCGAC at 2360, CCGAC at 2225, CCGAC at 2108, CCGAC at 2068, CCGAC at 1799, CCGAC at 1755, CCGAC at 1745, CCGAC at 1463, CCGAC at 1281, CCGAC at 1110, CCGAC at 990, CCGAC at 824.
  2. Positive strand, negative direction: 0.
  3. Negative strand, positive direction: 5, CCGAC at 3800, CCGAC at 1963, CCGAC at 997, CCGAC at 897, CCGAC at 791.
  4. Positive strand, positive direction: 15, CCGAC at 3639, CCGAC at 3587, CCGAC at 3525, CCGAC at 3348, CCGAC at 2914, CCGAC at 2886, CCGAC at 2809, CCGAC at 2769, CCGAC at 2319, CCGAC at 1818, CCGAC at 1030, CCGAC at 480, CCGAC at 416, CCGAC at 276, CCGAC at 263.
  5. inverse complement, negative strand, negative direction: 20, GTCGG at 4490, GTCGG at 4481, GTCGG at 4346, GTCGG at 4034, GTCGG at 3727, GTCGG at 3683, GTCGG at 3295, GTCGG at 3205, GTCGG at 3125, GTCGG at 2767, GTCGG at 2651, GTCGG at 2432, GTCGG at 2265, GTCGG at 2006, GTCGG at 1195, GTCGG at 1062, GTCGG at 896, GTCGG at 729, GTCGG at 505, GTCGG at 36.
  6. inverse complement, negative strand, positive direction: 1, GTCGG at 1529.
  7. inverse complement, positive strand, negative direction: 0.
  8. inverse complement, positive strand, positive direction: 15, GTCGG at 3998, GTCGG at 3896, GTCGG at 3101, GTCGG at 2897, GTCGG at 2527, GTCGG at 2391, GTCGG at 2353, GTCGG at 2009, GTCGG at 1604, GTCGG at 1268, GTCGG at 932, GTCGG at 832, GTCGG at 614, GTCGG at 512, GTCGG at 65.

Cold (4560-2846) UTRs

  1. Negative strand, negative direction: CCGAC at 4275, CCGAC at 4144, CCGAC at 3993, CCGAC at 3718, CCGAC at 3223, CCGAC at 3084, CCGAC at 3040.
  2. inverse complement, negative strand, negative direction: GTCGG at 4490, GTCGG at 4481, GTCGG at 4346, GTCGG at 4034, GTCGG at 3727, GTCGG at 3683, GTCGG at 3295, GTCGG at 3205, GTCGG at 3125.

Cold negative direction (2811-2596) proximal promoters

  1. Negative strand, negative direction: GTCGG at 2767, CCGAC at 2695, GTCGG at 2651.

Cold negative direction (2596-1) distal promoters

  1. Negative strand, negative direction: CCGAC at 2561, CCGAC at 2360, CCGAC at 2225, CCGAC at 2108, CCGAC at 2068, CCGAC at 1799, CCGAC at 1755, CCGAC at 1745, CCGAC at 1463, CCGAC at 1281, CCGAC at 1110, CCGAC at 990, CCGAC at 824.
  2. inverse complement, negative strand, negative direction: GTCGG at 2432, GTCGG at 2265, GTCGG at 2006, GTCGG at 1195, GTCGG at 1062, GTCGG at 896, GTCGG at 729, GTCGG at 505, GTCGG at 36.

Cold positive direction (4050-1) distal promoters

  1. Negative strand, positive direction: CCGAC at 3800, CCGAC at 1963, GTCGG at 1529, CCGAC at 997, CCGAC at 897, CCGAC at 791.
  2. Positive strand, positive direction: CCGAC at 3639, CCGAC at 3587, CCGAC at 3525, CCGAC at 3348, CCGAC at 2914, CCGAC at 2886, CCGAC at 2809, CCGAC at 2769, CCGAC at 2319, CCGAC at 1818, CCGAC at 1030, CCGAC at 480, CCGAC at 416, CCGAC at 276, CCGAC at 263.
  3. inverse complement, positive strand, positive direction: 15, GTCGG at 3998, GTCGG at 3896, GTCGG at 3101, GTCGG at 2897, GTCGG at 2527, GTCGG at 2391, GTCGG at 2353, GTCGG at 2009, GTCGG at 1604, GTCGG at 1268, GTCGG at 932, GTCGG at 832, GTCGG at 614, GTCGG at 512, GTCGG at 65.

Cold-responsive element random dataset samplings

  1. Coldr0: 6, CCGAC at 3063, CCGAC at 2510, CCGAC at 1598, CCGAC at 1318, CCGAC at 878, CCGAC at 48.
  2. Coldr1: 7, CCGAC at 3037, CCGAC at 2353, CCGAC at 2132, CCGAC at 1838, CCGAC at 1765, CCGAC at 1729, CCGAC at 958.
  3. Coldr2: 3, CCGAC at 3706, CCGAC at 1868, CCGAC at 1718.
  4. Coldr3: 3, CCGAC at 4506, CCGAC at 2428, CCGAC at 2363.
  5. Coldr4: 4, CCGAC at 4356, CCGAC at 3678, CCGAC at 398, CCGAC at 383.
  6. Coldr5: 2, CCGAC at 1543, CCGAC at 96.
  7. Coldr6: 4, CCGAC at 4297, CCGAC at 3539, CCGAC at 3407, CCGAC at 2843.
  8. Coldr7: 3, CCGAC at 3556, CCGAC at 2419, CCGAC at 2412.
  9. Coldr8: 5, CCGAC at 2906, CCGAC at 1992, CCGAC at 1942, CCGAC at 1105, CCGAC at 430.
  10. Coldr9: 9, CCGAC at 4192, CCGAC at 4078, CCGAC at 2767, CCGAC at 2520, CCGAC at 1568, CCGAC at 976, CCGAC at 511, CCGAC at 391, CCGAC at 50.
  11. Coldr0ci: 4, GTCGG at 4188, GTCGG at 4121, GTCGG at 1418, GTCGG at 867.
  12. Coldr1ci: 7, GTCGG at 4548, GTCGG at 3559, GTCGG at 3004, GTCGG at 1165, GTCGG at 1070, GTCGG at 592, GTCGG at 511.
  13. Coldr2ci: 4, GTCGG at 3197, GTCGG at 1606, GTCGG at 90, GTCGG at 11.
  14. Coldr3ci: 3, GTCGG at 1888, GTCGG at 1485, GTCGG at 645.
  15. Coldr4ci: 4, GTCGG at 4242, GTCGG at 2663, GTCGG at 2470, GTCGG at 2028.
  16. Coldr5ci: 6, GTCGG at 3539, GTCGG at 3177, GTCGG at 2902, GTCGG at 2880, GTCGG at 1053, GTCGG at 463.
  17. Coldr6ci: 4, GTCGG at 2689, GTCGG at 1230, GTCGG at 515, GTCGG at 475.
  18. Coldr7ci: 3, GTCGG at 3352, GTCGG at 2048, GTCGG at 1473.
  19. Coldr8ci: 4, GTCGG at 3903, GTCGG at 3403, GTCGG at 2556, GTCGG at 818.
  20. Coldr9ci: 3, GTCGG at 2936, GTCGG at 2776, GTCGG at 1271.

Coldr arbitrary (evens) (4560-2846) UTRs

  1. Coldr0: CCGAC at 3063.
  2. Coldr2: CCGAC at 3706.
  3. Coldr4: CCGAC at 4356, CCGAC at 3678.
  4. Coldr6: CCGAC at 4297, CCGAC at 3539, CCGAC at 3407.
  5. Coldr8: CCGAC at 2906.
  6. Coldr0ci: GTCGG at 4188, GTCGG at 4121.
  7. Coldr2ci: GTCGG at 3197.
  8. Coldr4ci: GTCGG at 4242.
  9. Coldr8ci: 4GTCGG at 3903, GTCGG at 3403.

Coldr alternate (odds) (4560-2846) UTRs

  1. Coldr1: CCGAC at 3037.
  2. Coldr3: CCGAC at 4506.
  3. Coldr7: CCGAC at 3556.
  4. Coldr9: CCGAC at 4192, CCGAC at 4078.
  5. Coldr1ci: GTCGG at 4548, GTCGG at 3559, GTCGG at 3004.
  6. Coldr5ci: GTCGG at 3539, GTCGG at 3177, GTCGG at 2902, GTCGG at 2880.
  7. Coldr7ci: GTCGG at 3352.
  8. Coldr9ci: GTCGG at 2936.

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

  1. Coldr6: CCGAC at 2843.

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

  1. Coldr4: CCGAC at 4356.
  2. Coldr6: CCGAC at 4297.

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

  1. Coldr4ci: GTCGG at 2663.
  2. Coldr6ci: GTCGG at 2689.

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

  1. Coldr9: CCGAC at 2767.
  2. Coldr9ci: GTCGG at 2776.

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

  1. Coldr9: CCGAC at 4192, CCGAC at 4078.

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

  1. Coldr0ci: GTCGG at 4188, GTCGG at 4121.
  2. Coldr4ci: GTCGG at 4242.

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

  1. Coldr0: CCGAC at 2510, CCGAC at 1598, CCGAC at 1318, CCGAC at 878, CCGAC at 48.
  2. Coldr2: CCGAC at 1868, CCGAC at 1718.
  3. Coldr4: CCGAC at 398, CCGAC at 383.
  4. Coldr8: CCGAC at 1992, CCGAC at 1942, CCGAC at 1105, CCGAC at 430.
  5. Coldr0ci: GTCGG at 1418, GTCGG at 867.
  6. Coldr2ci: GTCGG at 1606, GTCGG at 90, GTCGG at 11.
  7. Coldr4ci: GTCGG at 2470, GTCGG at 2028.
  8. Coldr6ci: GTCGG at 1230, GTCGG at 515, GTCGG at 475.
  9. Coldr8ci: GTCGG at 2556, GTCGG at 818.

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

  1. Coldr1: CCGAC at 2353, CCGAC at 2132, CCGAC at 1838, CCGAC at 1765, CCGAC at 1729, CCGAC at 958.
  2. Coldr3: CCGAC at 2428, CCGAC at 2363.
  3. Coldr5: CCGAC at 1543, CCGAC at 96.
  4. Coldr7: CCGAC at 2419, CCGAC at 2412.
  5. Coldr9: CCGAC at 2520, CCGAC at 1568, CCGAC at 976, CCGAC at 511, CCGAC at 391, CCGAC at 50.
  6. Coldr1ci: GTCGG at 1165, GTCGG at 1070, GTCGG at 592, GTCGG at 511.
  7. Coldr3ci: GTCGG at 1888, GTCGG at 1485, GTCGG at 645.
  8. Coldr5ci: GTCGG at 1053, GTCGG at 463.
  9. Coldr7ci: GTCGG at 2048, GTCGG at 1473.
  10. Coldr9ci: GTCGG at 1271.

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

  1. Coldr1: CCGAC at 3037, CCGAC at 2353, CCGAC at 2132, CCGAC at 1838, CCGAC at 1765, CCGAC at 1729, CCGAC at 958.
  2. Coldr3: CCGAC at 2428, CCGAC at 2363.
  3. Coldr5: CCGAC at 1543, CCGAC at 96.
  4. Coldr7: CCGAC at 3556, CCGAC at 2419, CCGAC at 2412.
  5. Coldr9: CCGAC at 2767, CCGAC at 2520, CCGAC at 1568, CCGAC at 976, CCGAC at 511, CCGAC at 391, CCGAC at 50.
  6. Coldr1ci: GTCGG at 3559, GTCGG at 3004, GTCGG at 1165, GTCGG at 1070, GTCGG at 592, GTCGG at 511.
  7. Coldr3ci: GTCGG at 1888, GTCGG at 1485, GTCGG at 645.
  8. Coldr5ci: GTCGG at 3539, GTCGG at 3177, GTCGG at 2902, GTCGG at 2880, GTCGG at 1053, GTCGG at 463.
  9. Coldr7ci: GTCGG at 3352, GTCGG at 2048, GTCGG at 1473.
  10. Coldr9ci: GTCGG at 2936, GTCGG at 2776, GTCGG at 1271.

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

  1. Coldr0: CCGAC at 3063, CCGAC at 2510, CCGAC at 1598, CCGAC at 1318, CCGAC at 878, CCGAC at 48.
  2. Coldr2: CCGAC at 3706, CCGAC at 1868, CCGAC at 1718.
  3. Coldr4: CCGAC at 3678, CCGAC at 398, CCGAC at 383.
  4. Coldr6: CCGAC at 3539, CCGAC at 3407, CCGAC at 2843.
  5. Coldr8: CCGAC at 2906, CCGAC at 1992, CCGAC at 1942, CCGAC at 1105, CCGAC at 430.
  6. Coldr0ci: GTCGG at 1418, GTCGG at 867.
  7. Coldr2ci: GTCGG at 3197, GTCGG at 1606, GTCGG at 90, GTCGG at 11.
  8. Coldr4ci: GTCGG at 2663, GTCGG at 2470, GTCGG at 2028.
  9. Coldr6ci: GTCGG at 2689, GTCGG at 1230, GTCGG at 515, GTCGG at 475.
  10. Coldr8ci: GTCGG at 3903, GTCGG at 3403, GTCGG at 2556, GTCGG at 818.

Cold-responsive element analysis and results

Main article: Complex locus A1BG and ZNF497 § Cold-responsive elements

The randoms have fourteen consensus sequences in the ZSCAN22-A1BG UTR with an occurrence of 1.4. The reals have sixteen sequences with an occurrence of 8.0 which is much larger than the randoms.

The randoms had core promoters: one in the arbitrary negative direction and two in the positive direction for occurrences of 0.1 and 0.2, respectively. The reals have no sequences in the core promoters.

The randoms had two in the negative direction for an occurrence of 0.2 and two in the positive direction also for an occurrence of 0.2. The reals have three sequences in the negative direction only for an occurrence of 1.5.

In the distal promoters, the randoms had twenty-five in the negative direction for an occurrence of 2.5. There were forty-two in the positive direction for an occurrence of 4.2.

The reals have twenty-two sequences in the negative direction for an occurrence of 11.0 and thirty-six in the positive direction for an occurrence of 18.0. Both of these are systematically higher than the randoms.

With the exceptions of the core promoters, the real UTR, proximal and distal promoters have systematically many more sequences than the randoms. This suggests that these promoters are likely active or activable.

A "putative cold-responsive element (CRE) [...] is specified by a conserved 5-bp core sequence (CCGAC) typical for C-repeat (CRT)/dehydration-responsive elements (DRE) that are recognized by cold-specific transcription factors (TFs) [16]."[1]

Reals or randoms Promoters direction Numbers Strands Occurrences Averages (± 0.1)
Reals UTR negative 16 2 8 8 ± 1 (--7,+-9)
Randoms UTR arbitrary negative 14 10 1.4 1.4
Randoms UTR alternate negative 14 10 1.4 1.4
Reals Core negative 0 2 0 0
Randoms Core arbitrary negative 1 10 0.1 0.05
Randoms Core alternate negative 0 10 0 0.05
Reals Core positive 0 2 0 0
Randoms Core arbitrary positive 0 10 0 0.1
Randoms Core alternate positive 2 10 0.2 0.1
Reals Proximal negative 3 2 1.5 1.5 ± 1.5 (--3,+-0)
Randoms Proximal arbitrary negative 2 10 0.2 0.2
Randoms Proximal alternate negative 2 10 0.2 0.2
Reals Proximal positive 0 2 0 0
Randoms Proximal arbitrary positive 2 10 0.2 0.25
Randoms Proximal alternate positive 3 10 0.3 0.25
Reals Distal negative 22 2 11 11 ± 11 (--22,+-0)
Randoms Distal arbitrary negative 25 10 2.5 2.75
Randoms Distal alternate negative 30 10 3.0 2.75
Reals Distal positive 36 2 18 18 ± 12 (-+6,++30)
Randoms Distal arbitrary positive 42 10 4.2 3.95
Randoms Distal alternate positive 37 10 3.7 3.95

Comparison:

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

Acknowledgements

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

See also

References

  1. ↑ 1.0 1.1 1.2 Björn Pietzenuk, Catarine Markus, Hervé Gaubert, Navratan Bagwan, Aldo Merotto, Etienne Bucher & Ales Pecinka (11 October 2016). "Recurrent evolution of heat-responsiveness in Brassicaceae COPIA elements". Genome Biology. 17: 209. doi:10.1186/s13059-016-1072-3. Retrieved 14 September 2020.

External links

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