Msn2,4p gene transcriptions

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

"[msn2p] is a transcription factor that binds to stress-response elements (STREs) resulting in the induction of more than 200 genes.10,11 STRE has a core pentameric cis-acting sequence CCCCT and is located in promoter regions of the induced genes."[1]

Human genes

Main article: Human genes

Gene expressions

Main article: Gene expressions

Interactions

Main article: Interaction gene transcriptions

Consensus sequences

Main article: Consensus sequence gene transcriptions

The upstream activating sequence (UAS) for the Msn2,4p transcription factor is 5'-CCCCT-3'.[2]

Binding site for

Complement copies

Main article: Complement copy gene transcriptions

Inverse copies

Main article: Inverse copy gene transcriptions

Complement-inverse copies

Main article: Complement-inverse copy gene transcriptions

Enhancer activity

Main article: Enhancer activity copy gene transcriptions

Promoter occurrences

Main article: Promoter occurrence gene transcriptions

Hypotheses

Main article: Hypotheses
  1. A1BG has no regulatory elements in either promoter.
  2. A1BG is not transcribed by a regulatory element.
  3. No regulatory element participates in the transcription of A1BG.

Stress-response element samplings

Copying CCCCT in "⌘F" yields one between ZSCAN22 and A1BG and three between ZNF497 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence CCCCT (starting with SuccessablesSTRE.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 CCCCT, 1, CCCCT at 2924.
  2. positive strand, negative direction, looking for CCCCT, 2, CCCCT at 3059, CCCCT at 617.
  3. positive strand, positive direction, looking for CCCCT, 11, CCCCT at 4043, CCCCT at 3665, CCCCT at 3656, CCCCT at 3543, CCCCT at 3452, CCCCT at 2657, CCCCT at 2287, CCCCT at 1867, CCCCT at 492, CCCCT at 321, CCCCT at 57.
  4. negative strand, positive direction, looking for CCCCT, 3, CCCCT at 3615, CCCCT at 1073, CCCCT at 86.
  5. complement, negative strand, negative direction, looking for GGGGA, 2, GGGGA at 3059, GGGGA at 617.
  6. complement, positive strand, negative direction, looking for GGGGA, 1, GGGGA at 2924.
  7. complement, positive strand, positive direction, looking for GGGGA, 3, GGGGA at 3615, GGGGA at 1073, GGGGA at86.
  8. complement, negative strand, positive direction, looking for GGGGA, 11, GGGGA at 4043, GGGGA at 3665, GGGGA at 3656, GGGGA at 3543, GGGGA at 3452, GGGGA at 2657, GGGGA at 2287, GGGGA at 492, GGGGA at 321, GGGGA at 57.
  9. inverse complement, negative strand, negative direction, looking for AGGGG, 0.
  10. inverse complement, positive strand, negative direction, looking for AGGGG, 0.
  11. inverse complement, positive strand, positive direction, looking for AGGGG, 6, AGGGG at 3555, AGGGG at 3199, AGGGG at 3078, AGGGG at 1072, AGGGG at 174, AGGGG at 84.
  12. inverse complement, negative strand, positive direction, looking for AGGGG, 11, AGGGG at 4435, AGGGG at 3981, AGGGG at 3664, AGGGG at 3654, AGGGG at 3468, AGGGG at 2656, AGGGG at 2291, AGGGG at 1790, AGGGG at 320, AGGGG at 259, AGGGG at 246.
  13. inverse negative strand, negative direction, looking for TCCCC, 0.
  14. inverse positive strand, negative direction, looking for TCCCC, 0.
  15. inverse positive strand, positive direction, looking for TCCCC, 11, TCCCC at 4435, TCCCC at 3981, TCCCC at 3664, TCCCC at 3654, TCCCC at 3468, TCCCC at 2656, TCCCC at 2291, TCCCC at 1790, TCCCC at 320, TCCCC at 259, TCCCC at 246.
  16. inverse negative strand, positive direction, looking for TCCCC, 6, TCCCC at 3555, TCCCC at 3199, TCCCC at 3078, TCCCC at 1072, TCCCC at 174, TCCCC at 84.

STRE (4560-2846) UTRs

  1. Negative strand, negative direction: CCCCT at 2924.
  1. Positive strand, negative direction: CCCCT at 3059.

STRE positive direction (4445-4265) core promoters

  1. Negative strand, positive direction: AGGGG at 4435.

STRE negative direction (2596-1) distal promoters

  1. Positive strand, negative direction: CCCCT at 617.

STRE positive direction (4050-1) distal promoters

  1. Negative strand, positive direction: CCCCT at 3615, CCCCT at 1073, CCCCT at 86.
  2. Negative strand, positive direction: AGGGG at 3981, AGGGG at 3664, AGGGG at 3654, AGGGG at 3468, AGGGG at 2656, AGGGG at 2291, AGGGG at 1790, AGGGG at 320, AGGGG at 259, AGGGG at 246.
  3. Positive strand, positive direction: CCCCT at 4043, CCCCT at 3665, CCCCT at 3656, CCCCT at 3543, CCCCT at 3452, CCCCT at 2657, CCCCT at 2287, CCCCT at 1867, CCCCT at 492, CCCCT at 321, CCCCT at 57.
  4. Positive strand, positive direction: AGGGG at 3555, AGGGG at 3199, AGGGG at 3078, AGGGG at 1072, AGGGG at 174, AGGGG at 84.

STRE random dataset samplings

  1. STREr0: 7, CCCCT at 3639, CCCCT at 2872, CCCCT at 1862, CCCCT at 1655, CCCCT at 1625, CCCCT at 586, CCCCT at 469.
  2. STREr1: 10, CCCCT at 4330, CCCCT at 3109, CCCCT at 2579, CCCCT at 2414, CCCCT at 2209, CCCCT at 2030, CCCCT at 1368, CCCCT at 1098, CCCCT at 867, CCCCT at 126.
  3. STREr2: 9, CCCCT at 3916, CCCCT at 3216, CCCCT at 1049, CCCCT at 955, CCCCT at 926, CCCCT at 893, CCCCT at 711, CCCCT at 669, CCCCT at 643.
  4. STREr3: 13, CCCCT at 4055, CCCCT at 3828, CCCCT at 3351, CCCCT at 3221, CCCCT at 2627, CCCCT at 2496, CCCCT at 2485, CCCCT at 2136, CCCCT at 1858, CCCCT at 779, CCCCT at 375, CCCCT at 120, CCCCT at 110.
  5. STREr4: 10, CCCCT at 4446, CCCCT at 3229, CCCCT at 3107, CCCCT at 2859, CCCCT at 2754, CCCCT at 2618, CCCCT at 1520, CCCCT at 1479, CCCCT at 1039, CCCCT at 201.
  6. STREr5: 10, CCCCT at 3761, CCCCT at 3578, CCCCT at 3243, CCCCT at 3138, CCCCT at 2847, CCCCT at 2352, CCCCT at 1859, CCCCT at 1852, CCCCT at 1469, CCCCT at 1404.
  7. STREr6: 8, CCCCT at 4407, CCCCT at 4340, CCCCT at 4223, CCCCT at 3778, CCCCT at 3602, CCCCT at 3559, CCCCT at 2452, CCCCT at 49.
  8. STREr7: 9, CCCCT at 3806, CCCCT at 2908, CCCCT at 2816, CCCCT at 1620, CCCCT at 902, CCCCT at 780, CCCCT at 754, CCCCT at 542, CCCCT at 184.
  9. STREr8: 5, CCCCT at 3826, CCCCT at 3387, CCCCT at 2450, CCCCT at 2318, CCCCT at 905.
  10. STREr9: 6, CCCCT at 2827, CCCCT at 2573, CCCCT at 2223, CCCCT at 1342, CCCCT at 961, CCCCT at 265.
  11. STREr0ci: 14, AGGGG at 4404, AGGGG at 4394, AGGGG at 3864, AGGGG at 3738, AGGGG at 3506, AGGGG at 3014, AGGGG at 2944, AGGGG at 2793, AGGGG at 2465, AGGGG at 1034, AGGGG at 1026, AGGGG at 921, AGGGG at 452, AGGGG at 67.
  12. STREr1ci: 14, AGGGG at 4538, AGGGG at 4015, AGGGG at 3318, AGGGG at 3179, AGGGG at 3134, AGGGG at 2820, AGGGG at 2654, AGGGG at 2611, AGGGG at 2512, AGGGG at 1983, AGGGG at 1180, AGGGG at 846, AGGGG at 669, AGGGG at 554.
  13. STREr2ci: 8, AGGGG at 4296, AGGGG at 3902, AGGGG at 2840, AGGGG at 2281, AGGGG at 1426, AGGGG at 1282, AGGGG at 677, AGGGG at 661.
  14. STREr3ci: 5, AGGGG at 2865, AGGGG at 1921, AGGGG at 1624, AGGGG at 818, AGGGG at 698.
  15. STREr4ci: 7, AGGGG at 3728, AGGGG at 3649, AGGGG at 3568, AGGGG at 2938, AGGGG at 2208, AGGGG at 1990, AGGGG at 407.
  16. STREr5ci: 11, AGGGG at 4261, AGGGG at 3908, AGGGG at 3902, AGGGG at 2753, AGGGG at 1809, AGGGG at 1307, AGGGG at 769, AGGGG at 639, AGGGG at 518, AGGGG at 250, AGGGG at 38.
  17. STREr6ci: 6, AGGGG at 2793, AGGGG at 2111, AGGGG at 1756, AGGGG at 1682, AGGGG at 1160, AGGGG at 110.
  18. STREr7ci: 9, AGGGG at 4372, AGGGG at 4319, AGGGG at 4294, AGGGG at 3713, AGGGG at 1783, AGGGG at 1729, AGGGG at 1458, AGGGG at 1190, AGGGG at 912.
  19. STREr8ci: 3, AGGGG at 2918, AGGGG at 1737, AGGGG at 237.
  20. STREr9ci: 6, AGGGG at 2438, AGGGG at 2417, AGGGG at 2174, AGGGG at 1579, AGGGG at 1333, AGGGG at 790.

STREr arbitrary (evens) (4560-2846) UTRs

  1. STREr0: CCCCT at 3639, CCCCT at 2872.
  2. STREr2: CCCCT at 3916, CCCCT at 3216.
  3. STREr4: CCCCT at 4446, CCCCT at 3229, CCCCT at 3107, CCCCT at 2859.
  4. STREr6: CCCCT at 4407, CCCCT at 4340, CCCCT at 4223, CCCCT at 3778, CCCCT at 3602, CCCCT at 3559.
  5. STREr8: CCCCT at 3826, CCCCT at 3387.
  6. STREr0ci: AGGGG at 4404, AGGGG at 4394, AGGGG at 3864, AGGGG at 3738, AGGGG at 3506, AGGGG at 3014, AGGGG at 2944.
  7. STREr2ci: AGGGG at 4296, AGGGG at 3902.
  8. STREr4ci: AGGGG at 3728, AGGGG at 3649, AGGGG at 3568, AGGGG at 2938.
  9. STREr8ci: AGGGG at 2918.

STREr alternate (odds) (4560-2846) UTRs

  1. STREr1: CCCCT at 4330, CCCCT at 3109.
  2. STREr3: CCCCT at 4055, CCCCT at 3828, CCCCT at 3351, CCCCT at 3221.
  3. STREr5: CCCCT at 3761, CCCCT at 3578, CCCCT at 3243, CCCCT at 3138, CCCCT at 2847.
  4. STREr7: CCCCT at 3806, CCCCT at 2908.
  5. STREr1ci: AGGGG at 4538, AGGGG at 4015, AGGGG at 3318, AGGGG at 3179, AGGGG at 3134.
  6. STREr3ci: AGGGG at 2865.
  7. STREr5ci: AGGGG at 4261, AGGGG at 3908, AGGGG at 3902.
  8. STREr7ci: AGGGG at 4372, AGGGG at 4319, AGGGG at 4294, AGGGG at 3713.

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

  1. STREr2ci: AGGGG at 2840.

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

  1. STREr7: CCCCT at 2816.
  2. STREr9: CCCCT at 2827.
  3. STREr1ci: AGGGG at 2820.

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

  1. STREr1: CCCCT at 4330.
  2. STREr7ci: AGGGG at 4372, AGGGG at 4319, AGGGG at 4294.

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

  1. STREr6: CCCCT at 4407, CCCCT at 4340.
  2. STREr0ci: AGGGG at 4404, AGGGG at 4394.
  3. STREr2ci: AGGGG at 4296.

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

  1. STREr4: CCCCT at 2754, CCCCT at 2618.
  2. STREr0ci: AGGGG at 2793.
  3. STREr6ci: AGGGG at 2793.

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

  1. STREr3: CCCCT at 2627.
  2. STREr1ci: AGGGG at 2654, AGGGG at 2611.
  3. STREr5ci: AGGGG at 2753.

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

  1. STREr3: CCCCT at 4055.
  2. STREr5ci: AGGGG at 4261.

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

  1. STREr6: CCCCT at 4223.

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

  1. STREr0: CCCCT at 1862, CCCCT at 1655, CCCCT at 1625, CCCCT at 586, CCCCT at 469.
  2. STREr2: CCCCT at 1049, CCCCT at 955, CCCCT at 926, CCCCT at 893, CCCCT at 711, CCCCT at 669, CCCCT at 643.
  3. STREr4: CCCCT at 1520, CCCCT at 1479, CCCCT at 1039, CCCCT at 201.
  4. STREr6: CCCCT at 2452, CCCCT at 49.
  5. STREr8: CCCCT at 2450, CCCCT at 2318, CCCCT at 905.
  6. STREr0ci: AGGGG at 2465, AGGGG at 1034, AGGGG at 1026, AGGGG at 921, AGGGG at 452, AGGGG at 67.
  7. STREr2ci: AGGGG at 2281, AGGGG at 1426, AGGGG at 1282, AGGGG at 677, AGGGG at 661.
  8. STREr4ci: AGGGG at 2208, AGGGG at 1990, AGGGG at 407.
  9. STREr6ci: AGGGG at 2111, AGGGG at 1756, AGGGG at 1682, AGGGG at 1160, AGGGG at 110.
  10. STREr8ci: AGGGG at 1737, AGGGG at 237.

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

  1. STREr1: CCCCT at 2579, CCCCT at 2414, CCCCT at 2209, CCCCT at 2030, CCCCT at 1368, CCCCT at 1098, CCCCT at 867, CCCCT at 126.
  2. STREr3: CCCCT at 2496, CCCCT at 2485, CCCCT at 2136, CCCCT at 1858, CCCCT at 779, CCCCT at 375, CCCCT at 120, CCCCT at 110.
  3. STREr5: CCCCT at 2352, CCCCT at 1859, CCCCT at 1852, CCCCT at 1469, CCCCT at 1404.
  4. STREr7: CCCCT at 1620, CCCCT at 902, CCCCT at 780, CCCCT at 754, CCCCT at 542, CCCCT at 184.
  5. STREr9: CCCCT at 2573, CCCCT at 2223, CCCCT at 1342, CCCCT at 961, CCCCT at 265.
  6. STREr1ci: AGGGG at 2512, AGGGG at 1983, AGGGG at 1180, AGGGG at 846, AGGGG at 669, AGGGG at 554.
  7. STREr3ci: AGGGG at 1921, AGGGG at 1624, AGGGG at 818, AGGGG at 698.
  8. STREr5ci: AGGGG at 1809, AGGGG at 1307, AGGGG at 769, AGGGG at 639, AGGGG at 518, AGGGG at 250, AGGGG at 38.
  9. STREr7ci: AGGGG at 1783, AGGGG at 1729, AGGGG at 1458, AGGGG at 1190, AGGGG at 912.
  10. STREr9ci: AGGGG at 2438, AGGGG at 2417, AGGGG at 2174, AGGGG at 1579, AGGGG at 1333, AGGGG at 790.

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

  1. STREr1: CCCCT at 3109, CCCCT at 2579, CCCCT at 2414, CCCCT at 2209, CCCCT at 2030, CCCCT at 1368, CCCCT at 1098, CCCCT at 867, CCCCT at 126.
  2. STREr3: CCCCT at 3828, CCCCT at 3351, CCCCT at 3221, CCCCT at 2627, CCCCT at 2496, CCCCT at 2485, CCCCT at 2136, CCCCT at 1858, CCCCT at 779, CCCCT at 375, CCCCT at 120, CCCCT at 110.
  3. STREr5: CCCCT at 3761, CCCCT at 3578, CCCCT at 3243, CCCCT at 3138, CCCCT at 2847, CCCCT at 2352, CCCCT at 1859, CCCCT at 1852, CCCCT at 1469, CCCCT at 1404.
  4. STREr7: CCCCT at 3806, CCCCT at 2908, CCCCT at 2816, CCCCT at 1620, CCCCT at 902, CCCCT at 780, CCCCT at 754, CCCCT at 542, CCCCT at 184.
  5. STREr9: CCCCT at 2827, CCCCT at 2573, CCCCT at 2223, CCCCT at 1342, CCCCT at 961, CCCCT at 265.
  6. STREr1ci: AGGGG at 4015, AGGGG at 3318, AGGGG at 3179, AGGGG at 3134, AGGGG at 2820, AGGGG at 2654, AGGGG at 2611, AGGGG at 2512, AGGGG at 1983, AGGGG at 1180, AGGGG at 846, AGGGG at 669, AGGGG at 554.
  7. STREr3ci: AGGGG at 2865, AGGGG at 1921, AGGGG at 1624, AGGGG at 818, AGGGG at 698.
  8. STREr5ci: AGGGG at 3908, AGGGG at 3902, AGGGG at 2753, AGGGG at 1809, AGGGG at 1307, AGGGG at 769, AGGGG at 639, AGGGG at 518, AGGGG at 250, AGGGG at 38.
  9. STREr7ci: AGGGG at 3713, AGGGG at 1783, AGGGG at 1729, AGGGG at 1458, AGGGG at 1190, AGGGG at 912.
  10. STREr9ci: AGGGG at 2438, AGGGG at 2417, AGGGG at 2174, AGGGG at 1579, AGGGG at 1333, AGGGG at 790.

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

  1. STREr0: CCCCT at 3639, CCCCT at 2872, CCCCT at 1862, CCCCT at 1655, CCCCT at 1625, CCCCT at 586, CCCCT at 469.
  2. STREr2: CCCCT at 3916, CCCCT at 3216, CCCCT at 1049, CCCCT at 955, CCCCT at 926, CCCCT at 893, CCCCT at 711, CCCCT at 669, CCCCT at 643.
  3. STREr4: CCCCT at 3229, CCCCT at 3107, CCCCT at 2859, CCCCT at 2754, CCCCT at 2618, CCCCT at 1520, CCCCT at 1479, CCCCT at 1039, CCCCT at 201.
  4. STREr6: CCCCT at 3778, CCCCT at 3602, CCCCT at 3559, CCCCT at 2452, CCCCT at 49.
  5. STREr8: CCCCT at 3826, CCCCT at 3387, CCCCT at 2450, CCCCT at 2318, CCCCT at 905.
  6. STREr0ci: AGGGG at 3864, AGGGG at 3738, AGGGG at 3506, AGGGG at 3014, AGGGG at 2944, AGGGG at 2793, AGGGG at 2465, AGGGG at 1034, AGGGG at 1026, AGGGG at 921, AGGGG at 452, AGGGG at 67.
  7. STREr2ci: AGGGG at 3902, AGGGG at 2840, AGGGG at 2281, AGGGG at 1426, AGGGG at 1282, AGGGG at 677, AGGGG at 661.
  8. STREr4ci: AGGGG at 3728, AGGGG at 3649, AGGGG at 3568, AGGGG at 2938, AGGGG at 2208, AGGGG at 1990, AGGGG at 407.
  9. STREr6ci: AGGGG at 2793, AGGGG at 2111, AGGGG at 1756, AGGGG at 1682, AGGGG at 1160, AGGGG at 110.
  10. STREr8ci: AGGGG at 2918, AGGGG at 1737, AGGGG at 237.

STRE analysis and results

Main article: Complex locus A1BG and ZNF497 § STREs

"STRE has a core pentameric cis-acting sequence CCCCT and is located in promoter regions of the induced genes."[1]

Reals or randoms Promoters direction Numbers Strands Occurrences Averages (± 0.1)
Reals UTR negative 2 2 1 1 ± 0 (--1,+-1)
Randoms UTR arbitrary negative 30 10 3.0 2.8 ± 0.2 (3.0,2.6)
Randoms UTR alternate negative 26 10 2.6 2.8 ± 0.2 (3.0,2.6)
Reals Core negative 0 2 0 0
Randoms Core arbitrary negative 1 10 0.1 0.2
Randoms Core alternate negative 3 10 0.3 0.2
Reals Core positive 1 2 0.5 0.5 ± 0.5 (-+1,++0)
Randoms Core arbitrary positive 4 10 0.4 0.45
Randoms Core alternate positive 5 10 0.5 0.45
Reals Proximal negative 0 2 0 0
Randoms Proximal arbitrary negative 4 10 0.4 0.4
Randoms Proximal alternate negative 4 10 0.4 0.4
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 1 2 0.5 0.5 ± 0.5 (--0,+-1)
Randoms Distal arbitrary negative 42 10 4.2 5.1 ± 0.9 (4.2,6.0)
Randoms Distal alternate negative 60 10 6.0 5.1 ± 0.9 (4.2,6.0)
Reals Distal positive 30 2 15 15 ± 2 (-+13,++17)
Randoms Distal arbitrary positive 86 10 8.6 7.8
Randoms Distal alternate positive 70 10 7.0 7.8

Comparison:

The occurrences of real STRE UTRs and negative distals are less than the randoms, positive cores and distals greater the randoms. This suggests that the real STREs 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 Sotirios‐Spyridon Vamvakas, John Kapolos, Lambros Farmakis, Gregoria Koskorellou, Fotios Genneos (14 May 2019). "Ser625 of msn2 transcription factor is indispensable for ethanol tolerance and alcoholic fermentation process". Biotechnology Progress. 35 (5): ee2837. doi:10.1002/btpr.2837. Retrieved 6 February 2021.
  2. ↑ Hongting Tang, Yanling Wu, Jiliang Deng, Nanzhu Chen, Zhaohui Zheng, Yongjun Wei, Xiaozhou Luo, and Jay D. Keasling (6 August 2020). "Promoter Architecture and Promoter Engineering in Saccharomyces cerevisiae". Metabolites. 10 (8): 320–39. doi:10.3390/metabo10080320. PMID 32781665 Check |pmid= value (help). Retrieved 18 September 2020.

External links

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