Yap1p,2p gene transcriptions: Difference between revisions

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| Reals || UTR || negative || 1 || 2 || 0.5 || 0.5  
| Reals || UTR || negative || 1 || 2 || 0.5 || 0.5  
|-
|-
| Randoms || UTR || arbitrary negative || 1 || 10 || 0.1 || 0.1
| Randoms || UTR || arbitrary negative || 1 || 10 || 0.1 || 0.15
|-
|-
| Randoms || UTR || alternate negative || 1 || 10 || 0.1 || 0.1
| Randoms || UTR || alternate negative || 2 || 10 || 0.2 || 0.15
|-
|-
| Reals || Core || negative || 0 || 2 || 0 || 0  
| Reals || Core || negative || 0 || 2 || 0 || 0  
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| Reals || Distal || negative || 0 || 2 || 0 || 0  
| Reals || Distal || negative || 0 || 2 || 0 || 0  
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| Randoms || Distal || arbitrary negative || 2 || 10 || 0.2 || 0.15
| Randoms || Distal || arbitrary negative || 3 || 10 || 0.3 || 0.3
|-
|-
| Randoms || Distal || alternate negative || 0 || 10 || 0 || 0.15
| Randoms || Distal || alternate negative || 3 || 10 || 0.3 || 0.3
|-
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| Reals || Distal || positive || 0 || 2 || 0 || 0  
| Reals || Distal || positive || 0 || 2 || 0 || 0  
|-
|-
| Randoms || Distal || arbitrary positive || 0 || 10 || 0 || 0.15
| Randoms || Distal || arbitrary positive || 3 || 10 || 0.3 || 0.35
|-
|-
| Randoms || Distal || alternate positive || 3 || 10 || 0.3 || 0.15
| Randoms || Distal || alternate positive || 4 || 10 || 0.4 || 0.35
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Revision as of 19:57, 24 March 2023

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

"The activity of the native TRX2 promoter, which is regulated by the transcription factor Yap1p, can be altered by sensing NADPH/NADP+ ratios, but its sensitivity is low. Increasing the number of the UAS-containing Yap1p binding sites greatly enhanced the cascade response effect, and this novel biosensor was useful at selecting cell populations with higher NADPH/NADP+ ratios [139]."[1]

"Saccharomyces cerevisiae contains eight members of a novel and fungus-specific family of bZIP proteins that is defined by four atypical residues on the DNA-binding surface. Two of these proteins, Yap1 and Yap2, are transcriptional activators involved in pleiotropic drug resistance. Although initially described as AP-1 factors, at least four Yap proteins bind most efficiently to TTACTAA, a sequence that differs at position ±2 from the optimal AP-1 site (TGACTCA); further, a Yap-like derivative of the AP-1 factor Gcn4 (A239Q S242F) binds efficiently to the Yap recognition sequence."[2]

Human genes

Main article: Human genes

Interactions

Main article: Interaction gene transcriptions

Consensus sequences

Main article: Consensus sequence gene transcriptions

The upstream activating sequence (UAS) for Yap1p/2p is TTACTAA, which is found in genes GSH1, TRX2, YCF1, GLR1, induced by oxidative stress such as H2O2, for regulation of genes expressed in response to environmental changes.[1]

Yap samplings

Main article: Model samplings

Copying TTACTAA in "⌘F" yields none between ZSCAN22 and A1BG and none between ZNF497 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence TTACTAA (starting with SuccessablesYap.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 TTACTAA, 0.
  2. positive strand, negative direction, looking for TTACTAA, 1, TTACTAA at 3472.
  3. positive strand, positive direction, looking for TTACTAA, 0.
  4. negative strand, positive direction, looking for TTACTAA, 0.
  5. complement, negative strand, negative direction, looking for AATGATT, 1, AATGATT at 3472.
  6. complement, positive strand, negative direction, looking for AATGATT, 0.
  7. complement, positive strand, positive direction, looking for AATGATT, 0.
  8. complement, negative strand, positive direction, looking for AATGATT, 0.
  9. inverse complement, negative strand, negative direction, looking for TTAGTAA, 0.
  10. inverse complement, positive strand, negative direction, looking for TTAGTAA, 0.
  11. inverse complement, positive strand, positive direction, looking for TTAGTAA, 0.
  12. inverse complement, negative strand, positive direction, looking for TTAGTAA, 0.
  13. inverse negative strand, negative direction, looking for AATCATT, 0.
  14. inverse positive strand, negative direction, looking for AATCATT, 0.
  15. inverse positive strand, positive direction, looking for AATCATT, 0.
  16. inverse negative strand, positive direction, looking for AATCATT, 0.

Yap (4560-2846) UTRs

  1. Positive strand, negative direction: TTACTAA at 3472.

Yap random dataset samplings

  1. Yapr0: 0.
  2. Yapr1: 1, TTACTAA at 4451.
  3. Yapr2: 1, TTACTAA at 2374.
  4. Yapr3: 0.
  5. Yapr4: 1, TTACTAA at 3669.
  6. Yapr5: 0.
  7. Yapr6: 1, TTACTAA at 1423.
  8. Yapr7: 0.
  9. Yapr8: 0.
  10. Yapr9: 0.
  11. Yapr0ci: 0.
  12. Yapr1ci: 1, TTAGTAA at 1724.
  13. Yapr2ci: 0.
  14. Yapr3ci: 1, TTAGTAA at 916.
  15. Yapr4ci: 1, TTAGTAA at 2301.
  16. Yapr5ci: 0.
  17. Yapr6ci: 0.
  18. Yapr7ci: 0.
  19. Yapr8ci: 0.
  20. Yapr9ci: 1, TTAGTAA at 4015.

Yapr arbitrary (evens) (4560-2846) UTRs

  1. Yapr4: TTACTAA at 3669.

Yapr alternate (odds) (4560-2846) UTRs

  1. Yapr1: TTACTAA at 4451.
  2. Yapr9ci: TTAGTAA at 4015.

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

  1. Yapr2: TTACTAA at 2374.
  2. Yapr6: TTACTAA at 1423.
  3. Yapr4ci: TTAGTAA at 2301.

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

  1. Yapr1ci: TTAGTAA at 1724.
  2. Yapr3ci: TTAGTAA at 916.
  3. Yapr9ci: TTAGTAA at 4015.

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

  1. Yapr1ci: TTAGTAA at 1724.
  2. Yapr3ci: TTAGTAA at 916.
  3. Yapr9ci: TTAGTAA at 4015.

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

  1. Yapr2: TTACTAA at 2374.
  2. Yapr4: TTACTAA at 3669.
  3. Yapr6: TTACTAA at 1423.
  4. Yapr4ci: TTAGTAA at 2301.

Yap analysis and results

Main article: Complex locus A1BG and ZNF497 § Yaps

At "least four Yap proteins bind most efficiently to TTACTAA, a sequence that differs at position ±2 from the optimal AP-1 site (TGACTCA)".[2][1]

Reals or randoms Promoters direction Numbers Strands Occurrences Averages (± 0.1)
Reals UTR negative 1 2 0.5 0.5
Randoms UTR arbitrary negative 1 10 0.1 0.15
Randoms UTR alternate negative 2 10 0.2 0.15
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 0 2 0 0
Randoms Core arbitrary positive 0 10 0 0
Randoms Core alternate positive 0 10 0 0
Reals Proximal negative 0 2 0 0
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 0 2 0 0
Randoms Distal arbitrary negative 3 10 0.3 0.3
Randoms Distal alternate negative 3 10 0.3 0.3
Reals Distal positive 0 2 0 0
Randoms Distal arbitrary positive 3 10 0.3 0.35
Randoms Distal alternate positive 4 10 0.4 0.35

Comparison:

The occurrences of real Yap UTRs are greater than the randoms. This suggests that the real Yaps 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 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.
  2. ↑ 2.0 2.1 Lisete Fernandes, Claudina Rodrigues-Pousada, Kevin Struhl (December 1997). "Yap, a novel family of eight bZIP proteins in Saccharomyces cerevisiae with distinct biological functions". Molecular and Cellular Biology. 17 (12): 6982–6993. doi:10.1128/MCB.17.12.6982. Retrieved 11 March 2021.

External links

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