Aft1p gene transcriptions: Difference between revisions

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{{AE}} Henry A. Hoff
{{AE}} Henry A. Hoff
Aft1 is Affinity Capture-Western; Two-hybrid.<ref name=RefSeq852809>{{ cite web
|author=RefSeq
|title=AFT1 DNA-binding transcription factor AFT1 [ Saccharomyces cerevisiae S288C ]
|publisher=National Center for Biotechnology Information, U.S. National Library of Medicine
|location=8600 Rockville Pike, Bethesda MD, 20894 USA
|date=18 September 2021
|url=https://www.ncbi.nlm.nih.gov/gene/852809
|accessdate=19 October 2021 }}</ref>


==Consensus sequences==
==Consensus sequences==


The upstream activating sequence (UAS) for Aft1p is 5'-PyPuCACCCPu-3' or 5'-(C/T)(A/G)CACCC(A/G).<ref name=Tang>{{ cite journal
The upstream activating sequence (UAS) for Aft1p is PyPuCACCCPu or (C/T)(A/G)CACCC(A/G).<ref name=Tang>{{ cite journal
|author=Hongting Tang, Yanling Wu, Jiliang Deng, Nanzhu Chen, Zhaohui Zheng, Yongjun Wei, Xiaozhou Luo, and Jay D. Keasling
|author=Hongting Tang, Yanling Wu, Jiliang Deng, Nanzhu Chen, Zhaohui Zheng, Yongjun Wei, Xiaozhou Luo, and Jay D. Keasling
|title=Promoter Architecture and Promoter Engineering in ''Saccharomyces cerevisiae''
|title=Promoter Architecture and Promoter Engineering in ''Saccharomyces cerevisiae''
Line 24: Line 33:
# Aft1p does not participate in the transcription of A1BG.
# Aft1p does not participate in the transcription of A1BG.


==Samplings==
==AFT1 samplings==
{{main|Model samplings}}
{{main|Model samplings}}
Copying 5'-TGCACCC-3' in "⌘F" yields none between ZSCAN22 and A1BG and one 5'-TGCACCCG-3' between ZNF497 and A1BG as can be found by the computer programs.
Copying TGCACCC in "⌘F" yields none between ZSCAN22 and A1BG and one TGCACCCG between ZNF497 and A1BG as can be found by the computer programs.
 
For the Basic programs testing consensus sequence (C/T)(A/G)CACCC(A/G) (starting with SuccessablesAFT.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:
# negative strand, negative direction, looking for (C/T)(A/G)CACCC(A/G), 0.
# negative strand, positive direction, looking for (C/T)(A/G)CACCC(A/G), 1, TGCACCCG at 3324.
# positive strand, negative direction, looking for (C/T)(A/G)CACCC(A/G), 0.
# positive strand, positive direction, looking for (C/T)(A/G)CACCC(A/G), 0.
# inverse complement, negative strand, negative direction, looking for (C/T)GGGTG(C/T)(A/G), 1, TGGGTGTG at 1804.
# inverse complement, negative strand, positive direction, looking for (C/T)GGGTG(C/T)(A/G), 0.
# inverse complement, positive strand, negative direction, looking for (C/T)GGGTG(C/T)(A/G), 3, TGGGTGTG at 3185, CGGGTGCG at 2196, CGGGTGCG at 379.
# inverse complement, positive strand, positive direction, looking for (C/T)GGGTG(C/T)(A/G), 0.
 
===AFT (4560-2846) UTRs===
 
# Positive strand, negative direction: TGGGTGTG at 3185.
 
===AFT negative direction (2596-1) distal promoters===
 
# Negative strand, negative direction: TGGGTGTG at 1804.
# Positive strand, negative direction: CGGGTGCG at 2196, CGGGTGCG at 379.
 
===AFT positive direction (4050-1) distal promoters===
 
# Negative strand, positive direction: TGCACCCG at 3324.
 
==AFT random dataset samplings==
 
# AFTr0: 0.
# AFTr1: 1, CGCACCCA at 237.
# AFTr2: 0.
# AFTr3: 0.
# AFTr4: 0.
# AFTr5: 0.
# AFTr6: 0.
# AFTr7: 0.
# AFTr8: 1, CACACCCG at 1053.
# AFTr9: 0.
# AFTr0ci: 1, TGGGTGCG at 643.
# AFTr1ci: 2, TGGGTGTA at 4170, TGGGTGTA at 2489.
# AFTr2ci: 1, TGGGTGCA at 2005.
# AFTr3ci: 0.
# AFTr4ci: 0.
# AFTr5ci: 1, TGGGTGTA at 2219.
# AFTr6ci: 0.
# AFTr7ci: 0.
# AFTr8ci: 0.
# AFTr9ci: 1, TGGGTGCG at 3727.
 
===AFTr alternate (odds) (4560-2846) UTRs===
 
# AFTr1ci: TGGGTGTA at 4170.
# AFTr9ci: TGGGTGCG at 3727.
 
===AFTr arbitrary positive direction (odds) (4265-4050) proximal promoters===
 
# AFTr1ci: TGGGTGTA at 4170.
 
===AFTr arbitrary negative direction (evens) (2596-1) distal promoters===
 
# AFTr8: CACACCCG at 1053.
# AFTr0ci: TGGGTGCG at 643.
# AFTr2ci: TGGGTGCA at 2005.
 
===AFTr alternate negative direction (odds) (2596-1) distal promoters===
 
# AFTr1: CGCACCCA at 237.
# AFTr1ci: TGGGTGTA at 2489.
# AFTr5ci: TGGGTGTA at 2219.
 
===AFTr arbitrary positive direction (odds) (4050-1) distal promoters===
 
# AFTr1: CGCACCCA at 237.
# AFTr1ci: TGGGTGTA at 2489.
# AFTr5ci: TGGGTGTA at 2219.
# AFTr9ci: TGGGTGCG at 3727.
 
===AFTr alternate positive direction (evens) (4050-1) distal promoters===
 
# AFTr8: CACACCCG at 1053.
# AFTr0ci: TGGGTGCG at 643.
# AFTr2ci: TGGGTGCA at 2005.


For the Basic programs testing consensus sequence 5'-(C/T)(A/G)CACCC(A/G)-3' (starting with SuccessablesAFT.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:
==AFT analysis and results==
# negative strand, negative direction, looking for 5'-(C/T)(A/G)CACCC(A/G)-3', 0.
{{main|Complex locus A1BG and ZNF497#AFTs}}
# negative strand, positive direction, looking for 5'-(C/T)(A/G)CACCC(A/G)-3', 1, 5'-TGCACCCG-3' at 3324.
The upstream activating sequence (UAS) for Aft1p is PyPuCACCCPu or (C/T)(A/G)CACCC(A/G).<ref name=Tang/>
# positive strand, negative direction, looking for 5'-(C/T)(A/G)CACCC(A/G)-3', 0.
# positive strand, positive direction, looking for 5'-(C/T)(A/G)CACCC(A/G)-3', 0.
# complement, negative strand, negative direction, looking for 5'-(A/G)(C/T)GTGGG(C/T)-3', 0.
# complement, negative strand, positive direction, looking for 5'-(A/G)(C/T)GTGGG(C/T)-3', 0.
# complement, positive strand, negative direction, looking for 5'-(A/G)(C/T)GTGGG(C/T)-3', 0.
# complement, positive strand, positive direction, looking for 5'-(A/G)(C/T)GTGGG(C/T)-3', 1, 5'-ACGTGGGC-3' at 3324.
# inverse complement, negative strand, negative direction, looking for 5'-(C/T)GGGTG(C/T)(A/G)-3', 0.
# inverse complement, negative strand, positive direction, looking for 5'-(C/T)GGGTG(C/T)(A/G)-3', 0.
# inverse complement, positive strand, negative direction, looking for 5'-(C/T)GGGTG(C/T)(A/G)-3', 0.
# inverse complement, positive strand, positive direction, looking for 5'-(C/T)GGGTG(C/T)(A/G)-3', 0.
# inverse negative strand, negative direction, looking for 5'-(A/G)CCCAC(A/G)(C/T)-3', 0.
# inverse negative strand, positive direction, looking for 5'-(A/G)CCCAC(A/G)(C/T)-3', 0.
# inverse positive strand, negative direction, looking for 5'-(A/G)CCCAC(A/G)(C/T)-3', 0.
# inverse positive strand, positive direction, looking for 5'-(A/G)CCCAC(A/G)(C/T)-3', 0.


===AFT core promoters===
{|class="wikitable"
{{main|Core promoter gene transcriptions}}
|-
! Reals or randoms !! Promoters !! direction !! Numbers !! Strands !! Occurrences !! Averages (± 0.1)
|-
| Reals || UTR || negative || 1 || 2 || 0.5 || 0.5
|-
| Randoms || UTR || arbitrary negative || 0 || 10 || 0 || 0.1
|-
| Randoms || UTR || alternate negative || 2 || 10 || 0.2 || 0.1
|-
| 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 || 1 || 10 || 0.1 || 0.05
|-
| Randoms || Proximal || alternate positive || 0 || 10 || 0 || 0.05
|-
| Reals || Distal || negative || 3 || 2 || 1.5 || 1.5 ± 0.5 (--1,+-2)
|-
| Randoms || Distal || arbitrary negative || 3 || 10 || 0.3 || 0.3
|-
| Randoms || Distal || alternate negative || 3 || 10 || 0.3 || 0.3
|-
| Reals || Distal || positive || 1 || 2 || 0.5 || 0.5
|-
| Randoms || Distal || arbitrary positive || 4 || 10 || 0.4 || 0.35
|-
| Randoms || Distal || alternate positive || 3 || 10 || 0.3 || 0.35
|}


===AFT proximal promoters===
Comparison:
{{main|Proximal promoter gene transcriptions}}


===AFT distal promoters===
The occurrences of real AFTs are greater than the randoms. This suggests that the real AFTs are likely active or activable.
{{main|Distal promoter gene transcriptions}}
Negative strand, positive direction: 5'-TGCACCCG-3' at 3324 and complement.


==Acknowledgements==
==Acknowledgements==
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[[Category:Resources last modified in October 2020]]

Latest revision as of 15:48, 3 October 2022

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

Aft1 is Affinity Capture-Western; Two-hybrid.[1]

Consensus sequences

The upstream activating sequence (UAS) for Aft1p is PyPuCACCCPu or (C/T)(A/G)CACCC(A/G).[2]

Hypotheses

  1. A1BG has no Aft1p in either promoter.
  2. A1BG is not transcribed by an Aft1p.
  3. Aft1p does not participate in the transcription of A1BG.

AFT1 samplings

Main article: Model samplings

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

For the Basic programs testing consensus sequence (C/T)(A/G)CACCC(A/G) (starting with SuccessablesAFT.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 (C/T)(A/G)CACCC(A/G), 0.
  2. negative strand, positive direction, looking for (C/T)(A/G)CACCC(A/G), 1, TGCACCCG at 3324.
  3. positive strand, negative direction, looking for (C/T)(A/G)CACCC(A/G), 0.
  4. positive strand, positive direction, looking for (C/T)(A/G)CACCC(A/G), 0.
  5. inverse complement, negative strand, negative direction, looking for (C/T)GGGTG(C/T)(A/G), 1, TGGGTGTG at 1804.
  6. inverse complement, negative strand, positive direction, looking for (C/T)GGGTG(C/T)(A/G), 0.
  7. inverse complement, positive strand, negative direction, looking for (C/T)GGGTG(C/T)(A/G), 3, TGGGTGTG at 3185, CGGGTGCG at 2196, CGGGTGCG at 379.
  8. inverse complement, positive strand, positive direction, looking for (C/T)GGGTG(C/T)(A/G), 0.

AFT (4560-2846) UTRs

  1. Positive strand, negative direction: TGGGTGTG at 3185.

AFT negative direction (2596-1) distal promoters

  1. Negative strand, negative direction: TGGGTGTG at 1804.
  2. Positive strand, negative direction: CGGGTGCG at 2196, CGGGTGCG at 379.

AFT positive direction (4050-1) distal promoters

  1. Negative strand, positive direction: TGCACCCG at 3324.

AFT random dataset samplings

  1. AFTr0: 0.
  2. AFTr1: 1, CGCACCCA at 237.
  3. AFTr2: 0.
  4. AFTr3: 0.
  5. AFTr4: 0.
  6. AFTr5: 0.
  7. AFTr6: 0.
  8. AFTr7: 0.
  9. AFTr8: 1, CACACCCG at 1053.
  10. AFTr9: 0.
  11. AFTr0ci: 1, TGGGTGCG at 643.
  12. AFTr1ci: 2, TGGGTGTA at 4170, TGGGTGTA at 2489.
  13. AFTr2ci: 1, TGGGTGCA at 2005.
  14. AFTr3ci: 0.
  15. AFTr4ci: 0.
  16. AFTr5ci: 1, TGGGTGTA at 2219.
  17. AFTr6ci: 0.
  18. AFTr7ci: 0.
  19. AFTr8ci: 0.
  20. AFTr9ci: 1, TGGGTGCG at 3727.

AFTr alternate (odds) (4560-2846) UTRs

  1. AFTr1ci: TGGGTGTA at 4170.
  2. AFTr9ci: TGGGTGCG at 3727.

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

  1. AFTr1ci: TGGGTGTA at 4170.

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

  1. AFTr8: CACACCCG at 1053.
  2. AFTr0ci: TGGGTGCG at 643.
  3. AFTr2ci: TGGGTGCA at 2005.

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

  1. AFTr1: CGCACCCA at 237.
  2. AFTr1ci: TGGGTGTA at 2489.
  3. AFTr5ci: TGGGTGTA at 2219.

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

  1. AFTr1: CGCACCCA at 237.
  2. AFTr1ci: TGGGTGTA at 2489.
  3. AFTr5ci: TGGGTGTA at 2219.
  4. AFTr9ci: TGGGTGCG at 3727.

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

  1. AFTr8: CACACCCG at 1053.
  2. AFTr0ci: TGGGTGCG at 643.
  3. AFTr2ci: TGGGTGCA at 2005.

AFT analysis and results

Main article: Complex locus A1BG and ZNF497 § AFTs

The upstream activating sequence (UAS) for Aft1p is PyPuCACCCPu or (C/T)(A/G)CACCC(A/G).[2]

Reals or randoms Promoters direction Numbers Strands Occurrences Averages (± 0.1)
Reals UTR negative 1 2 0.5 0.5
Randoms UTR arbitrary negative 0 10 0 0.1
Randoms UTR alternate negative 2 10 0.2 0.1
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 1 10 0.1 0.05
Randoms Proximal alternate positive 0 10 0 0.05
Reals Distal negative 3 2 1.5 1.5 ± 0.5 (--1,+-2)
Randoms Distal arbitrary negative 3 10 0.3 0.3
Randoms Distal alternate negative 3 10 0.3 0.3
Reals Distal positive 1 2 0.5 0.5
Randoms Distal arbitrary positive 4 10 0.4 0.35
Randoms Distal alternate positive 3 10 0.3 0.35

Comparison:

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

Acknowledgements

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

See also

References

  1. ↑ RefSeq (18 September 2021). "AFT1 DNA-binding transcription factor AFT1 [ Saccharomyces cerevisiae S288C ]". 8600 Rockville Pike, Bethesda MD, 20894 USA: National Center for Biotechnology Information, U.S. National Library of Medicine. Retrieved 19 October 2021.
  2. ↑ 2.0 2.1 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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