Zinc responsive element gene transcriptions: Difference between revisions

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|pmid=17933919
|pmid=17933919
|accessdate=10 February 2021 }}</ref>
|accessdate=10 February 2021 }}</ref>
==Consensus sequences==
{{main|Consensus sequence gene transcriptions}}
A zinc-responsive element consensus (MHHAACCBYNMRGGT) is (A/C)(A/C/T)(A/C/T)AACC(C/G/T)(C/T)N(A/C)(A/G)GGT.<ref name=Nicola/>


==ZRE samplings==
==ZRE samplings==
{{main|Model samplings}}
{{main|Model samplings}}
Copying a responsive elements consensus sequence AAAAAAAA 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.
Copying a responsive elements consensus sequence (A/C)(A/C/T)(A/C/T)AACC(C/G/T)(C/T)N(A/C)(A/G)GGT 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. The addition of degenerate nucleotides increases the possible occurrences to 216 from 1.
 
For the Basic programs testing consensus sequence AAAAAAAA (starting with SuccessablesAAA.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 AAAAAAAA, 0.
# positive strand, negative direction, looking for AAAAAAAA, 0.
# positive strand, positive direction, looking for AAAAAAAA, 0.
# negative strand, positive direction, looking for AAAAAAAA, 0.
# complement, negative strand, negative direction, looking for TTTTTTTT, 0.
# complement, positive strand, negative direction, looking for TTTTTTTT, 0.
# complement, positive strand, positive direction, looking for TTTTTTTT, 0.
# complement, negative strand, positive direction, looking for TTTTTTTT, 0.
# inverse complement, negative strand, negative direction, looking for TTTTTTTT, 0.
# inverse complement, positive strand, negative direction, looking for TTTTTTTT, 0.
# inverse complement, positive strand, positive direction, looking for TTTTTTTT, 0.
# inverse complement, negative strand, positive direction, looking for TTTTTTTT, 0.
# inverse negative strand, negative direction, looking for AAAAAAAA, 0.
# inverse positive strand, negative direction, looking for AAAAAAAA, 0.
# inverse positive strand, positive direction, looking for AAAAAAAA, 0.
# inverse negative strand, positive direction, looking for AAAAAAAA, 0.
 
===ZRE UTR gene transcriptions===
{{main|UTR promoter gene transcriptions}}
 
===ZRE core promoters===
{{main|Core promoter gene transcriptions}}
 
===ZRE proximal promoters===
{{main|Proximal promoter gene transcriptions}}


===ZRE distal promoters===
For the Basic programs testing consensus sequence (A/C)(A/C/T)(A/C/T)AACC(C/G/T)(C/T)N(A/C)(A/G)GGT (starting with SuccessablesZRE.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:
{{main|Distal promoter gene transcriptions}}
# negative strand, negative direction, looking for (A/C)(A/C/T)(A/C/T)AACC(C/G/T)(C/T)N(A/C)(A/G)GGT, 0.
# positive strand, negative direction, looking for (A/C)(A/C/T)(A/C/T)AACC(C/G/T)(C/T)N(A/C)(A/G)GGT, 0.
# positive strand, positive direction, looking for (A/C)(A/C/T)(A/C/T)AACC(C/G/T)(C/T)N(A/C)(A/G)GGT, 0.
# negative strand, positive direction, looking for (A/C)(A/C/T)(A/C/T)AACC(C/G/T)(C/T)N(A/C)(A/G)GGT, 0.
# complement, negative strand, negative direction, looking for (G/T)(A/G/T)(A/G/T)TTGG(C/G/A)(A/G)N(G/T)(C/T)CCA, 0.
# complement, positive strand, negative direction, looking for (G/T)(A/G/T)(A/G/T)TTGG(C/G/A)(A/G)N(G/T)(C/T)CCA, 0.
# complement, positive strand, positive direction, looking for (G/T)(A/G/T)(A/G/T)TTGG(C/G/A)(A/G)N(G/T)(C/T)CCA, 0.
# complement, negative strand, positive direction, looking for (G/T)(A/G/T)(A/G/T)TTGG(C/G/A)(A/G)N(G/T)(C/T)CCA, 0.
# inverse complement, negative strand, negative direction, looking for ACC(C/T)(G/T)N(A/G)(A/C/G)GGTT(A/G/T)(A/G/T)(G/T), 0.
# inverse complement, positive strand, negative direction, looking for ACC(C/T)(G/T)N(A/G)(A/C/G)GGTT(A/G/T)(A/G/T)(G/T), 0.
# inverse complement, positive strand, positive direction, looking for ACC(C/T)(G/T)N(A/G)(A/C/G)GGTT(A/G/T)(A/G/T)(G/T), 0.
# inverse complement, negative strand, positive direction, looking for ACC(C/T)(G/T)N(A/G)(A/C/G)GGTT(A/G/T)(A/G/T)(G/T), 0.
# inverse negative strand, negative direction, looking for TGG(A/G)(A/C)N(C/T)(C/G/T)CCAA(A/C/T)(A/C/T)(A/C), 0.
# inverse positive strand, negative direction, looking for TGG(A/G)(A/C)N(C/T)(C/G/T)CCAA(A/C/T)(A/C/T)(A/C), 0.
# inverse positive strand, positive direction, looking for TGG(A/G)(A/C)N(C/T)(C/G/T)CCAA(A/C/T)(A/C/T)(A/C), 0.
# inverse negative strand, positive direction, looking for TGG(A/G)(A/C)N(C/T)(C/G/T)CCAA(A/C/T)(A/C/T)(A/C), 0.


==Acknowledgements==
==Acknowledgements==
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* [[A1BG response element positive results]]
* [[A1BG response element positive results]]
* [[Complex locus A1BG and ZNF497]]
* [[Complex locus A1BG and ZNF497]]
* [[Zap1p gene transcriptions]]
{{Div col end}}
{{Div col end}}


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[[Category:Resources last modified in February 2021]]
[[Category:Resources last modified in March 2021]]

Latest revision as of 19:02, 15 March 2021

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

"A robust set of genes that responded consistently to Zn limitation was identified, and the set enabled the definition of the Zn-specific Zap1p regulon, comprised of 26 genes and characterized by a broader zinc-responsive element consensus (MHHAACCBYNMRGGT) than so far described."[1]

"In order to better define the Zap1p regulon, Lyons and coworkers analyzed the genome-wide transcriptional response of a S. cerevisiae zap1 mutant strain and a control strain to zinc abundance or depletion (50). A combinatorial analysis identified a subset of 46 zinc-responsive genes whose expression was reduced in the zap1 mutant and that possessed a zinc-responsive element (ZRE) (5′-ACCYYNAAGGT-3′). Among the members of this updated defined Zap1p regulon were the well-characterized plasma membrane, vacuole, and endoplasmic reticulum zinc transporters."[1]

Consensus sequences

Main article: Consensus sequence gene transcriptions

A zinc-responsive element consensus (MHHAACCBYNMRGGT) is (A/C)(A/C/T)(A/C/T)AACC(C/G/T)(C/T)N(A/C)(A/G)GGT.[1]

ZRE samplings

Main article: Model samplings

Copying a responsive elements consensus sequence (A/C)(A/C/T)(A/C/T)AACC(C/G/T)(C/T)N(A/C)(A/G)GGT 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. The addition of degenerate nucleotides increases the possible occurrences to 216 from 1.

For the Basic programs testing consensus sequence (A/C)(A/C/T)(A/C/T)AACC(C/G/T)(C/T)N(A/C)(A/G)GGT (starting with SuccessablesZRE.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 (A/C)(A/C/T)(A/C/T)AACC(C/G/T)(C/T)N(A/C)(A/G)GGT, 0.
  2. positive strand, negative direction, looking for (A/C)(A/C/T)(A/C/T)AACC(C/G/T)(C/T)N(A/C)(A/G)GGT, 0.
  3. positive strand, positive direction, looking for (A/C)(A/C/T)(A/C/T)AACC(C/G/T)(C/T)N(A/C)(A/G)GGT, 0.
  4. negative strand, positive direction, looking for (A/C)(A/C/T)(A/C/T)AACC(C/G/T)(C/T)N(A/C)(A/G)GGT, 0.
  5. complement, negative strand, negative direction, looking for (G/T)(A/G/T)(A/G/T)TTGG(C/G/A)(A/G)N(G/T)(C/T)CCA, 0.
  6. complement, positive strand, negative direction, looking for (G/T)(A/G/T)(A/G/T)TTGG(C/G/A)(A/G)N(G/T)(C/T)CCA, 0.
  7. complement, positive strand, positive direction, looking for (G/T)(A/G/T)(A/G/T)TTGG(C/G/A)(A/G)N(G/T)(C/T)CCA, 0.
  8. complement, negative strand, positive direction, looking for (G/T)(A/G/T)(A/G/T)TTGG(C/G/A)(A/G)N(G/T)(C/T)CCA, 0.
  9. inverse complement, negative strand, negative direction, looking for ACC(C/T)(G/T)N(A/G)(A/C/G)GGTT(A/G/T)(A/G/T)(G/T), 0.
  10. inverse complement, positive strand, negative direction, looking for ACC(C/T)(G/T)N(A/G)(A/C/G)GGTT(A/G/T)(A/G/T)(G/T), 0.
  11. inverse complement, positive strand, positive direction, looking for ACC(C/T)(G/T)N(A/G)(A/C/G)GGTT(A/G/T)(A/G/T)(G/T), 0.
  12. inverse complement, negative strand, positive direction, looking for ACC(C/T)(G/T)N(A/G)(A/C/G)GGTT(A/G/T)(A/G/T)(G/T), 0.
  13. inverse negative strand, negative direction, looking for TGG(A/G)(A/C)N(C/T)(C/G/T)CCAA(A/C/T)(A/C/T)(A/C), 0.
  14. inverse positive strand, negative direction, looking for TGG(A/G)(A/C)N(C/T)(C/G/T)CCAA(A/C/T)(A/C/T)(A/C), 0.
  15. inverse positive strand, positive direction, looking for TGG(A/G)(A/C)N(C/T)(C/G/T)CCAA(A/C/T)(A/C/T)(A/C), 0.
  16. inverse negative strand, positive direction, looking for TGG(A/G)(A/C)N(C/T)(C/G/T)CCAA(A/C/T)(A/C/T)(A/C), 0.

Acknowledgements

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

See also

References

  1. ↑ 1.0 1.1 1.2 Raffaele De Nicola, Lucie A. Hazelwood, Erik A. F. De Hulster, Michael C. Walsh, Theo A. Knijnenburg, Marcel J. T. Reinders, Graeme M. Walker, Jack T. Pronk, Jean-Marc Daran, Pascale Daran-Lapujade (December 2007). "Physiological and Transcriptional Responses of Saccharomyces cerevisiae to Zinc Limitation in Chemostat Cultures". Applied and Environmental Microbiology. 73 (23): 7680–92. doi:10.1128/AEM.01445-07. PMID 17933919. Retrieved 10 February 2021.

External links

Retrieved from "https://www.wikidoc.org/index.php?title=Zinc_responsive_element_gene_transcriptions&oldid=1694514"