Zinc responsive element gene transcriptions

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

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

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:

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

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

References

↑ ^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

[Nicola-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.

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transcriptions MYB recognition element gene transcriptions Myelocytomatosis transcription factor gene transcriptions Myocyte enhancer factor gene transcriptions N-boxes Ndt80p gene transcriptions Nuclear factor 1 Nuclear factor 𝜿B Nuclear factor gene transcriptions Nuclear factor of activated T cell gene transcriptions (NFAT) Nuclear factor Y gene transcriptions Nutrient-sensing response element gene transcriptions Oaf1p gene transcriptions ORE1 binding site gene transcriptions p53 response element gene transcriptions P63 DNA-binding site gene transcriptions P box gene transcriptions Pdr1,3p gene transcriptions Peroxisome proliferator hormone response element gene transcriptions Phosphate starvation-response transcription factor gene transcriptions Pollen1 element gene transcriptions Polycomb response element gene transcriptions Preinitiation complex Preinitiation complex gene transcriptions Pribnow box gene transcriptions Prolamin box gene transcriptions Promoter gene transcriptions 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transcriptions Ste12p gene transcriptions Sterol response element gene transcriptions Sucrose box gene transcriptions Synaptic Activity-Responsive Elements TACTAAC box gene transcriptions TAGteam gene transcriptions Tapetum box gene transcriptions TATA binding protein associated factor gene transcriptions TATA binding protein gene transcriptions TATA box gene transcriptions TAT box gene transcriptions TATC box gene transcriptions Tbf1 regulatory factor gene transcriptions T box gene transcriptions TCCACCATA element gene transcriptions TC element gene transcriptions TCT gene transcriptions TEA consensus sequence gene transcriptions Tec1p gene transcriptions Telomeric repeat DNA-binding factor gene transcriptions Tetradecanoylphorbol-13-acetate response element gene transcriptions TGF-β control elements (TCEs) TGF-β inhibitory elements (TIEs) Thyroid hormone response element gene transcriptions Transcriptional regulation Transcription bubble gene transcriptions Transcription factor gene transcriptions Transcription factor 3 gene transcriptions Transcription factory gene transcriptions Transcription start site gene transcriptions Translational control sequence gene transcriptions U box gene transcriptions Unfolded protein response element gene transcriptions Upstream response element gene transcriptions Upstream stimulatory factor gene transcriptions UTR promoter gene transcriptions V and P box gene transcriptions V box gene transcriptions Vhr1p gene transcriptions Vitamin D response element gene transcriptions W box gene transcriptions X box gene transcriptions Xbp1p gene transcriptions X core promoter element gene transcriptions Xenobiotic response element gene transcriptions Xenobiotic responsive element gene transcriptions Yap1p,2p gene transcriptions Y box gene transcriptions YY1 gene transcriptions Zap1p gene transcriptions Z box gene transcriptions Zinc responsive element gene transcriptions

Zinc responsive element gene transcriptions

Contents

Consensus sequences

ZRE samplings

Acknowledgements

See also

References

External links

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