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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recognition element gene transcriptions DREB box gene transcriptions E2 box gene transcriptions EIF4E basal element gene transcriptions EIN3 binding site gene transcriptions Enhancer activity copy gene transcriptions E box gene transcriptions Element gene transcriptions Endoplasmic reticulum stress response element gene transcriptions Endosperm expression gene transcriptions Enhancer box gene transcriptions Estrogen response element gene transcriptions Ethylene responsive element gene transcriptions Families of TATA box genes F box gene transcriptions Focused promoter gene transcriptions Forkhead box gene transcriptions Fur box gene transcriptions GAAC element gene transcriptions Gal4p gene transcriptions Γ-interferon activated sequence gene transcriptions GARE gene transcriptions GA responsive complex gene transcriptions GATA gene transcriptions G box gene transcriptions GC box gene transcriptions GCC box gene transcriptions Gcn4p gene transcriptions Gcr1p gene transcriptions Gene 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gene transcriptions Hsf1p gene transcriptions HY box gene transcriptions Hybrid C, A boxes Hybrid C, G boxes Hybrid C, T boxes Hypoxia-inducible factor gene transcriptions Hypoxia response elements I box gene transcriptions Immunoglobulin like domain containing family Initiator element gene transcriptions Initiator-like element gene transcriptions Inositol/choline-responsive elements Interaction gene transcriptions Interferon regulatory factors Inverse copy gene transcriptions Jasmonic acid-responsive element gene transcriptions K-boxes Kozak sequence gene transcriptions Kruppel-associated box gene transcriptions Krüppel-like factor gene transcriptions L box gene transcriptions Leu3 gene transcriptions M35 box gene transcriptions MADS box gene transcriptions Maf recognition element gene transcriptions M box gene transcriptions Mcm1 regulatory factor gene transcriptions Met3 gene transcriptions Met31p box gene transcriptions Metal responsive element gene transcriptions Middle sporulation element gene transcriptions Mig1p gene transcriptions Model samplings Motif ten element gene transcriptions Msn2,4p gene transcriptions Musashi binding element gene transcriptions MYB recognition element gene transcriptions Myelocytomatosis transcription factor gene transcriptions Myocyte enhancer factor gene transcriptions N-boxes Nanos/Pumilio response element 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 Proximal promoter gene transcriptions Promoter occurrence gene transcriptions Pyrimidine box gene transcriptions Q element gene transcriptions Rap1 regulatory factor gene transcriptions Reb1 general regulatory factor gene transcriptions Retinoblastoma control element gene transcriptions Retinoic acid response element gene transcriptions Rgt1p gene transcriptions Rlm1p gene transcriptions RNA polymerase II gene transcriptions RNA polymerase II holoenzyme complex Root specific element gene transcriptions ROR-response element gene transcriptions Rox1p gene transcriptions Rpn4p gene transcriptions R response element gene transcriptions SARE gene transcriptions Seed-specific element gene transcriptions Serum response element gene transcriptions Servenius sequence gene transcriptions Shoot specific element gene transcriptions Sip4p gene transcriptions Smp1p gene transcriptions Sp1 gene transcriptions Spaceflight gene expressions Specificity protein gene transcriptions STAT gene 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 actin/cytoskeleton/contractile family TATA box albumin family TATA box aldolase family TATA box alkaline phosphatase family TATA box annexin family TATA box cytochrome superfamily TATA box gene transcriptions TATA box heat shock family TATA box histone family TATA box human genes TATA box keratin family TATA box lipase family TATA box peptidase family TATA box platelet-derived growth factor family TATA box selenium-binding family TATA box serine protease family TATA box serpin superfamily TATA box transforming growth factor superfamily TATA box trefoil family TATA box tumor necrosis factor superfamily TATA box zinc metalloenzyme family 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 Tryptophan residue 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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