Metal responsive element gene transcriptions

Editor-In-Chief: Henry A. Hoff

Metal responsive elements (MRE)s, or TGC boxes, may occur in the core promoter of some human DNA genes.

TGC boxes

Notation: let the symbol MT stand for metallothionein.

"The metallothionein (MT) genes provide a good example of eucaryotic promoter architecture. MT genes specify the synthesis of low-molecular-weight metal-binding proteins. They are transcriptionally regulated by the metal ions cadmium and zinc (11), glucocorticoid hormones (18), interferon (14), interleukin-1 (22), and tumor promoters (2). The metal ion regulation of MTs is conferred by a short sequence element called the metal-responsive element (MRE [21]) or TGC box (31, 34), which functions as a metal ion-dependent enhancer."^[1]

Consensus sequences

"The promoter regulatory sequences are identified by homology to published GRE (21), MRE (35), and GC box (15) consensus sequences."^[1]

Here "is a consensus sequence for the MREs of the rat MT-1 gene."^[1] In the direction of transcription on the DNA template strand: 3'-CNNTGCRCYCGGGNC-5', where R = purine; Y = pyrimidine; and N = any nucleotide (nt).^[1]

"[T]hree potential metal response elements (MREs) [overlap] the E-boxes in the repeats, (TGCACGT with TGCRCNC being the consensus sequence; 17,18)."^[2]

The reproducible consensus sequence seems to be 3'-TGCRCNC-5', specifically 3'-TGC(A/G)CNC-5'.

"To execute the transcriptional regulation, [Metal-responsive transcription factor-1] MTF-1 binds to the specific site, called [metal responsive element] MRE (core sequence = TGCRCNC), in the promoter region of target gene (Günther et al. 2012a)."^[3]

MREs

Six MREs lie in the proximal promoter of the rat MT-1 gene upstream of the TATA box to almost -200 nts from the transcription start site.^[1]

Hypotheses

A1BG has no MREs in either promoter.
A1BG is not transcribed by an MRE.
MREs do not participate in the transcription of A1BG.

Samplings

Copying a responsive elements consensus sequence 5'-TGCGCCC-3' 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.

For the Basic programs (starting with SuccessablesMRE.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 (+), including extending the number of nts from 958 to 4445, the programs are, are looking for, and found:

negative strand in the negative direction is SuccessablesMRE--.bas, looking for 5'-T-G-C-(A/G)-C-(A/C/G/T)-C-3', 0,
negative strand in the positive direction is SuccessablesMRE-+.bas, looking for 5'-T-G-C-(A/G)-C-(A/C/G/T)-C-3', 11, 5'-TGCGCCC-3' at 453, 5'-TGCACAC-3' at 549, 5'-TGCACAC-3' at 1221, 5'-TGCGCCC-3' at 1247, 5'-TGCACTC-3' at 1373, 5'-TGCGCCC-3' at 1399, 5'-TGCACTC-3' at 1473, 5'-TGCGCCC-3' at 1499, 5'-TGCGCCC-3' at 1657, 5'-TGCACAC-3' at 2963, 5'-TGCACCC-3' at 3323,
positive strand in the negative direction is SuccessablesMRE+-.bas, looking for 5'-T-G-C-(A/G)-C-(A/C/G/T)-C-3', 7, 5'-TGCGCTC-3' at 891, 5'-TGCACTC-3' at 1348, 5'-TGCACTC-3' at 2001, 5'-TGCACTC-3' at 2427, 5'-TGCACCC-3' at 2762, 5'-TGCACTC-3' at 3290, 5'-TGCACTC-3' at 4341,
positive strand in the positive direction is SuccessablesMRE++.bas, looking for 5'-T-G-C-(A/G)-C-(A/C/G/T)-C-3', 2, 5'-TGCGCCC-3' at 872, 5'-TGCGCCC-3' at 972,
complement, negative strand, negative direction is SuccessablesMREc--.bas, looking for 5'-A-C-G-(T/C)-G-(A/C/G/T)-G-3', 7, 5'-ACGCGAG-3' at 891, 5'-ACGTGAG-3' at 1348, 5'-ACGTGAG-3' at 2001, 5'-ACGTGAG-3' at 2427, 5'-ACGTGGG-3' at 2762, 5'-ACGTGAG-3' at 3290, 5'-ACGTGAG-3' at 4341,
complement, negative strand, positive direction is SuccessablesMREc-+.bas, looking for 5'-A-C-G-(T/C)-G-(A/C/G/T)-G-3', 2, 5'-ACGCGGG-3' at 872, 5'-ACGCGGG-3' at 972,
complement, positive strand, negative direction is SuccessablesMREc+-.bas, looking for 5'-A-C-G-(T/C)-G-(A/C/G/T)-G-3', 0,
complement, positive strand, negative direction is SuccessablesMREc++.bas, looking for 5'-A-C-G-(T/C)-G-(A/C/G/T)-G-3', 11, 5'-ACGCGGG-3' at 453, 5'-ACGTGTG-3' at 549, 5'-ACGTGTG-3' at 1221, 5'-ACGCGGG-3' at 1247, 5'-ACGTGAG-3' at 1373, 5'-ACGCGGG-3' at 1399, 5'-ACGTGAG-3' at 1473, 5'-ACGCGGG-3' at 1499, 5'-ACGCGGG-3' at 1657, 5'-ACGTGTG-3' at 2963, 5'-ACGTGGG-3' at 3323,
inverse complement, negative strand, negative direction is SuccessablesMREci--.bas, looking for 5'-G-(A/C/G/T)-G-(T/C)-G-C-A-3', 2, 5'-GTGTGCA-3' at 531, 5'-GAGTGCA-3' at 1772,
inverse complement, negative strand, positive direction is SuccessablesMREci-+.bas, looking for 5'-G-(A/C/G/T)-G-(T/C)-G-C-A-3', 10, 5'-GCGTGCA-3' at 546, 5'-GCGCGCA-3' at 684, 5'-GGGCGCA-3' at 876, 5'-GGGCGCA-3' at 976, 5'-GCGTGCA-3' at 1218, 5'-GTGCGCA-3' at 1523, 5'-GAGTGCA-3' at 1786, 5'-GAGTGCA-3' at 2326, 5'-GGGTGCA-3' at 2800, 5'-GGGTGCA-3' at 3883,
inverse complement, positive strand, negative direction is SuccessablesMREci+-.bas, looking for 5'-G-(A/C/G/T)-G-(T/C)-G-C-A-3', 2, 5'-GAGTGCA-3' at 1470, 5'-GTGTGCA-3' at 2863,
inverse complement, positive strand, positive direction is SuccessablesMREci++.bas, looking for 5'-G-(A/C/G/T)-G-(T/C)-G-C-A-3', 0,
inverse, negative strand, negative direction, is SuccessablesMREi--.bas, looking for 5'-C-(A/C/G/T)-C-(A/G)-C-G-T-3', 2, 5'-CTCACGT-3' at 1470, 5'-CACACGT-3' at 2863,
inverse, negative strand, positive direction, is SuccessablesMREi-+.bas, looking for 5'-C-(A/C/G/T)-C-(A/G)-C-G-T-3', 0,
inverse, positive strand, negative direction, is SuccessablesMREi+-.bas, looking for 5'-C-(A/C/G/T)-C-(A/G)-C-G-T-3', 2, 5'-CACACGT-3' at 531, 5'-CTCACGT-3' at 1772,
inverse, positive strand, positive direction, is SuccessablesMREi++.bas, looking for 5'-C-(A/C/G/T)-C-(A/G)-C-G-T-3', 10, 5'-CGCACGT-3' at 546, 5'-CGCGCGT-3' at 684, 5'-CCCGCGT-3' at 876, 5'-CCCGCGT-3' at 976, 5'-CGCACGT-3' at 1218, 5'-CACGCGT-3' at 1523, 5'-CTCACGT-3' at 1786, 5'-CTCACGT-3' at 2326, 5'-CCCACGT-3' at 2800, 5'-CCCACGT-3' at 3883.

MRE proximal promoters

Positive strand, negative direction: 5'-TGCACTC-3' at 4341.

MRE distal promoters

Negative strand, negative direction: 5'-GAGTGCA-3', 1772, 5'-GTGTGCA-3', 531, and complements.

Negative strand, positive direction: 5'-GGGTGCA-3' at 3883, 5'-TGCACCC-3' at 3323, 5'-TGCACAC-3' at 2963, 5'-GGGTGCA-3' at 2800, 5'-GAGTGCA-3' at 2326, 5'-GAGTGCA-3' at 1786, 5'-TGCGCCC-3' at 1657, 5'-GTGCGCA-3' at 1523, 5'-TGCGCCC-3' at 1499, 5'-TGCACTC-3' at 1473, 5'-TGCGCCC-3' at 1399, 5'-TGCACTC-3' at 1373, 5'-TGCGCCC-3' at 1247, 5'-TGCACAC-3' at 1221, 5'-GCGTGCA-3' at 1218, 5'-GGGCGCA-3' at 976, 5'-GGGCGCA-3' at 876, 5'-GCGCGCA-3' at 684, 5'-TGCACAC-3' at 549, 5'-GCGTGCA-3' at 546, 5'-TGCGCCC-3' at 453, and complements.

Positive strand, negative direction: 5'-TGCACTC-3' at 3290, 5'-GTGTGCA-3' at 2863, 5'-TGCACCC-3' at 2762, 5'-TGCACTC-3' at 2427, 5'-TGCACTC-3' at 2001, 5'-GAGTGCA-3' at 1470, 5'-TGCACTC-3' at 1348, 5'-TGCGCTC-3' at 891, and complements.

Positive strand, positive direction: 5'-TGCGCCC-3' at 972, 5'-TGCGCCC-3' at 872, and complements.

Acknowledgements

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

Initial content for this page in some instances came from Wikiversity.

References

↑ ^1.0 ^1.1 ^1.2 ^1.3 ^1.4 Robert D. Andersen, Susan J. Taplitz, Sandy Wong, Greg Bristol, Bill Larkin, and Harvey R. Herschman (1987). "Metal-Dependent Binding of a Factor In Vivo to the Metal-Responsive Elements of the Metallothionein 1 Gene Promoter". Molecular and Cellular Biology. 7 (10): 3574–81. doi:10.1128/MCB.7.10.3574 Check |doi= value (help). Retrieved 2013-04-15. Unknown parameter |month= ignored (help); Unknown parameter |pdf= ignored (help); zero width space character in |doi= at position 9 (help)
↑ Barbara Levinson, Rebecca Conant, Rhonda Schnur, Soma Das, Seymour Packman and Jane Gitschier (1996). "A Repeated Element in the Regulatory Region of the MNK Gene and Its Deletion in A Patient With Occipital Horn Syndrome". Human Molecular Genetics. 5 (11): 1737–42. doi:10.1093/hmg/5.11.1737. Retrieved 2013-04-15.
↑ Sang Yoon Lee & Yoon Kwon Nam (3 July 2017). "Molecular cloning of metal-responsive transcription factor-1 (MTF-1) and transcriptional responses to metal and heat stresses in Pacific abalone, Haliotis discus hannai". Fisheries and Aquatic Sciences. 20: 9. doi:10.1186/s41240-017-0055-y. Retrieved 16 October 2020.

External links

Template:Sisterlinks

[Andersen-1] 1.0 ^1.1 ^1.2 ^1.3 ^1.4 Robert D. Andersen, Susan J. Taplitz, Sandy Wong, Greg Bristol, Bill Larkin, and Harvey R. Herschman (1987). "Metal-Dependent Binding of a Factor In Vivo to the Metal-Responsive Elements of the Metallothionein 1 Gene Promoter". Molecular and Cellular Biology. 7 (10): 3574–81. doi:10.1128/MCB.7.10.3574 Check |doi= value (help). Retrieved 2013-04-15. Unknown parameter |month= ignored (help); Unknown parameter |pdf= ignored (help); zero width space character in |doi= at position 9 (help)

[Levinson-2] Barbara Levinson, Rebecca Conant, Rhonda Schnur, Soma Das, Seymour Packman and Jane Gitschier (1996). "A Repeated Element in the Regulatory Region of the MNK Gene and Its Deletion in A Patient With Occipital Horn Syndrome". Human Molecular Genetics. 5 (11): 1737–42. doi:10.1093/hmg/5.11.1737. Retrieved 2013-04-15.

[Lee-3] Sang Yoon Lee & Yoon Kwon Nam (3 July 2017). "Molecular cloning of metal-responsive transcription factor-1 (MTF-1) and transcriptional responses to metal and heat stresses in Pacific abalone, Haliotis discus hannai". Fisheries and Aquatic Sciences. 20: 9. doi:10.1186/s41240-017-0055-y. Retrieved 16 October 2020.

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Hybrid C, T boxes Hypoxia-inducible factor gene transcriptions Hypoxia response elements I box gene transcriptions 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 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 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 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