Antioxidant-electrophile responsive element gene transcriptions: Difference between revisions

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Revision as of 23:24, 4 November 2020

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

The "perfect ARE sequence [GCTGAGTCA] is strongly conserved across mammals [...]."^[1]

Consensus sequences

5'-GTGAGGTCGC-3'^[2]

5'-GCTGAGT-3', 5'-GCAGGCT-3' of 5'-GC(A/C/T)(A/G/T)(A/G/T)(C/G/T)T(A/C)A-3'^[1], an antioxidant response element (ARE).

Hypotheses

A1BG has no Antioxidant-electrophile responsive element in either promoter.
A1BG is not transcribed by an Antioxidant-electrophile responsive element.
Antioxidant-electrophile responsive element does not participate in the transcription of A1BG.

AERE (Otsuki) samplings

Copying an antioxidant-electrophile responsive elements consensus sequence 5'-GTGAGGTCGC-3' and putting the sequence in "⌘F" finds no location between ZNF497 and A1BG or none locations between ZSCAN22 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence 5'-GTGAGGTCGC-3' (starting with SuccessablesAERE.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 5'-GTGAGGTCGC-3', 0.
negative strand, positive direction, looking for 5'-GTGAGGTCGC-3', 0.
positive strand, negative direction, looking for 5'-GTGAGGTCGC-3', 0.
positive strand, positive direction, looking for 5'-GTGAGGTCGC-3', 0.
complement, negative strand, negative direction, looking for 5'-CACTCCAGCG-3', 0.
complement, negative strand, positive direction, looking for 5'-CACTCCAGCG-3', 0.
complement, positive strand, negative direction, looking for 5'-CACTCCAGCG-3', 0.
complement, positive strand, positive direction, looking for 5'-CACTCCAGCG-3', 0.
inverse complement, negative strand, negative direction, looking for 5'-GCGACCTCAC-3', 0.
inverse complement, negative strand, positive direction, looking for 5'-GCGACCTCAC-3', 0.
inverse complement, positive strand, negative direction, looking for 5'-GCGACCTCAC-3', 0.
inverse complement, positive strand, positive direction, looking for 5'-GCGACCTCAC-3', 0.
inverse negative strand, negative direction, looking for 5'-CGCTGGAGTG-3', 0.
inverse negative strand, positive direction, looking for 5'-CGCTGGAGTG-3', 0.
inverse positive strand, negative direction, looking for 5'-CGCTGGAGTG-3', 0.
inverse positive strand, positive direction, looking for 5'-CGCTGGAGTG-3', 0.

AERE (Otsuki) core promoters

AERE (Otsuki) proximal promoters

AERE (Otsuki) distal promoters

AERE (Lacher) samplings

Copying 5'-GCTGAGT-3', 5'-GCAGGCT-3' of 5'-GC(A/C/T)(A/G/T)(A/G/T)(C/G/T)T(A/C)A-3' and putting the sequence in "⌘F" finds no location between ZNF497 and A1BG or none locations between ZSCAN22 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence 5'-GTGAGGTCGC-3' (starting with SuccessablesAERE.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 5'-GTGAGGTCGC-3', 0.
negative strand, positive direction, looking for 5'-GTGAGGTCGC-3', 0.
positive strand, negative direction, looking for 5'-GTGAGGTCGC-3', 0.
positive strand, positive direction, looking for 5'-GTGAGGTCGC-3', 0.
complement, negative strand, negative direction, looking for 5'-CACTCCAGCG-3', 0.
complement, negative strand, positive direction, looking for 5'-CACTCCAGCG-3', 0.
complement, positive strand, negative direction, looking for 5'-CACTCCAGCG-3', 0.
complement, positive strand, positive direction, looking for 5'-CACTCCAGCG-3', 0.
inverse complement, negative strand, negative direction, looking for 5'-GCGACCTCAC-3', 0.
inverse complement, negative strand, positive direction, looking for 5'-GCGACCTCAC-3', 0.
inverse complement, positive strand, negative direction, looking for 5'-GCGACCTCAC-3', 0.
inverse complement, positive strand, positive direction, looking for 5'-GCGACCTCAC-3', 0.
inverse negative strand, negative direction, looking for 5'-CGCTGGAGTG-3', 0.
inverse negative strand, positive direction, looking for 5'-CGCTGGAGTG-3', 0.
inverse positive strand, negative direction, looking for 5'-CGCTGGAGTG-3', 0.
inverse positive strand, positive direction, looking for 5'-CGCTGGAGTG-3', 0.

AERE (Lacher) core promoters

AERE (Lacher) proximal promoters

AERE (Lacher) distal promoters

References

↑ ^1.0 ^1.1 Sarah E. Lacher, Daniel C. Levings, Samuel Freeman, Matthew Slattery (October 2018). "Identification of a functional antioxidant response element at the HIF1A locus". Redox Biology. 19: 401–411. doi:10.1016/j.redox.2018.08.014. Retrieved 6 October 2020.
↑ Akihito Otsuki, Mikiko Suzuki, Fumiki Katsuoka, Kouhei Tsuchida, Hiromi Suda, Masanobu Morita, Ritsuko Shimizu, Masayuki Yamamoto (February 2016). "Unique cistrome defined as CsMBE is strictly required for Nrf2-sMaf heterodimer function in cytoprotection". Free Radical Biology and Medicine. 91: 45–57. doi:10.1016/j.freeradbiomed.2015.12.005. PMID 26677805. Retrieved 21 August 2020.

Acknowledgements

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

External links

[Lacher-1] 1.0 ^1.1 Sarah E. Lacher, Daniel C. Levings, Samuel Freeman, Matthew Slattery (October 2018). "Identification of a functional antioxidant response element at the HIF1A locus". Redox Biology. 19: 401–411. doi:10.1016/j.redox.2018.08.014. Retrieved 6 October 2020.

[Otsuki-2] Akihito Otsuki, Mikiko Suzuki, Fumiki Katsuoka, Kouhei Tsuchida, Hiromi Suda, Masanobu Morita, Ritsuko Shimizu, Masayuki Yamamoto (February 2016). "Unique cistrome defined as CsMBE is strictly required for Nrf2-sMaf heterodimer function in cytoprotection". Free Radical Biology and Medicine. 91: 45–57. doi:10.1016/j.freeradbiomed.2015.12.005. PMID 26677805. Retrieved 21 August 2020.

[1]

[2]

@@ Line 41: / Line 41: @@
 # Antioxidant-electrophile responsive element does not participate in the transcription of A1BG.
-==Samplings==
+==AERE (Otsuki) samplings==
-Copying an antioxidant-electrophile responsive elements consensus sequence 5'-GTGAGGTCGC-3' and putting the sequence in "⌘F" finds no location between ZNF497 and A1BG or none locations between ZSCAN22 and A1BG as can be found by the computer programs. Copying 5'-GCTGAGT-3', 5'-GCAGGCT-3' of 5'-GC(A/C/T)(A/G/T)(A/G/T)(C/G/T)T(A/C)A-3' and putting the sequence in "⌘F" finds no location between ZNF497 and A1BG or none locations between ZSCAN22 and A1BG as can be found by the computer programs.
+Copying an antioxidant-electrophile responsive elements consensus sequence 5'-GTGAGGTCGC-3' and putting the sequence in "⌘F" finds no location between ZNF497 and A1BG or none locations between ZSCAN22 and A1BG as can be found by the computer programs.
 For the Basic programs testing consensus sequence 5'-GTGAGGTCGC-3' (starting with SuccessablesAERE.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:
@@ Line 70: / Line 70: @@
 ===AERE (Otsuki) distal promoters===
+{{main|Distal promoter gene transcriptions}}
+==AERE (Lacher) samplings==
+Copying 5'-GCTGAGT-3', 5'-GCAGGCT-3' of 5'-GC(A/C/T)(A/G/T)(A/G/T)(C/G/T)T(A/C)A-3' and putting the sequence in "⌘F" finds no location between ZNF497 and A1BG or none locations between ZSCAN22 and A1BG as can be found by the computer programs.
+For the Basic programs testing consensus sequence 5'-GTGAGGTCGC-3' (starting with SuccessablesAERE.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 5'-GTGAGGTCGC-3', 0.
+# negative strand, positive direction, looking for 5'-GTGAGGTCGC-3', 0.
+# positive strand, negative direction, looking for 5'-GTGAGGTCGC-3', 0.
+# positive strand, positive direction, looking for 5'-GTGAGGTCGC-3', 0.
+# complement, negative strand, negative direction, looking for 5'-CACTCCAGCG-3', 0.
+# complement, negative strand, positive direction, looking for 5'-CACTCCAGCG-3', 0.
+# complement, positive strand, negative direction, looking for 5'-CACTCCAGCG-3', 0.
+# complement, positive strand, positive direction, looking for 5'-CACTCCAGCG-3', 0.
+# inverse complement, negative strand, negative direction, looking for 5'-GCGACCTCAC-3', 0.
+# inverse complement, negative strand, positive direction, looking for 5'-GCGACCTCAC-3', 0.
+# inverse complement, positive strand, negative direction, looking for 5'-GCGACCTCAC-3', 0.
+# inverse complement, positive strand, positive direction, looking for 5'-GCGACCTCAC-3', 0.
+# inverse negative strand, negative direction, looking for 5'-CGCTGGAGTG-3', 0.
+# inverse negative strand, positive direction, looking for 5'-CGCTGGAGTG-3', 0.
+# inverse positive strand, negative direction, looking for 5'-CGCTGGAGTG-3', 0.
+# inverse positive strand, positive direction, looking for 5'-CGCTGGAGTG-3', 0.
+===AERE (Lacher) core promoters===
+{{main|Core promoter gene transcriptions}}
+===AERE (Lacher) proximal promoters===
+{{main|Proximal promoter gene transcriptions}}
+===AERE (Lacher) distal promoters===
 {{main|Distal promoter gene transcriptions}}

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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