Xenobiotic response element gene transcriptions: Difference between revisions

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Copying a responsive elements consensus sequence GCGTG 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 GCGTG and putting the sequence in "⌘F" finds six between ZNF497 and A1BG or none between ZSCAN22 and A1BG as can be found by the computer programs.


For the Basic programs testing consensus sequence GCGTG (starting with SuccessablesXRE.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:
For the Basic programs testing consensus sequence GCGTG (starting with SuccessablesXRE.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.
# negative strand, negative direction, looking for GCGTG, 0.
# positive strand, negative direction, looking for AAAAAAAA, 0.
# positive strand, negative direction, looking for GCGTG, 4, GCGTG at 3046, GCGTG at 1896, GCGTG at 1243, GCGTG at 740.
# positive strand, positive direction, looking for AAAAAAAA, 0.
# positive strand, positive direction, looking for GCGTG, 13, GCGTG at 2565, GCGTG at 1555, GCGTG at 1551, GCGTG at 1299, GCGTG at 1135, GCGTG at 1131, GCGTG at 1051, GCGTG at 1047, GCGTG at 977, GCGTG at 877, GCGTG at 799, GCGTG at 795, GCGTG at 685.
# negative strand, positive direction, looking for AAAAAAAA, 0.
# negative strand, positive direction, looking for GCGTG, 6, GCGTG at 2554, GCGTG at 1719, GCGTG at 1242, GCGTG at 1216, GCGTG at 1019, GCGTG at 544.
# complement, negative strand, negative direction, looking for TTTTTTTT, 0.
# complement, negative strand, negative direction, looking for CGCAC, 4, CGCAC at 3046, CGCAC at 1896, CGCAC at 1243, CGCAC at 740.
# complement, positive strand, negative direction, looking for TTTTTTTT, 0.
# complement, positive strand, negative direction, looking for CGCAC, 0.
# complement, positive strand, positive direction, looking for TTTTTTTT, 0.
# complement, positive strand, positive direction, looking for CGCAC, 6, CGCAC at 2554, CGCAC at 1719, CGCAC at 1242, CGCAC at 1216, CGCAC at 1019, CGCAC at 544.
# complement, negative strand, positive direction, looking for TTTTTTTT, 0.
# complement, negative strand, positive direction, looking for CGCAC, 13, CGCAC at 2565, CGCAC at 1555, CGCAC at 1551, CGCAC at 1299, CGCAC at 1135, CGCAC at 1131, CGCAC at 1051, CGCAC at 1047, CGCAC at 977, CGCAC at 877, CGCAC at 799, CGCAC at 795, CGCAC at 685.
# inverse complement, negative strand, negative direction, looking for TTTTTTTT, 0.
# inverse complement, negative strand, negative direction, looking for CACGC, 3, CACGC at 2196, CACGC at 447, CACGC at 379.
# inverse complement, positive strand, negative direction, looking for TTTTTTTT, 0.
# inverse complement, positive strand, negative direction, looking for CACGC, 5, CACGC at 3280, CACGC at 2207, CACGC at 1991, CACGC at 963, CACGC at 663.
# inverse complement, positive strand, positive direction, looking for TTTTTTTT, 0.
# inverse complement, positive strand, positive direction, looking for CACGC, 14, CACGC at 1763, CACGC at 1725, CACGC at 1589, CACGC at 1521, CACGC at 1253, CACGC at 1244, CACGC at 1169, CACGC at 1160, CACGC at 1085, CACGC at 1017, CACGC at 665, CACGC at 581, CACGC at 497, CACGC at 488.
# inverse complement, negative strand, positive direction, looking for TTTTTTTT, 0.
# inverse complement, negative strand, positive direction, looking for CACGC, 11, CACGC at 1553, CACGC at 1301, CACGC at 1133, CACGC at 1049, CACGC at 987, CACGC at 969, CACGC at 887, CACGC at 869, CACGC at 803, CACGC at 797, CACGC at 776.
# inverse negative strand, negative direction, looking for AAAAAAAA, 0.
# inverse negative strand, negative direction, looking for GTGCG, 5, GTGCG at 3280, GTGCG at 2207, GTGCG at 1991, GTGCG at 963, GTGCG at 663.
# inverse positive strand, negative direction, looking for AAAAAAAA, 0.
# inverse positive strand, negative direction, looking for GTGCG, 3, GTGCG at 2196, GTGCG at 447, GTGCG at 379.
# inverse positive strand, positive direction, looking for AAAAAAAA, 0.
# inverse positive strand, positive direction, looking for GTGCG, 11, GTGCG at 1553, GTGCG at 1301, GTGCG at 1133, GTGCG at 1049, GTGCG at 987, GTGCG at 969, GTGCG at 887, GTGCG at 869, GTGCG at 803, GTGCG at 797, GTGCG at 776.
# inverse negative strand, positive direction, looking for AAAAAAAA, 0.
# inverse negative strand, positive direction, looking for GTGCG, 14, GTGCG at 1763, GTGCG at 1725, GTGCG at 1589, GTGCG at 1521, GTGCG at 1253, GTGCG at 1244, GTGCG at 1169, GTGCG at 1160, GTGCG at 1085, GTGCG at 1017, GTGCG at 665, GTGCG at 581, GTGCG at 497, GTGCG at 488.


===XRE UTRs===
===XRE UTRs===
{{main|UTR promoter gene transcriptions}}
{{main|UTR promoter gene transcriptions}}
Positive strand, negative direction: CACGC at 3280, GCGTG at 3046.


===XRE core promoters===
===XRE distal promoters===
{{main|Core promoter gene transcriptions}}
{{main|Distal promoter gene transcriptions}}
Negative strand, negative direction: CACGC at 2196, CACGC at 447, CACGC at 379.


===XRE proximal promoters===
Positive strand, negative direction: CACGC at 2207, CACGC at 1991, GCGTG at 1896, GCGTG at 1243, CACGC at 963, GCGTG at 740, CACGC at 663.
{{main|Proximal promoter gene transcriptions}}


===XRE distal promoters===
Negative strand, positive direction: GCGTG at 2554, GCGTG at 1719, CACGC at 1553, CACGC at 1301, GCGTG at 1242, GCGTG at 1216, CACGC at 1133, CACGC at 1049, GCGTG at 1019, CACGC at 987, CACGC at 969, CACGC at 887, CACGC at 869, CACGC at 803, CACGC at 797, CACGC at 776, GCGTG at 544.
{{main|Distal promoter gene transcriptions}}
 
Positive strand, positive direction: GCGTG at 2565, CACGC at 1763, CACGC at 1725, CACGC at 1589, GCGTG at 1555, GCGTG at 1551, CACGC at 1521, GCGTG at 1299, CACGC at 1253, CACGC at 1244, CACGC at 1169, CACGC at 1160, GCGTG at 1135, GCGTG at 1131, CACGC at 1085, GCGTG at 1051, GCGTG at 1047, CACGC at 1017, GCGTG at 977, GCGTG at 877, GCGTG at 799, GCGTG at 795, GCGTG at 685, CACGC at 665, CACGC at 581, CACGC at 497, CACGC at 488.


==See also==
==See also==

Revision as of 02:44, 17 February 2021

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

The classical recognition motif of the AhR/ARNT complex, referred to as either the AhR-, dioxin- or xenobiotic- responsive element (AHRE, DRE or XRE), contains the core sequence 5'-GCGTG-3'.[1]

The AhR/ARNT heterodimer directly binds the AHRE/DRE/XRE core sequence in an asymmetric manner such that ARNT binds to 5'-GTG-3' and AhR binding 5'-TC/TGC-3'.[2][3][4]

Human genes

Consensus sequences

The classical recognition motif of the AhR/ARNT complex, referred to as either the AhR-, dioxin- or xenobiotic- responsive element (AHRE, DRE or XRE) has the consensus sequence 5'-(T/G)NGCGTG(A/C)(G/C)A-3'[5][6] in the promoter region of AhR responsive genes.

"Sequence alignment of the mouse CYPIA1 upstream DREs has revealed a consensus sequence [...] which contains an invariant 6-bp core sequence, TNGCGTG, and several variable nucleotides flanking this core that we have previously shown to be important for TCDD-AhR-DRE complex formation (Denison et al., 1988a)."[6]

The quinone reductase (QRDRE) gene contains TCCCCTTGCGTG which has the DRE core of TNGCGTG.[6]

AHRE samplings

Main article: Model samplings

Copying a responsive elements consensus sequence (G/T)NGCGTG(A/C)(C/G)A 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 testing consensus sequence AAAAAAAA (starting with SuccessablesXRE.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 AAAAAAAA, 0.
  2. positive strand, negative direction, looking for AAAAAAAA, 0.
  3. positive strand, positive direction, looking for AAAAAAAA, 0.
  4. negative strand, positive direction, looking for AAAAAAAA, 0.
  5. complement, negative strand, negative direction, looking for TTTTTTTT, 0.
  6. complement, positive strand, negative direction, looking for TTTTTTTT, 0.
  7. complement, positive strand, positive direction, looking for TTTTTTTT, 0.
  8. complement, negative strand, positive direction, looking for TTTTTTTT, 0.
  9. inverse complement, negative strand, negative direction, looking for TTTTTTTT, 0.
  10. inverse complement, positive strand, negative direction, looking for TTTTTTTT, 0.
  11. inverse complement, positive strand, positive direction, looking for TTTTTTTT, 0.
  12. inverse complement, negative strand, positive direction, looking for TTTTTTTT, 0.
  13. inverse negative strand, negative direction, looking for AAAAAAAA, 0.
  14. inverse positive strand, negative direction, looking for AAAAAAAA, 0.
  15. inverse positive strand, positive direction, looking for AAAAAAAA, 0.
  16. inverse negative strand, positive direction, looking for AAAAAAAA, 0.

AAA UTRs

Main article: UTR promoter gene transcriptions

AAA core promoters

Main article: Core promoter gene transcriptions

AAA proximal promoters

Main article: Proximal promoter gene transcriptions

AAA distal promoters

Main article: Distal promoter gene transcriptions

DIOX samplings

Main article: Model samplings

Copying a dioxin-responsive element (DIOX) consensus sequence TNGCGTG 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 testing consensus sequence TNGCGTG (starting with SuccessablesDIOX.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 TNGCGTG, 0.
  2. positive strand, negative direction, looking for TNGCGTG, 0.
  3. positive strand, positive direction, looking for TNGCGTG, 2, TGGCGTG at 2565, TCGCGTG at 1131.
  4. negative strand, positive direction, looking for TNGCGTG, 0.
  5. complement, negative strand, negative direction, looking for ANCGCAC, 0.
  6. complement, positive strand, negative direction, looking for ANCGCAC, 0.
  7. complement, positive strand, positive direction, looking for ANCGCAC, 0.
  8. complement, negative strand, positive direction, looking for ANCGCAC, 2, ACCGCAC at 2565, AGCGCAC at 1131.
  9. inverse complement, negative strand, negative direction, looking for CACGCNA, 2, CACGCCA at 2198, CACGCCA at 381.
  10. inverse complement, positive strand, negative direction, looking for CACGCNA, 3, CACGCCA at 3282, CACGCCA at 2209, CACGCCA at 1993.
  11. inverse complement, positive strand, positive direction, looking for CACGCNA, 1, CACGCGA at 1727.
  12. inverse complement, negative strand, positive direction, looking for CACGCNA, 0.
  13. inverse negative strand, negative direction, looking for GTGCGNT, 3, GTGCGGT at 3282, GTGCGGT at 2209, GTGCGGT at 1993.
  14. inverse positive strand, negative direction, looking for GTGCGNT, 2, GTGCGGT at 2198, GTGCGGT at 381.
  15. inverse positive strand, positive direction, looking for GTGCGNT, 0.
  16. inverse negative strand, positive direction, looking for GTGCGNT, 1, GTGCGCT at 1727.

DRE UTRs

Main article: UTR promoter gene transcriptions

Positive strand, negative direction: CACGCCA at 3282.

DRE distal promoters

Main article: Distal promoter gene transcriptions

Negative strand, negative direction: CACGCCA at 2198, CACGCCA at 381.

Positive strand, negative direction: CACGCCA at 2209, CACGCCA at 1993.

Positive strand, positive direction: TGGCGTG at 2565, CACGCGA at 1727, TCGCGTG at 1131.

Xenobiotic response element samplings

Main article: Model samplings

"The megalin (LRP2) gene promoter region [shows] eight consensus sequence of XRE 5′-GCGTG-3′."[7]

"The AHR-ARNT heterodimer then binds to the xenobiotic response element (XRE), defined by the consensus 5′-GCGTG-3′ motif, within the promoter region of target genes to activate transcription."[8]

Copying a responsive elements consensus sequence GCGTG and putting the sequence in "⌘F" finds six between ZNF497 and A1BG or none between ZSCAN22 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence GCGTG (starting with SuccessablesXRE.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 GCGTG, 0.
  2. positive strand, negative direction, looking for GCGTG, 4, GCGTG at 3046, GCGTG at 1896, GCGTG at 1243, GCGTG at 740.
  3. positive strand, positive direction, looking for GCGTG, 13, GCGTG at 2565, GCGTG at 1555, GCGTG at 1551, GCGTG at 1299, GCGTG at 1135, GCGTG at 1131, GCGTG at 1051, GCGTG at 1047, GCGTG at 977, GCGTG at 877, GCGTG at 799, GCGTG at 795, GCGTG at 685.
  4. negative strand, positive direction, looking for GCGTG, 6, GCGTG at 2554, GCGTG at 1719, GCGTG at 1242, GCGTG at 1216, GCGTG at 1019, GCGTG at 544.
  5. complement, negative strand, negative direction, looking for CGCAC, 4, CGCAC at 3046, CGCAC at 1896, CGCAC at 1243, CGCAC at 740.
  6. complement, positive strand, negative direction, looking for CGCAC, 0.
  7. complement, positive strand, positive direction, looking for CGCAC, 6, CGCAC at 2554, CGCAC at 1719, CGCAC at 1242, CGCAC at 1216, CGCAC at 1019, CGCAC at 544.
  8. complement, negative strand, positive direction, looking for CGCAC, 13, CGCAC at 2565, CGCAC at 1555, CGCAC at 1551, CGCAC at 1299, CGCAC at 1135, CGCAC at 1131, CGCAC at 1051, CGCAC at 1047, CGCAC at 977, CGCAC at 877, CGCAC at 799, CGCAC at 795, CGCAC at 685.
  9. inverse complement, negative strand, negative direction, looking for CACGC, 3, CACGC at 2196, CACGC at 447, CACGC at 379.
  10. inverse complement, positive strand, negative direction, looking for CACGC, 5, CACGC at 3280, CACGC at 2207, CACGC at 1991, CACGC at 963, CACGC at 663.
  11. inverse complement, positive strand, positive direction, looking for CACGC, 14, CACGC at 1763, CACGC at 1725, CACGC at 1589, CACGC at 1521, CACGC at 1253, CACGC at 1244, CACGC at 1169, CACGC at 1160, CACGC at 1085, CACGC at 1017, CACGC at 665, CACGC at 581, CACGC at 497, CACGC at 488.
  12. inverse complement, negative strand, positive direction, looking for CACGC, 11, CACGC at 1553, CACGC at 1301, CACGC at 1133, CACGC at 1049, CACGC at 987, CACGC at 969, CACGC at 887, CACGC at 869, CACGC at 803, CACGC at 797, CACGC at 776.
  13. inverse negative strand, negative direction, looking for GTGCG, 5, GTGCG at 3280, GTGCG at 2207, GTGCG at 1991, GTGCG at 963, GTGCG at 663.
  14. inverse positive strand, negative direction, looking for GTGCG, 3, GTGCG at 2196, GTGCG at 447, GTGCG at 379.
  15. inverse positive strand, positive direction, looking for GTGCG, 11, GTGCG at 1553, GTGCG at 1301, GTGCG at 1133, GTGCG at 1049, GTGCG at 987, GTGCG at 969, GTGCG at 887, GTGCG at 869, GTGCG at 803, GTGCG at 797, GTGCG at 776.
  16. inverse negative strand, positive direction, looking for GTGCG, 14, GTGCG at 1763, GTGCG at 1725, GTGCG at 1589, GTGCG at 1521, GTGCG at 1253, GTGCG at 1244, GTGCG at 1169, GTGCG at 1160, GTGCG at 1085, GTGCG at 1017, GTGCG at 665, GTGCG at 581, GTGCG at 497, GTGCG at 488.

XRE UTRs

Main article: UTR promoter gene transcriptions

Positive strand, negative direction: CACGC at 3280, GCGTG at 3046.

XRE distal promoters

Main article: Distal promoter gene transcriptions

Negative strand, negative direction: CACGC at 2196, CACGC at 447, CACGC at 379.

Positive strand, negative direction: CACGC at 2207, CACGC at 1991, GCGTG at 1896, GCGTG at 1243, CACGC at 963, GCGTG at 740, CACGC at 663.

Negative strand, positive direction: GCGTG at 2554, GCGTG at 1719, CACGC at 1553, CACGC at 1301, GCGTG at 1242, GCGTG at 1216, CACGC at 1133, CACGC at 1049, GCGTG at 1019, CACGC at 987, CACGC at 969, CACGC at 887, CACGC at 869, CACGC at 803, CACGC at 797, CACGC at 776, GCGTG at 544.

Positive strand, positive direction: GCGTG at 2565, CACGC at 1763, CACGC at 1725, CACGC at 1589, GCGTG at 1555, GCGTG at 1551, CACGC at 1521, GCGTG at 1299, CACGC at 1253, CACGC at 1244, CACGC at 1169, CACGC at 1160, GCGTG at 1135, GCGTG at 1131, CACGC at 1085, GCGTG at 1051, GCGTG at 1047, CACGC at 1017, GCGTG at 977, GCGTG at 877, GCGTG at 799, GCGTG at 795, GCGTG at 685, CACGC at 665, CACGC at 581, CACGC at 497, CACGC at 488.

See also

References

  1. ↑ Shen ES, Whitlock JP (April 1992). "Protein-DNA interactions at a dioxin-responsive enhancer. Mutational analysis of the DNA-binding site for the liganded Ah receptor". The Journal of Biological Chemistry. 267 (10): 6815–9. PMID 1313023.
  2. ↑ Wharton KA, Franks RG, Kasai Y, Crews ST (December 1994). "Control of CNS midline transcription by asymmetric E-box-like elements: similarity to xenobiotic responsive regulation". Development. 120 (12): 3563–9. PMID 7821222.
  3. ↑ Bacsi SG, Reisz-Porszasz S, Hankinson O (March 1995). "Orientation of the heterodimeric aryl hydrocarbon (dioxin) receptor complex on its asymmetric DNA recognition sequence". Molecular Pharmacology. 47 (3): 432–8. PMID 7700240.
  4. ↑ Swanson HI, Chan WK, Bradfield CA (November 1995). "DNA binding specificities and pairing rules of the Ah receptor, ARNT, and SIM proteins". The Journal of Biological Chemistry. 270 (44): 26292–302. doi:10.1074/jbc.270.44.26292. PMID 7592839.
  5. ↑ Lusska A, Shen E, Whitlock JP (March 1993). "Protein-DNA interactions at a dioxin-responsive enhancer. Analysis of six bona fide DNA-binding sites for the liganded Ah receptor". The Journal of Biological Chemistry. 268 (9): 6575–80. PMID 8384216.
  6. ↑ 6.0 6.1 6.2 Yao EF, Denison MS (June 1992). "DNA sequence determinants for binding of transformed Ah receptor to a dioxin-responsive enhancer". Biochemistry. 31 (21): 5060–7. doi:10.1021/bi00136a019. PMID 1318077.
  7. ↑ Mahmoud Mohamed Mokhtar, Emad Gamil Khidr, Hesham Mohamed Shaban, Shady Allam, Bakheet E. M. Elsadek, Salama Abdou Salama & Shawkey Saddik Ali (28 February 2020). "The effect of aryl hydrocarbon receptor ligands on gentamicin-induced nephrotoxicity in rats". Environmental Science and Pollution Research. 27 (May): 16189–16202. doi:10.1007/s11356-020-08073-z. Retrieved 16 February 2021.
  8. ↑ Nathaniel G. Girer, Dwayne Carter, Nisha Bhattarai, Mehnaz Mustafa, Larry Denner, Craig Porter and Cornelis J. Elferink (22 February 2019). "Inducible loss of the aryl hydrocarbon receptor activates perigonadal white fat respiration and brown fat thermogenesis via fibroblast growth factor 21". International Journal of Molecular Sciences. 20 (4): 950. doi:10.3390/ijms20040950. |access-date= requires |url= (help)

External links

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