Peroxisome proliferator hormone response element gene transcriptions: Difference between revisions

Revision as of 19:08, 15 February 2021

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

Peroxisome proliferator hormone response elements (PPREs) consensus sequences are AGGGGA and TCCCCT.^[1]

Human genes

Consensus sequences

"After activation by ligands, PPARs/RXRs heterodimers bind to PPRE consensus sequence (AGGTCANAGGTCA) in the promoter of their target genes."^[2]

The DNA consensus sequence is AGGTCANAGGTCA, with N being any nucleotide.

PPRE samplings

For the Basic programs testing consensus sequence AGGTCANAGGTCA (starting with SuccessablesPPRE.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 AGGTCANAGGTCA, 0.
positive strand, negative direction, looking for AGGTCANAGGTCA, 0.
positive strand, positive direction, looking for AGGTCANAGGTCA, 0.
negative strand, positive direction, looking for AGGTCANAGGTCA, 0.
complement, negative strand, negative direction, looking for TCCAGTNTCCAGT, 0.
complement, positive strand, negative direction, looking for TCCAGTNTCCAGT, 0.
complement, positive strand, positive direction, looking for TCCAGTNTCCAGT, 0.
complement, negative strand, positive direction, looking for TCCAGTNTCCAGT, 0.
inverse complement, negative strand, negative direction, looking for TGACCTNTGACCT, 0.
inverse complement, positive strand, negative direction, looking for TGACCTNTGACCT, 0.
inverse complement, positive strand, positive direction, looking for TGACCTNTGACCT, 0.
inverse complement, negative strand, positive direction, looking for TGACCTNTGACCT, 0.
inverse negative strand, negative direction, looking for ACTGGANACTGGA, 0.
inverse positive strand, negative direction, looking for ACTGGANACTGGA, 0.
inverse positive strand, positive direction, looking for ACTGGANACTGGA, 0.
inverse negative strand, positive direction, looking for ACTGGANACTGGA, 0.

PPARA consensus sequences

Consensus sequence is 5'-CGACCCC-3'.^[3]

PPARA samplings

Copying the apparent consensus sequence for the PPARA (CGACCCC) and putting it in "⌘F" finds one located between ZSCAN22 and none between ZNF497 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence CGACCCC (starting with Successables PPARA.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 CGACCCC, 1, CGACCCC at 3037.
positive strand, negative direction, looking for CGACCCC, 0.
positive strand, positive direction, looking for CGACCCC, 1, CGACCCC at 279.
negative strand, positive direction, looking for CGACCCC, 0.
complement, negative strand, negative direction, looking for GCTGGGG, 0.
complement, positive strand, negative direction, looking for GCTGGGG, 1, GCTGGGG at 3037.
complement, positive strand, positive direction, looking for GCTGGGG, 0.
complement, negative strand, positive direction, looking for GCTGGGG, 1, GCTGGGG at 279.
inverse complement, negative strand, negative direction, looking for GGGGTCG, 1, GGGGTCG at 2766.
inverse complement, positive strand, negative direction, looking for GGGGTCG, 0.
inverse complement, positive strand, positive direction, looking for GGGGTCG, 0.
inverse complement, negative strand, positive direction, looking for GGGGTCG, 0.
inverse negative strand, negative direction, looking for CCCCAGC, 0.
inverse positive strand, negative direction, looking for CCCCAGC, 1, CCCCAGC at 2766.
inverse positive strand, positive direction, looking for CCCCAGC, 0.
inverse negative strand, positive direction, looking for CCCCAGC, 0.

PPARA UTRs

Negative strand, negative direction: CGACCCC at 3037.

PPARA proximal promoters

Positive strand, negative direction: CCCCAGC at 2766.

PPARA distal promoters

Positive strand, positive direction: CGACCCC at 279.

References

↑ 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.
↑ Mengli You, Shuping Yuan, Juanjuan Shi, Yongzhong Hou (1 June 2015). "PPARδ signaling regulates colorectal cancer". Current Pharmaceutical Design. 21 (21): 2956–2959. doi:10.2174/1381612821666150514104035. PMID 26004416. Retrieved 10 September 2020.
↑ Jianyin Long; Daniel L. Galvan; Koki Mise; Yashpal S. Kanwar; Li Li; Naravat Poungavrin; Paul A. Overbeek; Benny H. Chang; Farhad R. Danesh (28 May 2020). "Role for carbohydrate response element-binding protein (ChREBP) in high glucose-mediated repression of long noncoding RNA Tug1" (PDF). Journal of Biological Chemistry. 5 (28). doi:10.1074/jbc.RA120.013228. Retrieved 6 October 2020.

External links

[Yao-1] 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.

[You-2] Mengli You, Shuping Yuan, Juanjuan Shi, Yongzhong Hou (1 June 2015). "PPARδ signaling regulates colorectal cancer". Current Pharmaceutical Design. 21 (21): 2956–2959. doi:10.2174/1381612821666150514104035. PMID 26004416. Retrieved 10 September 2020.

[Long-3] Jianyin Long; Daniel L. Galvan; Koki Mise; Yashpal S. Kanwar; Li Li; Naravat Poungavrin; Paul A. Overbeek; Benny H. Chang; Farhad R. Danesh (28 May 2020). "Role for carbohydrate response element-binding protein (ChREBP) in high glucose-mediated repression of long noncoding RNA Tug1" (PDF). Journal of Biological Chemistry. 5 (28). doi:10.1074/jbc.RA120.013228. Retrieved 6 October 2020.

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[2]

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@@ Line 34: / Line 34: @@
 ==PPRE samplings==
-Copying the apparent consensus sequence for the PPRE (AGGGGA) and putting it in "⌘F" finds none located between ZSCAN22 or three between ZNF497 and A1BG as can be found by the computer programs.
 For the Basic programs testing consensus sequence AGGTCANAGGTCA (starting with SuccessablesPPRE.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:

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