Peroxisome proliferator hormone response element gene transcriptions

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

"After activation by ligands, PPARs/RXRs heterodimers bind to PPRE consensus sequence (AGGTCANAGGTCA) in the promoter of their target genes."^[1]

Peroxisome proliferator hormone response elements (PPREs) consensus sequences are AGGGGA and TCCCCT.^[2]

Human genes

Consensus sequences

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 (4560-2846) UTRs

Negative strand, negative direction: CGACCCC at 3037.

PPARA negative direction (2811-2596) proximal promoters

Negative strand, negative direction: GGGGTCG at 2766.

PPARA positive direction (4050-1) distal promoters

Positive strand, positive direction: CGACCCC at 279.

PPARA random dataset samplings

PPARAr0: 2, CGACCCC at 4084, CGACCCC at 3906.
PPARAr1: 0.
PPARAr2: 0.
PPARAr3: 0.
PPARAr4: 0.
PPARAr5: 1, CGACCCC at 3597.
PPARAr6: 1, CGACCCC at 2956.
PPARAr7: 1, CGACCCC at 2415.
PPARAr8: 1, CGACCCC at 1108.
PPARAr9: 0.
PPARAr0ci: 0.
PPARAr1ci: 1, GGGGTCG at 2011.
PPARAr2ci: 0.
PPARAr3ci: 0.
PPARAr4ci: 0.
PPARAr5ci: 0.
PPARAr6ci: 0.
PPARAr7ci: 0.
PPARAr8ci: 2, GGGGTCG at 1741, GGGGTCG at 246.
PPARAr9ci: 0.

PPARAr arbitrary (evens) (4560-2846) UTRs

PPARAr0: CGACCCC at 4084, CGACCCC at 3906.
PPARAr6: CGACCCC at 2956.

PPARAr alternate (odds) (4560-2846) UTRs

PPARAr5: CGACCCC at 3597.

PPARAr alternate positive direction (evens) (4265-4050) proximal promoters

PPARAr0: CGACCCC at 4084.

PPARAr arbitrary negative direction (evens) (2596-1) distal promoters

PPARAr8: CGACCCC at 1108.
PPARAr8ci: GGGGTCG at 1741, GGGGTCG at 246.

PPARAr alternate negative direction (odds) (2596-1) distal promoters

PPARAr7: CGACCCC at 2415.
PPARAr1ci: GGGGTCG at 2011.

PPARAr arbitrary positive direction (odds) (4050-1) distal promoters

PPARAr5: CGACCCC at 3597.
PPARAr7: CGACCCC at 2415.
PPARAr1ci: GGGGTCG at 2011.

PPARAr alternate positive direction (evens) (4050-1) distal promoters

PPARAr0: CGACCCC at 3906.
PPARAr6: CGACCCC at 2956.
PPARAr8: CGACCCC at 1108.
PPARAr8ci: GGGGTCG at 1741, GGGGTCG at 246.

PPARA analysis and results

Consensus sequence is CGACCCC.^[3]

Reals or randoms	Promoters	direction	Numbers	Strands	Occurrences	Averages (± 0.1)
Reals	UTR	negative	1	2	0.5	0.5 ± 0.5 (--1,+-0)
Randoms	UTR	arbitrary negative	3	10	0.3	0.2
Randoms	UTR	alternate negative	1	10	0.1	0.2
Reals	Core	negative	0	2	0	0
Randoms	Core	arbitrary negative	0	10	0	0
Randoms	Core	alternate negative	0	10	0	0
Reals	Core	positive	0	2	0	0
Randoms	Core	arbitrary positive	0	10	0	0
Randoms	Core	alternate positive	0	10	0	0
Reals	Proximal	negative	1	2	0.5	0.5 ± 0.5 (--1,+-0)
Randoms	Proximal	arbitrary negative	0	10	0	0
Randoms	Proximal	alternate negative	0	10	0	0
Reals	Proximal	positive	0	2	0	0
Randoms	Proximal	arbitrary positive	0	10	0	0.05
Randoms	Proximal	alternate positive	1	10	0.1	0.05
Reals	Distal	negative	0	2	0	0
Randoms	Distal	arbitrary negative	3	10	0.3	0.25
Randoms	Distal	alternate negative	2	10	0.2	0.25
Reals	Distal	positive	1	2	0.5	0.5 ± 0.5 (-+0,++1)
Randoms	Distal	arbitrary positive	3	10	0.3	0.4
Randoms	Distal	alternate positive	5	10	0.5	0.4

Comparison:

The occurrences of real PPARAs are greater than the randoms. This suggests that the real PPARAs are likely active or activable.

References

↑ 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.
↑ 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.
↑ ^3.0 ^3.1 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

[You-1] 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.

[Yao-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.

[Long-3] 3.0 ^3.1 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]

[3]

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