Peroxisome proliferator hormone response element gene transcriptions: Difference between revisions

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{{AE}} Henry A. Hoff
{{AE}} Henry A. Hoff
Peroxisome proliferator hormone response elements (PPREs) consensus sequences are AGGGGA and TCCCCT.<ref name=Yao>{{ cite journal
| vauthors = Yao EF, Denison MS
| title = DNA sequence determinants for binding of transformed Ah receptor to a dioxin-responsive enhancer
| journal = Biochemistry
| volume = 31
| issue = 21
| pages = 5060–7
| date = June 1992
| pmid = 1318077
| doi = 10.1021/bi00136a019 }}</ref>
==Human genes==
==Consensus sequences==


"After activation by ligands, PPARs/RXRs heterodimers bind to PPRE consensus sequence (AGGTCANAGGTCA) in the promoter of their target genes."<ref name=You>{{ cite journal
"After activation by ligands, PPARs/RXRs heterodimers bind to PPRE consensus sequence (AGGTCANAGGTCA) in the promoter of their target genes."<ref name=You>{{ cite journal
Line 30: Line 15:
|pmid=26004416
|pmid=26004416
|accessdate=10 September 2020 }}</ref>
|accessdate=10 September 2020 }}</ref>
Peroxisome proliferator hormone response elements (PPREs) consensus sequences are AGGGGA and TCCCCT.<ref name=Yao>{{ cite journal
| authors = Yao EF, Denison MS
| title = DNA sequence determinants for binding of transformed Ah receptor to a dioxin-responsive enhancer
| journal = Biochemistry
| volume = 31
| issue = 21
| pages = 5060–7
| date = June 1992
| pmid = 1318077
| doi = 10.1021/bi00136a019 }}</ref>
==Human genes==
==Consensus sequences==


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


==PPRE samplings==
==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:
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.
# negative strand, negative direction, looking for AGGTCANAGGTCA, 0.
# positive strand, negative direction, looking for AAAAAAAA, 0.
# positive strand, negative direction, looking for AGGTCANAGGTCA, 0.
# positive strand, positive direction, looking for AAAAAAAA, 0.
# positive strand, positive direction, looking for AGGTCANAGGTCA, 0.
# negative strand, positive direction, looking for AAAAAAAA, 0.
# negative strand, positive direction, looking for AGGTCANAGGTCA, 0.
# complement, negative strand, negative direction, looking for TTTTTTTT, 0.
# complement, negative strand, negative direction, looking for TCCAGTNTCCAGT, 0.
# complement, positive strand, negative direction, looking for TTTTTTTT, 0.
# complement, positive strand, negative direction, looking for TCCAGTNTCCAGT, 0.
# complement, positive strand, positive direction, looking for TTTTTTTT, 0.
# complement, positive strand, positive direction, looking for TCCAGTNTCCAGT, 0.
# complement, negative strand, positive direction, looking for TTTTTTTT, 0.
# complement, negative strand, positive direction, looking for TCCAGTNTCCAGT, 0.
# inverse complement, negative strand, negative direction, looking for TTTTTTTT, 0.
# inverse complement, negative strand, negative direction, looking for TGACCTNTGACCT, 0.
# inverse complement, positive strand, negative direction, looking for TTTTTTTT, 0.
# inverse complement, positive strand, negative direction, looking for TGACCTNTGACCT, 0.
# inverse complement, positive strand, positive direction, looking for TTTTTTTT, 0.
# inverse complement, positive strand, positive direction, looking for TGACCTNTGACCT, 0.
# inverse complement, negative strand, positive direction, looking for TTTTTTTT, 0.
# inverse complement, negative strand, positive direction, looking for TGACCTNTGACCT, 0.
# inverse negative strand, negative direction, looking for AAAAAAAA, 0.
# inverse negative strand, negative direction, looking for ACTGGANACTGGA, 0.
# inverse positive strand, negative direction, looking for AAAAAAAA, 0.
# inverse positive strand, negative direction, looking for ACTGGANACTGGA, 0.
# inverse positive strand, positive direction, looking for AAAAAAAA, 0.
# inverse positive strand, positive direction, looking for ACTGGANACTGGA, 0.
# inverse negative strand, positive direction, looking for AAAAAAAA, 0.
# inverse negative strand, positive direction, looking for ACTGGANACTGGA, 0.


===PPRE UTRs===
==PPARA consensus sequences==
{{main|UTR promoter gene transcriptions}}


===PPRE core promoters===
Consensus sequence is 5'-CGACCCC-3'.<ref name=Long>{{ cite journal
{{main|Core promoter gene transcriptions}}
|author=Jianyin Long
 
|author2=Daniel L. Galvan
===PPRE proximal promoters===
|author3=Koki Mise
{{main|Proximal promoter gene transcriptions}}
|author4=Yashpal S. Kanwar
 
|author5=Li Li
===PPRE distal promoters===
|author6=Naravat Poungavrin
{{main|Distal promoter gene transcriptions}}
|author7=Paul A. Overbeek
|author8=Benny H. Chang
|author9=Farhad R. Danesh
|title=Role for carbohydrate response element-binding protein (ChREBP) in high glucose-mediated repression of long noncoding RNA Tug1
|journal=Journal of Biological Chemistry
|date=28 May 2020
|volume=5
|issue=28
|pages=
|url=https://www.jbc.org/content/early/2020/05/28/jbc.RA120.013228.full.pdf
|arxiv=
|bibcode=
|doi=10.1074/jbc.RA120.013228
|pmid=
|accessdate=6 October 2020 }}</ref>


==PPARA samplings==
==PPARA samplings==
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# inverse negative strand, positive direction, looking for CCCCAGC, 0.
# inverse negative strand, positive direction, looking for CCCCAGC, 0.


===PPARA UTRs===
===PPARA (4560-2846) UTRs===
{{main|UTR promoter gene transcriptions}}
 
Negative strand, negative direction: CGACCCC at 3037.
# 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==
{{main|Complex locus A1BG and ZNF497#PPARAs}}
Consensus sequence is CGACCCC.<ref name=Long/>
 
{|class="wikitable"
|-
! 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
|}


===PPARA proximal promoters===
Comparison:
{{main|Proximal promoter gene transcriptions}}
Positive strand, negative direction: CCCCAGC at 2766.


===PPARA distal promoters===
The occurrences of real PPARAs are greater than the randoms. This suggests that the real PPARAs are likely active or activable.
{{main|Distal promoter gene transcriptions}}
Positive strand, positive direction: CGACCCC at 279.


==See also==
==See also==
{{div col|colwidth=20em}}
{{div col|colwidth=20em}}
* [[A1BG gene transcription core promoters]]
* [[A1BG gene transcriptions]]
* [[A1BG regulatory elements and regions]]
* [[A1BG response element negative results]]
* [[A1BG response element positive results]]
* [[Complex locus A1BG and ZNF497]]
* [[Complex locus A1BG and ZNF497]]
* [[Transcription factor]]
* [[Xenobiotic response element gene transcriptions]]
{{Div col end}}
{{Div col end}}


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==External links==
==External links==
* [http://www.genome.jp/ GenomeNet KEGG database]
* [http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene Home - Gene - NCBI]
* [http://www.ncbi.nlm.nih.gov/sites/gquery NCBI All Databases Search]
* [http://www.ncbi.nlm.nih.gov/ncbisearch/ NCBI Site Search]


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[[Category:Resources last modified in September 2020]]

Latest revision as of 12:58, 6 September 2023

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:

  1. negative strand, negative direction, looking for AGGTCANAGGTCA, 0.
  2. positive strand, negative direction, looking for AGGTCANAGGTCA, 0.
  3. positive strand, positive direction, looking for AGGTCANAGGTCA, 0.
  4. negative strand, positive direction, looking for AGGTCANAGGTCA, 0.
  5. complement, negative strand, negative direction, looking for TCCAGTNTCCAGT, 0.
  6. complement, positive strand, negative direction, looking for TCCAGTNTCCAGT, 0.
  7. complement, positive strand, positive direction, looking for TCCAGTNTCCAGT, 0.
  8. complement, negative strand, positive direction, looking for TCCAGTNTCCAGT, 0.
  9. inverse complement, negative strand, negative direction, looking for TGACCTNTGACCT, 0.
  10. inverse complement, positive strand, negative direction, looking for TGACCTNTGACCT, 0.
  11. inverse complement, positive strand, positive direction, looking for TGACCTNTGACCT, 0.
  12. inverse complement, negative strand, positive direction, looking for TGACCTNTGACCT, 0.
  13. inverse negative strand, negative direction, looking for ACTGGANACTGGA, 0.
  14. inverse positive strand, negative direction, looking for ACTGGANACTGGA, 0.
  15. inverse positive strand, positive direction, looking for ACTGGANACTGGA, 0.
  16. 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:

  1. negative strand, negative direction, looking for CGACCCC, 1, CGACCCC at 3037.
  2. positive strand, negative direction, looking for CGACCCC, 0.
  3. positive strand, positive direction, looking for CGACCCC, 1, CGACCCC at 279.
  4. negative strand, positive direction, looking for CGACCCC, 0.
  5. complement, negative strand, negative direction, looking for GCTGGGG, 0.
  6. complement, positive strand, negative direction, looking for GCTGGGG, 1, GCTGGGG at 3037.
  7. complement, positive strand, positive direction, looking for GCTGGGG, 0.
  8. complement, negative strand, positive direction, looking for GCTGGGG, 1, GCTGGGG at 279.
  9. inverse complement, negative strand, negative direction, looking for GGGGTCG, 1, GGGGTCG at 2766.
  10. inverse complement, positive strand, negative direction, looking for GGGGTCG, 0.
  11. inverse complement, positive strand, positive direction, looking for GGGGTCG, 0.
  12. inverse complement, negative strand, positive direction, looking for GGGGTCG, 0.
  13. inverse negative strand, negative direction, looking for CCCCAGC, 0.
  14. inverse positive strand, negative direction, looking for CCCCAGC, 1, CCCCAGC at 2766.
  15. inverse positive strand, positive direction, looking for CCCCAGC, 0.
  16. inverse negative strand, positive direction, looking for CCCCAGC, 0.

PPARA (4560-2846) UTRs

  1. Negative strand, negative direction: CGACCCC at 3037.

PPARA negative direction (2811-2596) proximal promoters

  1. Negative strand, negative direction: GGGGTCG at 2766.

PPARA positive direction (4050-1) distal promoters

  1. Positive strand, positive direction: CGACCCC at 279.

PPARA random dataset samplings

  1. PPARAr0: 2, CGACCCC at 4084, CGACCCC at 3906.
  2. PPARAr1: 0.
  3. PPARAr2: 0.
  4. PPARAr3: 0.
  5. PPARAr4: 0.
  6. PPARAr5: 1, CGACCCC at 3597.
  7. PPARAr6: 1, CGACCCC at 2956.
  8. PPARAr7: 1, CGACCCC at 2415.
  9. PPARAr8: 1, CGACCCC at 1108.
  10. PPARAr9: 0.
  11. PPARAr0ci: 0.
  12. PPARAr1ci: 1, GGGGTCG at 2011.
  13. PPARAr2ci: 0.
  14. PPARAr3ci: 0.
  15. PPARAr4ci: 0.
  16. PPARAr5ci: 0.
  17. PPARAr6ci: 0.
  18. PPARAr7ci: 0.
  19. PPARAr8ci: 2, GGGGTCG at 1741, GGGGTCG at 246.
  20. PPARAr9ci: 0.

PPARAr arbitrary (evens) (4560-2846) UTRs

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

PPARAr alternate (odds) (4560-2846) UTRs

  1. PPARAr5: CGACCCC at 3597.

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

  1. PPARAr0: CGACCCC at 4084.

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

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

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

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

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

  1. PPARAr5: CGACCCC at 3597.
  2. PPARAr7: CGACCCC at 2415.
  3. PPARAr1ci: GGGGTCG at 2011.

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

  1. PPARAr0: CGACCCC at 3906.
  2. PPARAr6: CGACCCC at 2956.
  3. PPARAr8: CGACCCC at 1108.
  4. PPARAr8ci: GGGGTCG at 1741, GGGGTCG at 246.

PPARA analysis and results

Main article: Complex locus A1BG and ZNF497 § PPARAs

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.

See also

References

  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.
  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.
  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.

External links


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