Estrogen response element gene transcriptions: Difference between revisions

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==ERE1 (Driscoll) samplings==
==ERE1 (Driscoll) samplings==


Copying a responsive elements consensus sequence GGTCA 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 GGTCA and putting the sequence in "⌘F" finds five between ZNF497 and A1BG or six between ZSCAN22 and A1BG as can be found by the computer programs.


For the Basic programs testing consensus sequence GGTCA (starting with SuccessablesERE1.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 GGTCA (starting with SuccessablesERE1.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: 6, GGTCA at 4415, GGTCA at 2654, GGTCA at 2601, GGTCA at 2211, GGTCA at 1532, GGTCA at 1352.
# positive strand, negative direction, looking for AAAAAAAA, 0.
# positive strand, negative direction, looking for AAAAAAAA, 0.
# negative strand, positive direction, looking for AAAAAAAA, 0.
# negative strand, positive direction, looking for AAAAAAAA, 0.
Line 122: Line 122:
# inverse complement, positive strand, positive direction, looking for TTTTTTTT, 0.
# inverse complement, positive strand, positive direction, looking for TTTTTTTT, 0.


===AAA (4560-2846) UTRs===
===ERE1 (4560-2846) UTRs===
 
# Negative strand, negative direction: GGTCA at 4415.


===AAA negative direction (2846-2811) core promoters===
===AAA negative direction (2846-2811) core promoters===


===AAA positive direction (4445-4265) core promoters===
===AAA positive direction (4445-4265) core promoters===


===AAA negative direction (2811-2596) proximal promoters===
===ERE1 negative direction (2811-2596) proximal promoters===
 
# Negative strand, negative direction: GGTCA at 2654, GGTCA at 2601.


===AAA positive direction (4265-4050) proximal promoters===
===AAA positive direction (4265-4050) proximal promoters===


===AAA negative direction (2596-1) distal promoters===
===ERE1 negative direction (2596-1) distal promoters===
 
# Negative strand, negative direction: GGTCA at 2211, GGTCA at 1532, GGTCA at 1352.


===AAA positive direction (4050-1) distal promoters===
===AAA positive direction (4050-1) distal promoters===

Revision as of 18:27, 11 March 2023

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

Human genes

Consensus sequences

"The [...] estrogen response element (ERE) [was] located on [...] −94 to −80 "AGGTTATTGCCTCCT" on the transcript, respectively."[1]

Note: GGTTA is the complement of CCAAT. AGGTTATTGCCTCCT is the complement of TCCAATAACGGAGGA.

"Our in silico analysis revealed a putative ERE sequence (GGTCAggaTGACA; wherein the non-consensus nucleotide A is underlined) starting at position −242 from the translation initiation codon (ATG, A being +1; [...])."[2]

"The estrogen receptor (ER)1 is a transcription factor that regulates the expression of estrogen-responsive genes by binding to a specific DNA sequence found in their regulatory regions. This sequence is called the estrogen response element (ERE). [...] The essential ERE was determined to have the consensus sequence 5′-GGTCAnnnTGACC-3′ (4, 7)."[3]

The "sequence requirements for a “minimal” consensus ERE [...] for ER binding encompasses a wide variety of possible combinations, which display stable ER binding. The optimal binding sequence is 5′-C(A/G)GGTCAnnnTGACC(T/C)G-3′. Any change from this optimal consensus diminishes ER-ERE affinity. The underlined core consensus sequence represents the minimum length for binding activity."[3]

ERE (Matsumoto) samplings

Copying an abridged consensus sequence for the estrogen response element of AGGTTA (ci=TAACCT) and putting it in "⌘F" finds none located between ZSCAN22 and A1BG and none between ZNF497 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence AGGTTA (starting with SuccessablesEREM.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: 0.
  2. positive strand, negative direction: 0.
  3. negative strand, positive direction: 0.
  4. positive strand, positive direction: 0.
  5. inverse complement, negative strand, negative direction: 0.
  6. inverse complement, positive strand, negative direction: 0.
  7. inverse complement, negative strand, positive direction: 0.
  8. inverse complement, positive strand, positive direction: 0.

For the Basic programs testing consensus sequence 5'-AGGTTATTGCCTCCT-3' (starting with SuccessablesERE.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 5'-AGGTTATTGCCTCCT-3', 0.
  2. negative strand, positive direction, looking for 5'-AGGTTATTGCCTCCT-3', 0.
  3. positive strand, negative direction, looking for 5'-AGGTTATTGCCTCCT-3', 0.
  4. positive strand, positive direction, looking for 5'-AGGTTATTGCCTCCT-3', 0.
  5. complement, negative strand, negative direction, looking for 5'-TCCAATAACGGAGGA-3', 0.
  6. complement, negative strand, positive direction, looking for 5'-TCCAATAACGGAGGA-3', 0.
  7. complement, positive strand, negative direction, looking for 5'-TCCAATAACGGAGGA-3', 0.
  8. complement, positive strand, positive direction, looking for 5'-TCCAATAACGGAGGA-3', 0.
  9. inverse complement, negative strand, negative direction, looking for 5'-AGGAGGCAATAACCT-3', 0.
  10. inverse complement, negative strand, positive direction, looking for 5'-AGGAGGCAATAACCT-3', 0.
  11. inverse complement, positive strand, negative direction, looking for 5'-AGGAGGCAATAACCT-3', 0.
  12. inverse complement, positive strand, positive direction, looking for 5'-AGGAGGCAATAACCT-3', 0.
  13. inverse negative strand, negative direction, looking for 5'-TCCTCCGTTATTGGA-3', 0.
  14. inverse negative strand, positive direction, looking for 5'-TCCTCCGTTATTGGA-3', 0.
  15. inverse positive strand, negative direction, looking for 5'-TCCTCCGTTATTGGA-3', 0.
  16. inverse positive strand, positive direction, looking for 5'-TCCTCCGTTATTGGA-3', 0.

ERE (Yasar) samplings

Copying an abridged consensus sequence for the estrogen response element of GGTCAGGAT and putting it in "⌘F" finds none located between ZSCAN22 and A1BG and none between ZNF497 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence 5'-GGTCAGGATGAC-3' (starting with SuccessablesERE2.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 5'-GGTCAGGATGAC-3', 0.
  2. negative strand, positive direction, looking for 5'-GGTCAGGATGAC-3', 0.
  3. positive strand, negative direction, looking for 5'-GGTCAGGATGAC-3', 0.
  4. positive strand, positive direction, looking for 5'-GGTCAGGATGAC-3', 0.
  5. complement, negative strand, negative direction, looking for 5'-CCAGTCCTACTG-3', 0.
  6. complement, negative strand, positive direction, looking for 5'-CCAGTCCTACTG-3', 0.
  7. complement, positive strand, negative direction, looking for 5'-CCAGTCCTACTG-3', 0.
  8. complement, positive strand, positive direction, looking for 5'-CCAGTCCTACTG-3', 0.
  9. inverse complement, negative strand, negative direction, looking for 5'-GTCATCCTGACC-3', 0.
  10. inverse complement, negative strand, positive direction, looking for 5'-GTCATCCTGACC-3', 0.
  11. inverse complement, positive strand, negative direction, looking for 5'-GTCATCCTGACC-3', 0.
  12. inverse complement, positive strand, positive direction, looking for 5'-GTCATCCTGACC-3', 0.
  13. inverse negative strand, negative direction, looking for 5'-CAGTAGGACTGG-3', 0.
  14. inverse negative strand, positive direction, looking for 5'-CAGTAGGACTGG-3', 0.
  15. inverse positive strand, negative direction, looking for 5'-CAGTAGGACTGG-3', 0.
  16. inverse positive strand, positive direction, looking for 5'-CAGTAGGACTGG-3', 0.

ERE1 (Driscoll) samplings

Copying a responsive elements consensus sequence GGTCA and putting the sequence in "⌘F" finds five between ZNF497 and A1BG or six between ZSCAN22 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence GGTCA (starting with SuccessablesERE1.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: 6, GGTCA at 4415, GGTCA at 2654, GGTCA at 2601, GGTCA at 2211, GGTCA at 1532, GGTCA at 1352.
  2. positive strand, negative direction, looking for AAAAAAAA, 0.
  3. negative strand, positive direction, looking for AAAAAAAA, 0.
  4. positive strand, positive direction, looking for AAAAAAAA, 0.
  5. inverse complement, negative strand, negative direction, looking for TTTTTTTT, 0.
  6. inverse complement, positive strand, negative direction, looking for TTTTTTTT, 0.
  7. inverse complement, negative strand, positive direction, looking for TTTTTTTT, 0.
  8. inverse complement, positive strand, positive direction, looking for TTTTTTTT, 0.

ERE1 (4560-2846) UTRs

  1. Negative strand, negative direction: GGTCA at 4415.

AAA negative direction (2846-2811) core promoters

AAA positive direction (4445-4265) core promoters

ERE1 negative direction (2811-2596) proximal promoters

  1. Negative strand, negative direction: GGTCA at 2654, GGTCA at 2601.

AAA positive direction (4265-4050) proximal promoters

ERE1 negative direction (2596-1) distal promoters

  1. Negative strand, negative direction: GGTCA at 2211, GGTCA at 1532, GGTCA at 1352.

AAA positive direction (4050-1) distal promoters

ERE1 (Driscoll) random dataset samplings

  1. RDr0: 0.
  2. RDr1: 0.
  3. RDr2: 0.
  4. RDr3: 0.
  5. RDr4: 0.
  6. RDr5: 0.
  7. RDr6: 0.
  8. RDr7: 0.
  9. RDr8: 0.
  10. RDr9: 0.
  11. RDr0ci: 0.
  12. RDr1ci: 0.
  13. RDr2ci: 0.
  14. RDr3ci: 0.
  15. RDr4ci: 0.
  16. RDr5ci: 0.
  17. RDr6ci: 0.
  18. RDr7ci: 0.
  19. RDr8ci: 0.
  20. RDr9ci: 0.

RDr arbitrary (evens) (4560-2846) UTRs

RDr alternate (odds) (4560-2846) UTRs

RDr arbitrary negative direction (evens) (2846-2811) core promoters

RDr alternate negative direction (odds) (2846-2811) core promoters

RDr arbitrary positive direction (odds) (4445-4265) core promoters

RDr alternate positive direction (evens) (4445-4265) core promoters

RDr arbitrary negative direction (evens) (2811-2596) proximal promoters

RDr alternate negative direction (odds) (2811-2596) proximal promoters

RDr arbitrary positive direction (odds) (4265-4050) proximal promoters

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

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

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

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

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

ERE1 (Driscoll) analysis and results

Main article: Complex locus A1BG and ZNF497 § ERE1s

"The underlined core consensus sequence [GGTCA] represents the minimum length for binding activity."[3]

Reals or randoms Promoters direction Numbers Strands Occurrences Averages (± 0.1)
Reals UTR negative 0 2 0 0
Randoms UTR arbitrary negative 0 10 0 0
Randoms UTR alternate negative 0 10 0 0
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 0 2 0 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
Randoms Proximal alternate positive 0 10 0 0
Reals Distal negative 0 2 0 0
Randoms Distal arbitrary negative 0 10 0 0
Randoms Distal alternate negative 0 10 0 0
Reals Distal positive 0 2 0 0
Randoms Distal arbitrary positive 0 10 0 0
Randoms Distal alternate positive 0 10 0 0

Comparison:

The occurrences of real ERE1s are greater than the randoms. This suggests that the real ERE1s are likely active or activable.

ERE2 (Driscoll) samplings

Copying a responsive elements consensus sequence TGACC 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 TGACC (starting with SuccessablesERE2.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. negative strand, positive direction, looking for AAAAAAAA, 0.
  4. positive strand, positive direction, looking for AAAAAAAA, 0.
  5. inverse complement, negative strand, negative direction, looking for TTTTTTTT, 0.
  6. inverse complement, positive strand, negative direction, looking for TTTTTTTT, 0.
  7. inverse complement, negative strand, positive direction, looking for TTTTTTTT, 0.
  8. inverse complement, positive strand, positive direction, looking for TTTTTTTT, 0.

AAA (4560-2846) UTRs

AAA negative direction (2846-2811) core promoters

AAA positive direction (4445-4265) core promoters

AAA negative direction (2811-2596) proximal promoters

AAA positive direction (4265-4050) proximal promoters

AAA negative direction (2596-1) distal promoters

AAA positive direction (4050-1) distal promoters

ERE2 (Driscoll) random dataset samplings

  1. RDr0: 0.
  2. RDr1: 0.
  3. RDr2: 0.
  4. RDr3: 0.
  5. RDr4: 0.
  6. RDr5: 0.
  7. RDr6: 0.
  8. RDr7: 0.
  9. RDr8: 0.
  10. RDr9: 0.
  11. RDr0ci: 0.
  12. RDr1ci: 0.
  13. RDr2ci: 0.
  14. RDr3ci: 0.
  15. RDr4ci: 0.
  16. RDr5ci: 0.
  17. RDr6ci: 0.
  18. RDr7ci: 0.
  19. RDr8ci: 0.
  20. RDr9ci: 0.

RDr arbitrary (evens) (4560-2846) UTRs

RDr alternate (odds) (4560-2846) UTRs

RDr arbitrary negative direction (evens) (2846-2811) core promoters

RDr alternate negative direction (odds) (2846-2811) core promoters

RDr arbitrary positive direction (odds) (4445-4265) core promoters

RDr alternate positive direction (evens) (4445-4265) core promoters

RDr arbitrary negative direction (evens) (2811-2596) proximal promoters

RDr alternate negative direction (odds) (2811-2596) proximal promoters

RDr arbitrary positive direction (odds) (4265-4050) proximal promoters

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

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

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

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

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

ERE2 (Driscoll) analysis and results

Main article: Complex locus A1BG and ZNF497 § ERE2s

"The underlined core consensus sequence [TGACC] represents the minimum length for binding activity."[3]

Reals or randoms Promoters direction Numbers Strands Occurrences Averages (± 0.1)
Reals UTR negative 0 2 0 0
Randoms UTR arbitrary negative 0 10 0 0
Randoms UTR alternate negative 0 10 0 0
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 0 2 0 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
Randoms Proximal alternate positive 0 10 0 0
Reals Distal negative 0 2 0 0
Randoms Distal arbitrary negative 0 10 0 0
Randoms Distal alternate negative 0 10 0 0
Reals Distal positive 0 2 0 0
Randoms Distal arbitrary positive 0 10 0 0
Randoms Distal alternate positive 0 10 0 0

Comparison:

The occurrences of real ERE2s are greater than the randoms. This suggests that the real ERE2s are likely active or activable.

See also

References

  1. ↑ Takuya Matsumoto, Saemi Kitajima, Chisato Yamamoto, Mitsuru Aoyagi, Yoshiharu Mitoma, Hiroyuki Harada and Yuji Nagashima (9 August 2020). "Cloning and tissue distribution of the ATP-binding cassette subfamily G member 2 gene in the marine pufferfish Takifugu rubripes" (PDF). Fisheries Science. 86: 873–887. doi:10.1007/s12562-020-01451-z. Retrieved 27 September 2020.
  2. ↑ Pelin Yaşar, Gamze Ayaz & Mesut Muyan (25 November 2016). "Estradiol-Estrogen Receptor α Mediates the Expression of the CXXC5 Gene through the Estrogen Response Element-Dependent Signaling Pathway". Scientific Reports. 6: 37808. doi:10.1038/srep37808. Retrieved 6 October 2020.
  3. ↑ 3.0 3.1 3.2 3.3 Mark D. Driscoll, G. Sathya, Mesut Muyan, Carolyn M. Klinge, Russell Hilf and Robert A. Bambara (November 1998). "Sequence Requirements for Estrogen Receptor Binding to Estrogen Response Elements". Journal of Biological Chemistry Nucleic Acids, Protein Synthesis, and Molecular Genetics. 273 (45): 29321–29330. doi:10.1074/jbc.273.45.29321. Retrieved 8 March 2023.

External links


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