Thyroid hormone response element gene transcriptions: Difference between revisions

Jump to navigation Jump to search
VisualWikitext
 
(3 intermediate revisions by the same user not shown)
Line 64: Line 64:
==THR random dataset samplings==
==THR random dataset samplings==


# RDr0: 0.
# THRr0: 1, AGGTCA at 699.
# RDr1: 0.
# THRr1: 1, AGGTCA at 1750.
# RDr2: 0.
# THRr2: 2, AGGTCA at 4381, AGGTCA at 3163.
# RDr3: 0.
# THRr3: 1, AGGTCA at 2303.
# RDr4: 0.
# THRr4: 0.
# RDr5: 0.
# THRr5: 1, AGGTCA at 4296.
# RDr6: 0.
# THRr6: 0.
# RDr7: 0.
# THRr7: 0.
# RDr8: 0.
# THRr8: 0.
# RDr9: 0.
# THRr9: 0.
# RDr0ci: 0.
# THRr0ci: 0.
# RDr1ci: 0.
# THRr1ci: 0.
# RDr2ci: 0.
# THRr2ci: 0.
# RDr3ci: 0.
# THRr3ci: 2, TGACCT at 4439, TGACCT at 2443.
# RDr4ci: 0.
# THRr4ci: 0.
# RDr5ci: 0.
# THRr5ci: 1, TGACCT at 2538.
# RDr6ci: 0.
# THRr6ci: 0.
# RDr7ci: 0.
# THRr7ci: 1, TGACCT at 3801.
# RDr8ci: 0.
# THRr8ci: 1, TGACCT at 540.
# RDr9ci: 0.
# THRr9ci: 0.


===RDr arbitrary (evens) (4560-2846) UTRs===
===THRr arbitrary (evens) (4560-2846) UTRs===


===RDr alternate (odds) (4560-2846) UTRs===
# THRr2: AGGTCA at 4381, AGGTCA at 3163.


===RDr arbitrary negative direction (evens) (2846-2811) core promoters===
===THRr alternate (odds) (4560-2846) UTRs===


===RDr alternate negative direction (odds) (2846-2811) core promoters===
# THRr5: AGGTCA at 4296.
# THRr3ci: TGACCT at 4439.
# THRr7ci: TGACCT at 3801.


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


===RDr alternate positive direction (evens) (4445-4265) core promoters===
# THRr5: AGGTCA at 4296.
# THRr3ci: TGACCT at 4439.


===RDr arbitrary negative direction (evens) (2811-2596) proximal promoters===
===THRr alternate positive direction (evens) (4445-4265) core promoters===


===RDr alternate negative direction (odds) (2811-2596) proximal promoters===
# THRr2: AGGTCA at 4381.


===RDr arbitrary positive direction (odds) (4265-4050) proximal promoters===
===THRr arbitrary negative direction (evens) (2596-1) distal promoters===


===RDr alternate positive direction (evens) (4265-4050) proximal promoters===
# THRr0: AGGTCA at 699.
# THRr2: AGGTCA at 3163.
# THRr8ci: TGACCT at 540.


===RDr arbitrary negative direction (evens) (2596-1) distal promoters===
===THRr alternate negative direction (odds) (2596-1) distal promoters===


===RDr alternate negative direction (odds) (2596-1) distal promoters===
# THRr1: AGGTCA at 1750.
# THRr3: AGGTCA at 2303.
# THRr3ci: TGACCT at 2443.
# THRr5ci: TGACCT at 2538.


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


===RDr alternate positive direction (evens) (4050-1) distal promoters===
# THRr1: AGGTCA at 1750.
# THRr3: AGGTCA at 2303.
# THRr3ci: TGACCT at 2443.
# THRr5ci: TGACCT at 2538.
# THRr7ci: TGACCT at 3801.
 
===THRr alternate positive direction (evens) (4050-1) distal promoters===
 
# THRr0: AGGTCA at 699.
# THRr2: AGGTCA at 3163.
# THRr8ci: TGACCT at 540.


==THR analysis and results==
==THR analysis and results==
Line 123: Line 141:
| Reals || UTR || negative || 1 || 2 || 0.5 || 0.5 ± 0.5 (--0,+-1)  
| Reals || UTR || negative || 1 || 2 || 0.5 || 0.5 ± 0.5 (--0,+-1)  
|-
|-
| Randoms || UTR || arbitrary negative || 0 || 10 || 0 || 0  
| Randoms || UTR || arbitrary negative || 2 || 10 || 0.2 || 0.25
|-
|-
| Randoms || UTR || alternate negative || 0 || 10 || 0 || 0  
| Randoms || UTR || alternate negative || 3 || 10 || 0.3 || 0.25
|-
|-
| Reals || Core || negative || 0 || 2 || 0 || 0  
| Reals || Core || negative || 0 || 2 || 0 || 0  
Line 135: Line 153:
| Reals || Core || positive || 1 || 2 || 0.5 || 0.5 ± 0.5 (-+1,++0)  
| Reals || Core || positive || 1 || 2 || 0.5 || 0.5 ± 0.5 (-+1,++0)  
|-
|-
| Randoms || Core || arbitrary positive || 0 || 10 || 0 || 0
| Randoms || Core || arbitrary positive || 2 || 10 || 0.2 || 0.15
|-
|-
| Randoms || Core || alternate positive || 0 || 10 || 0 || 0  
| Randoms || Core || alternate positive || 1 || 10 || 0.1 || 0.15
|-
|-
| Reals || Proximal || negative || 0 || 2 || 0 || 0  
| Reals || Proximal || negative || 0 || 2 || 0 || 0  
Line 153: Line 171:
| Reals || Distal || negative || 8 || 2 || 4 || 4 ± 2 (--2,+-6)  
| Reals || Distal || negative || 8 || 2 || 4 || 4 ± 2 (--2,+-6)  
|-
|-
| Randoms || Distal || arbitrary negative || 0 || 10 || 0 || 0
| Randoms || Distal || arbitrary negative || 3 || 10 || 0.3 || 0.35
|-
|-
| Randoms || Distal || alternate negative || 0 || 10 || 0 || 0  
| Randoms || Distal || alternate negative || 4 || 10 || 0.4 || 0.35
|-
|-
| Reals || Distal || positive || 4 || 2 || 2 || 2 ± 2 (-+4,++0)  
| Reals || Distal || positive || 4 || 2 || 2 || 2 ± 2 (-+4,++0)  
|-
|-
| Randoms || Distal || arbitrary positive || 0 || 10 || 0 || 0  
| Randoms || Distal || arbitrary positive || 5 || 10 || 0.5 || 0.4
|-
|-
| Randoms || Distal || alternate positive || 0 || 10 || 0 || 0  
| Randoms || Distal || alternate positive || 3 || 10 || 0.3 || 0.4
|}
|}


Comparison:
Comparison:


The occurrences of real THRs are greater than the randoms. This suggests that the real THRs are likely active or activable.
The occurrences of real THR UTRs, cores and distals are greater than the randoms. This suggests that the real THRs are likely active or activable.


==Acknowledgements==
==Acknowledgements==

Latest revision as of 23:06, 3 March 2023

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

"The arrangement of TREs within the promoter might regulate THR action by determining THR isoform binding, THR dimerization, and coregulators binding. In the classic view of how TH and its receptor stimulate gene expression, the gene promoter contains TREs consisting of a 6-bp consensus sequence (AGGTCA) organized as a direct repeat separated by 4 bp (DR4), a palindrome without spacing (PAL), or an inverted palindrome (LAP) separated by 4 to 6 bp (10–13)."[1]

Human genes

Consensus sequences

The "gene promoter contains TREs consisting of a 6-bp consensus sequence (AGGTCA) organized as a direct repeat separated by 4 bp (DR4), a palindrome without spacing (PAL), or an inverted palindrome (LAP) separated by 4 to 6 bp (10–13)."[1]

THR samplings

Copying the consensus sequence for the THR AGGTCA and putting the sequence in "⌘F" finds no locations between ZNF497 and A1BG or two locations between ZSCAN22 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence AGGTCA (starting with SuccessablesTHR.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 AGGTCA, 2, AGGTCA at 1532, AGGTCA at 1352.
  2. positive strand, negative direction, looking for AGGTCA, 7, AGGTCA at 4307, AGGTCA at 2585, AGGTCA at 2248, AGGTCA at 712, AGGTCA at 576, AGGTCA at 568, AGGTCA at 439.
  3. positive strand, positive direction, looking for AGGTCA, 0.
  4. negative strand, positive direction, looking for AGGTCA, 3, AGGTCA at 4269, AGGTCA at 2220, AGGTCA at 153.
  5. complement, negative strand, negative direction, looking for TCCAGT, 7, TCCAGT at 4307, TCCAGT at 2585, TCCAGT at 2248, TCCAGT at 712, TCCAGT at 576, TCCAGT at 568, TCCAGT at 439.
  6. complement, positive strand, negative direction, looking for TCCAGT, 2, TCCAGT at 1532, TCCAGT at 1352.
  7. complement, positive strand, positive direction, looking for TCCAGT, 3, TCCAGT at 4269, TCCAGT at 2220, TCCAGT at 153.
  8. complement, negative strand, positive direction, looking for TCCAGT, 0.
  9. inverse complement, negative strand, negative direction, looking for TGACCTT, 0.
  10. inverse complement, positive strand, negative direction, looking for TGACCTT, 0.
  11. inverse complement, positive strand, positive direction, looking for TGACCTT, 0.
  12. inverse complement, negative strand, positive direction, looking for TGACCTT, 2, TGACCTT at 4019, TGACCTT at 3785.
  13. inverse negative strand, negative direction, looking for ACTGGA, 0.
  14. inverse positive strand, negative direction, looking for ACTGGA, 0.
  15. inverse positive strand, positive direction, looking for ACTGGA, 2, ACTGGA at 4019, ACTGGA at 3785.
  16. inverse negative strand, positive direction, looking for ACTGGA, 0.

THR (4560-2846) UTRs

  1. Positive strand, negative direction: AGGTCA at 4307.

THR positive direction (4445-4265) core promoters

  1. Negative strand, positive direction: AGGTCA at 4269.

THR negative direction (2596-1) distal promoters

  1. Negative strand, negative direction: AGGTCA at 1532, AGGTCA at 1352.
  2. Positive strand, negative direction: AGGTCA at 2585, AGGTCA at 2248, AGGTCA at 712, AGGTCA at 576, AGGTCA at 568, AGGTCA at 439.

THR positive direction (4050-1) distal promoters

  1. Negative strand, positive direction: AGGTCA at 2220, AGGTCA at 153.
  2. Negative strand, positive direction: TGACCTT at 4019, TGACCTT at 3785.

THR random dataset samplings

  1. THRr0: 1, AGGTCA at 699.
  2. THRr1: 1, AGGTCA at 1750.
  3. THRr2: 2, AGGTCA at 4381, AGGTCA at 3163.
  4. THRr3: 1, AGGTCA at 2303.
  5. THRr4: 0.
  6. THRr5: 1, AGGTCA at 4296.
  7. THRr6: 0.
  8. THRr7: 0.
  9. THRr8: 0.
  10. THRr9: 0.
  11. THRr0ci: 0.
  12. THRr1ci: 0.
  13. THRr2ci: 0.
  14. THRr3ci: 2, TGACCT at 4439, TGACCT at 2443.
  15. THRr4ci: 0.
  16. THRr5ci: 1, TGACCT at 2538.
  17. THRr6ci: 0.
  18. THRr7ci: 1, TGACCT at 3801.
  19. THRr8ci: 1, TGACCT at 540.
  20. THRr9ci: 0.

THRr arbitrary (evens) (4560-2846) UTRs

  1. THRr2: AGGTCA at 4381, AGGTCA at 3163.

THRr alternate (odds) (4560-2846) UTRs

  1. THRr5: AGGTCA at 4296.
  2. THRr3ci: TGACCT at 4439.
  3. THRr7ci: TGACCT at 3801.

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

  1. THRr5: AGGTCA at 4296.
  2. THRr3ci: TGACCT at 4439.

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

  1. THRr2: AGGTCA at 4381.

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

  1. THRr0: AGGTCA at 699.
  2. THRr2: AGGTCA at 3163.
  3. THRr8ci: TGACCT at 540.

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

  1. THRr1: AGGTCA at 1750.
  2. THRr3: AGGTCA at 2303.
  3. THRr3ci: TGACCT at 2443.
  4. THRr5ci: TGACCT at 2538.

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

  1. THRr1: AGGTCA at 1750.
  2. THRr3: AGGTCA at 2303.
  3. THRr3ci: TGACCT at 2443.
  4. THRr5ci: TGACCT at 2538.
  5. THRr7ci: TGACCT at 3801.

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

  1. THRr0: AGGTCA at 699.
  2. THRr2: AGGTCA at 3163.
  3. THRr8ci: TGACCT at 540.

THR analysis and results

Main article: Complex locus A1BG and ZNF497 § THRs

The "gene promoter contains TREs consisting of a 6-bp consensus sequence (AGGTCA) organized as a direct repeat separated by 4 bp (DR4), a palindrome without spacing (PAL), or an inverted palindrome (LAP) separated by 4 to 6 bp (10–13)."[1]

Reals or randoms Promoters direction Numbers Strands Occurrences Averages (± 0.1)
Reals UTR negative 1 2 0.5 0.5 ± 0.5 (--0,+-1)
Randoms UTR arbitrary negative 2 10 0.2 0.25
Randoms UTR alternate negative 3 10 0.3 0.25
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 1 2 0.5 0.5 ± 0.5 (-+1,++0)
Randoms Core arbitrary positive 2 10 0.2 0.15
Randoms Core alternate positive 1 10 0.1 0.15
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 8 2 4 4 ± 2 (--2,+-6)
Randoms Distal arbitrary negative 3 10 0.3 0.35
Randoms Distal alternate negative 4 10 0.4 0.35
Reals Distal positive 4 2 2 2 ± 2 (-+4,++0)
Randoms Distal arbitrary positive 5 10 0.5 0.4
Randoms Distal alternate positive 3 10 0.3 0.4

Comparison:

The occurrences of real THR UTRs, cores and distals are greater than the randoms. This suggests that the real THRs are likely active or activable.

Acknowledgements

The content on this page was first contributed by: Henry A. Hoff.

See also

References

  1. ↑ 1.0 1.1 1.2 Vitor M S Pinto, Svetlana Minakhina, Shuiqing Qiu, Aniket Sidhaye, Michael P Brotherton, Amy Suhotliv, Fredric E Wondisford (1 September 2017). "Naturally Occurring Amino Acids in Helix 10 of the Thyroid Hormone Receptor Mediate Isoform-Specific TH Gene Regulation". Endocrinology. 158 (9): 3067–3078. doi:10.1210/en.2017-00314. PMID 28911178. Retrieved 5 September 2020.

External links

Retrieved from "https://www.wikidoc.org/index.php?title=Thyroid_hormone_response_element_gene_transcriptions&oldid=1733257"