Glucocorticoid response element gene transcriptions: Difference between revisions

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# A GRE does not participate in the transcription of A1BG.
# A GRE does not participate in the transcription of A1BG.


==Samplings==
==Glu samplings==
 
Copying an apparent consensus sequence of AGAACA and putting it in "⌘F" finds one located between ZSCAN22 and A1BG and two between ZNF497 and A1BG as can be found by the computer programs.
Copying an apparent consensus sequence of AGAACA and putting it in "⌘F" finds one located between ZSCAN22 and A1BG and two between ZNF497 and A1BG as can be found by the computer programs.


For the Basic programs testing consensus sequence AAAAAAAA (starting with SuccessablesAAA.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 AGAACA (starting with SuccessablesGlu.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, looking for AGAACA, 1, AGAACA at 281.
# negative strand, positive direction, looking for AAAAAAAA, 0.
# positive strand, negative direction, looking for AGAACA, 2, AGAACA at 3668, AGAACA at 287.
# positive strand, negative direction, looking for AAAAAAAA, 0.
# negative strand, positive direction, looking for AGAACA, 2, AGAACA at 4068, AGAACA at 3094.
# positive strand, positive direction, looking for AAAAAAAA, 0.
# positive strand, positive direction, looking for AGAACA, 0.
# complement, negative strand, negative direction, looking for TTTTTTTT, 0.
# inverse complement, negative strand, negative direction, looking for TGTTCT, 4, TGTTCT at 3759, TGTTCT at 3635, TGTTCT at 3340, TGTTCT at 3307.
# complement, negative strand, positive direction, looking for TTTTTTTT, 0.
# inverse complement, positive strand, negative direction, looking for TGTTCT, 1, TGTTCT at 45.
# complement, positive strand, negative direction, looking for TTTTTTTT, 0.
# inverse complement, negative strand, positive direction, looking for TGTTCT, 1, TGTTCT at 108.
# complement, positive strand, positive direction, looking for TTTTTTTT, 0.
# inverse complement, positive strand, positive direction, looking for TGTTCT, 0.
# inverse complement, negative strand, negative direction, looking for TTTTTTTT, 0.
 
# inverse complement, negative strand, positive direction, looking for TTTTTTTT, 0.
===Glu (4560-2846) UTRs===
# inverse complement, positive strand, negative direction, looking for TTTTTTTT, 0.
 
# inverse complement, positive strand, positive direction, looking for TTTTTTTT, 0.
# Negative strand, negative direction: TGTTCT at 3759, TGTTCT at 3635, TGTTCT at 3340, TGTTCT at 3307.
# inverse negative strand, negative direction, looking for AAAAAAAA, 0.
# Positive strand, negative direction: AGAACA at 3668.
# inverse negative strand, positive direction, looking for AAAAAAAA, 0.
 
# inverse positive strand, negative direction, looking for AAAAAAAA, 0.
===Glu positive direction (4265-4050) proximal promoters===
# inverse positive strand, positive direction, looking for AAAAAAAA, 0.
 
# Negative strand, positive direction: AGAACA at 4068.
 
===Glu negative direction (2596-1) distal promoters===
 
# Negative strand, negative direction: AGAACA at 281.
# Positive strand, negative direction: AGAACA at 287, TGTTCT at 45.
 
===Glu positive direction (4050-1) distal promoters===
 
# Negative strand, positive direction: AGAACA at 3094, TGTTCT at 108.
 
==Glu random dataset samplings==
 
# Glur0: 0.
# Glur1: 2, AGAACA at 4240, AGAACA at 2607.
# Glur2: 1, AGAACA at 908.
# Glur3: 0.
# Glur4: 0.
# Glur5: 1, AGAACA at 1196.
# Glur6: 1, AGAACA at 646.
# Glur7: 0.
# Glur8: 1 AGAACA at 4495.
# Glur9: 0.
# Glur0ci: 1, TGTTCT at 1979.
# Glur1ci: 1, TGTTCT at 1218.
# Glur2ci: 0.
# Glur3ci: 0.
# Glur4ci: 0.
# Glur5ci: 2, TGTTCT at 2442, TGTTCT at 958.
# Glur6ci: 1, TGTTCT at 827.
# Glur7ci: 1, TGTTCT at 1886.
# Glur8ci: 1, TGTTCT at 217.
# Glur9ci: 1, TGTTCT at 1534.
 
===Glur arbitrary (evens) (4560-2846) UTRs===
 
# Glur8: AGAACA at 4495.
 
===Glur alternate (odds) (4560-2846) UTRs===
 
# Glur1: AGAACA at 4240.
 
===Glur alternate negative direction (odds) (2811-2596) proximal promoters===
 
# Glur1: AGAACA at 2607.
 
===Glur arbitrary positive direction (odds) (4265-4050) proximal promoters===
 
# Glur1: AGAACA at 4240.
 
===Glur arbitrary negative direction (evens) (2596-1) distal promoters===
 
# Glur2: AGAACA at 908.
# Glur6: AGAACA at 646.
# Glur0ci: TGTTCT at 1979.
# Glur6ci: TGTTCT at 827.
# Glur8ci: TGTTCT at 217.
 
===Glur alternate negative direction (odds) (2596-1) distal promoters===
 
# Glur5: AGAACA at 1196.
# Glur1ci: TGTTCT at 1218.
# Glur5ci: TGTTCT at 2442, TGTTCT at 958.
# Glur7ci: TGTTCT at 1886.
# Glur9ci: TGTTCT at 1534.
 
===Glur arbitrary positive direction (odds) (4050-1) distal promoters===
 
# Glur1: AGAACA at 2607.
# Glur5: AGAACA at 1196.
# Glur1ci: TGTTCT at 1218.
# Glur5ci: TGTTCT at 2442, TGTTCT at 958.
# Glur7ci: TGTTCT at 1886.
# Glur9ci: TGTTCT at 1534.
 
===Glur alternate positive direction (evens) (4050-1) distal promoters===
 
# Glur2: AGAACA at 908.
# Glur6: AGAACA at 646.
# Glur0ci: TGTTCT at 1979.
# Glur6ci: TGTTCT at 827.
# Glur8ci: TGTTCT at 217.
 
==Glu response element analysis and results==
{{main|Complex locus A1BG and ZNF497#Glucocorticoid response elements}}
"DNA-binding by the GR-DBD has been well-characterized; it is highly sequence-specific, directly recognizing invariant guanine nucleotides of two AGAACA [TGTTCT] half sites called the glucocorticoid response element (GRE), and binds as a dimer in head-to-head orientation with mid-nanomolar affinity (4,12–18). [...] The consensus DNA glucocorticoid response element (GRE) is comprised of two half-sites (AGAACA) separated by a three base-pair spacer (13,15,60,61)."<ref name=Parsonnet/>
 
{|class="wikitable"
|-
! Reals or randoms !! Promoters !! direction !! Numbers !! Strands !! Occurrences !! Averages (± 0.1)
|-
| Reals || UTR || negative || 5 || 2 || 2.5 || 2.5 ± 1.5 (--4,+-1)
|-
| Randoms || UTR || arbitrary negative || 1 || 10 || 0.1 || 0.1
|-
| Randoms || UTR || alternate negative || 1 || 10 || 0.1 || 0.1
|-
| 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 || 0.05
|-
| Randoms || Proximal || alternate negative || 1 || 10 || 0.1 || 0.05
|-
| Reals || Proximal || positive || 1 || 2 || 0.5 || 0.5 ± 0.5 (-+1,++0)
|-
| Randoms || Proximal || arbitrary positive || 1 || 10 || 0.1 || 0.05
|-
| Randoms || Proximal || alternate positive || 0 || 10 || 0 || 0.05
|-
| Reals || Distal || negative || 3 || 2 || 1.5 || 1.5 ± 1.5 (--1,+-2)
|-
| Randoms || Distal || arbitrary negative || 5 || 10 || 0.5 || 0.55
|-
| Randoms || Distal || alternate negative || 6 || 10 || 0.6 || 0.55
|-
| Reals || Distal || positive || 2 || 2 || 1 || 1 ± 1 (-+2,++0)
|-
| Randoms || Distal || arbitrary positive || 7 || 10 || 0.7 || 0.6
|-
| Randoms || Distal || alternate positive || 5 || 10 || 0.5 || 0.6
|}
 
Comparison:


===AAA core promoters===
The occurrences of real Glucocorticoid UTRs, proximals and distals are greater than the randoms. This suggests that the real Glucocorticoid response elements are likely active or activable.
{{main|Core promoter gene transcriptions}}


===AAA proximal promoters===
==Pathways==
{{main|Proximal promoter gene transcriptions}}


===AAA distal promoters===
Stimulation of the pathway [[gluconeogenesis]], in particular, in the [[liver]] results in the synthesis of glucose from non-[[hexose]] substrates, such as [[amino acid]]s and [[glycerol]] from triglyceride breakdown, and is particularly important in [[carnivore]]s and certain [[herbivore]]s.
{{main|Distal promoter gene transcriptions}}


==Acknowledgements==
==Acknowledgements==

Latest revision as of 20:52, 29 August 2023

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

"DNA-binding by the GR-DBD has been well-characterized; it is highly sequence-specific, directly recognizing invariant guanine nucleotides of two AGAACA [TGTTCT] half sites called the glucocorticoid response element (GRE), and binds as a dimer in head-to-head orientation with mid-nanomolar affinity (4,12–18). [...] The consensus DNA glucocorticoid response element (GRE) is comprised of two half-sites (AGAACA) separated by a three base-pair spacer (13,15,60,61)."[1]

Human genes

Main article: Human genes

Interactions

Main article: Interaction gene transcriptions

Consensus sequences

Main article: Consensus sequence gene transcriptions

Hypotheses

Main article: Hypotheses
  1. A1BG has no GREs in either promoter.
  2. A1BG is not transcribed by a GRE.
  3. A GRE does not participate in the transcription of A1BG.

Glu samplings

Copying an apparent consensus sequence of AGAACA and putting it in "⌘F" finds one located between ZSCAN22 and A1BG and two between ZNF497 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence AGAACA (starting with SuccessablesGlu.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 AGAACA, 1, AGAACA at 281.
  2. positive strand, negative direction, looking for AGAACA, 2, AGAACA at 3668, AGAACA at 287.
  3. negative strand, positive direction, looking for AGAACA, 2, AGAACA at 4068, AGAACA at 3094.
  4. positive strand, positive direction, looking for AGAACA, 0.
  5. inverse complement, negative strand, negative direction, looking for TGTTCT, 4, TGTTCT at 3759, TGTTCT at 3635, TGTTCT at 3340, TGTTCT at 3307.
  6. inverse complement, positive strand, negative direction, looking for TGTTCT, 1, TGTTCT at 45.
  7. inverse complement, negative strand, positive direction, looking for TGTTCT, 1, TGTTCT at 108.
  8. inverse complement, positive strand, positive direction, looking for TGTTCT, 0.

Glu (4560-2846) UTRs

  1. Negative strand, negative direction: TGTTCT at 3759, TGTTCT at 3635, TGTTCT at 3340, TGTTCT at 3307.
  2. Positive strand, negative direction: AGAACA at 3668.

Glu positive direction (4265-4050) proximal promoters

  1. Negative strand, positive direction: AGAACA at 4068.

Glu negative direction (2596-1) distal promoters

  1. Negative strand, negative direction: AGAACA at 281.
  2. Positive strand, negative direction: AGAACA at 287, TGTTCT at 45.

Glu positive direction (4050-1) distal promoters

  1. Negative strand, positive direction: AGAACA at 3094, TGTTCT at 108.

Glu random dataset samplings

  1. Glur0: 0.
  2. Glur1: 2, AGAACA at 4240, AGAACA at 2607.
  3. Glur2: 1, AGAACA at 908.
  4. Glur3: 0.
  5. Glur4: 0.
  6. Glur5: 1, AGAACA at 1196.
  7. Glur6: 1, AGAACA at 646.
  8. Glur7: 0.
  9. Glur8: 1 AGAACA at 4495.
  10. Glur9: 0.
  11. Glur0ci: 1, TGTTCT at 1979.
  12. Glur1ci: 1, TGTTCT at 1218.
  13. Glur2ci: 0.
  14. Glur3ci: 0.
  15. Glur4ci: 0.
  16. Glur5ci: 2, TGTTCT at 2442, TGTTCT at 958.
  17. Glur6ci: 1, TGTTCT at 827.
  18. Glur7ci: 1, TGTTCT at 1886.
  19. Glur8ci: 1, TGTTCT at 217.
  20. Glur9ci: 1, TGTTCT at 1534.

Glur arbitrary (evens) (4560-2846) UTRs

  1. Glur8: AGAACA at 4495.

Glur alternate (odds) (4560-2846) UTRs

  1. Glur1: AGAACA at 4240.

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

  1. Glur1: AGAACA at 2607.

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

  1. Glur1: AGAACA at 4240.

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

  1. Glur2: AGAACA at 908.
  2. Glur6: AGAACA at 646.
  3. Glur0ci: TGTTCT at 1979.
  4. Glur6ci: TGTTCT at 827.
  5. Glur8ci: TGTTCT at 217.

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

  1. Glur5: AGAACA at 1196.
  2. Glur1ci: TGTTCT at 1218.
  3. Glur5ci: TGTTCT at 2442, TGTTCT at 958.
  4. Glur7ci: TGTTCT at 1886.
  5. Glur9ci: TGTTCT at 1534.

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

  1. Glur1: AGAACA at 2607.
  2. Glur5: AGAACA at 1196.
  3. Glur1ci: TGTTCT at 1218.
  4. Glur5ci: TGTTCT at 2442, TGTTCT at 958.
  5. Glur7ci: TGTTCT at 1886.
  6. Glur9ci: TGTTCT at 1534.

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

  1. Glur2: AGAACA at 908.
  2. Glur6: AGAACA at 646.
  3. Glur0ci: TGTTCT at 1979.
  4. Glur6ci: TGTTCT at 827.
  5. Glur8ci: TGTTCT at 217.

Glu response element analysis and results

Main article: Complex locus A1BG and ZNF497 § Glucocorticoid response elements

"DNA-binding by the GR-DBD has been well-characterized; it is highly sequence-specific, directly recognizing invariant guanine nucleotides of two AGAACA [TGTTCT] half sites called the glucocorticoid response element (GRE), and binds as a dimer in head-to-head orientation with mid-nanomolar affinity (4,12–18). [...] The consensus DNA glucocorticoid response element (GRE) is comprised of two half-sites (AGAACA) separated by a three base-pair spacer (13,15,60,61)."[1]

Reals or randoms Promoters direction Numbers Strands Occurrences Averages (± 0.1)
Reals UTR negative 5 2 2.5 2.5 ± 1.5 (--4,+-1)
Randoms UTR arbitrary negative 1 10 0.1 0.1
Randoms UTR alternate negative 1 10 0.1 0.1
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 0.05
Randoms Proximal alternate negative 1 10 0.1 0.05
Reals Proximal positive 1 2 0.5 0.5 ± 0.5 (-+1,++0)
Randoms Proximal arbitrary positive 1 10 0.1 0.05
Randoms Proximal alternate positive 0 10 0 0.05
Reals Distal negative 3 2 1.5 1.5 ± 1.5 (--1,+-2)
Randoms Distal arbitrary negative 5 10 0.5 0.55
Randoms Distal alternate negative 6 10 0.6 0.55
Reals Distal positive 2 2 1 1 ± 1 (-+2,++0)
Randoms Distal arbitrary positive 7 10 0.7 0.6
Randoms Distal alternate positive 5 10 0.5 0.6

Comparison:

The occurrences of real Glucocorticoid UTRs, proximals and distals are greater than the randoms. This suggests that the real Glucocorticoid response elements are likely active or activable.

Pathways

Stimulation of the pathway gluconeogenesis, in particular, in the liver results in the synthesis of glucose from non-hexose substrates, such as amino acids and glycerol from triglyceride breakdown, and is particularly important in carnivores and certain herbivores.

Acknowledgements

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

See also

References

  1. ↑ 1.0 1.1 Nicholas V Parsonnet, Nickolaus C Lammer, Zachariah E Holmes, Robert T Batey, Deborah S Wuttke (5 September 2019). "The glucocorticoid receptor DNA-binding domain recognizes RNA hairpin structures with high affinity". Nucleic Acids Research. 47 (15): 8180–8192. doi:10.1093/nar/gkz486. PMID 31147715. Retrieved 28 August 2020.

External links

Retrieved from "https://www.wikidoc.org/index.php?title=Glucocorticoid_response_element_gene_transcriptions&oldid=1735885"