Glucocorticoid response element gene transcriptions: Difference between revisions

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Line 87: Line 87:
# Glur3ci: 0.
# Glur3ci: 0.
# Glur4ci: 0.
# Glur4ci: 0.
# RDr5ci: 0.
# Glur5ci: 2, TGTTCT at 2442, TGTTCT at 958.
# RDr6ci: 0.
# Glur6ci: 1, TGTTCT at 827.
# RDr7ci: 0.
# Glur7ci: 1, TGTTCT at 1886.
# RDr8ci: 0.
# Glur8ci: 1, TGTTCT at 217.
# RDr9ci: 0.
# Glur9ci: 1, TGTTCT at 1534.


===Glur UTRs===
===Glur UTRs===
Line 103: Line 103:
# Glur1: AGAACA at 4240.
# Glur1: AGAACA at 4240.


===RDr distal promoters===
===Glur distal promoters===


# Glur2: AGAACA at 908.
# Glur2: AGAACA at 908.
# Glur6: AGAACA at 646.
# Glur6: AGAACA at 646.
# Glur0ci: TGTTCT at 1979.
# Glur0ci: TGTTCT at 1979.
# Glur6ci: TGTTCT at 827.
# Glur8ci: TGTTCT at 217.




# Glur1: AGAACA at 2607.
# Glur1: AGAACA at 2607.
# Glur5: AGAACA at 1196.
# Glur5: AGAACA at 1196.
# Glur5ci: TGTTCT at 2442, TGTTCT at 958.
# Glur9ci: TGTTCT at 1534.


==Glu response element analysis and results==
==Glu response element analysis and results==

Revision as of 06:55, 26 April 2022

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

Interactions

Consensus sequences

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, and complement.
  2. negative strand, positive direction, looking for AGAACA, 2, AGAACA at 4068, AGAACA at 3094, and complements.
  3. positive strand, negative direction, looking for AGAACA, 2, AGAACA at 3668, AGAACA at 287, and complements.
  4. positive strand, positive direction, looking for AGAACA, 0.
  5. complement, negative strand, negative direction, looking for TCTTGT, 2, TCTTGT at 3668, TCTTGT at 287.
  6. complement, negative strand, positive direction, looking for TCTTGT, 0.
  7. complement, positive strand, negative direction, looking for TCTTGT, 1, TCTTGT at 281.
  8. complement, positive strand, positive direction, looking for TCTTGT, 2, TCTTGT at 4068, TCTTGT at 3094.
  9. inverse complement, negative strand, negative direction, looking for TGTTCT, 4, TGTTCT at 3759, TGTTCT at 3635, TGTTCT at 3340, TGTTCT at 3307, and complements.
  10. inverse complement, negative strand, positive direction, looking for TGTTCT, 1, TGTTCT at 108, and complement.
  11. inverse complement, positive strand, negative direction, looking for TGTTCT, 1, TGTTCT at 45, and complement.
  12. inverse complement, positive strand, positive direction, looking for TGTTCT, 0.
  13. inverse negative strand, negative direction, looking for ACAAGA, 1, ACAAGA at 45.
  14. inverse negative strand, positive direction, looking for ACAAGA, 0.
  15. inverse positive strand, negative direction, looking for ACAAGA, 4, ACAAGA at 3759, ACAAGA at 3635, ACAAGA at 3340, ACAAGA at 3307.
  16. inverse positive strand, positive direction, looking for ACAAGA, 1, ACAAGA at 108.

Glu 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 proximal promoters

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

Glu distal promoters

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


  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 UTRs

  1. Glur8: AGAACA at 4495.

RDr core promoters

Glur proximal promoters

  1. Glur1: AGAACA at 4240.

Glur 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.


  1. Glur1: AGAACA at 2607.
  2. Glur5: AGAACA at 1196.
  3. Glur5ci: TGTTCT at 2442, TGTTCT at 958.
  4. Glur9ci: TGTTCT at 1534.

Glu response element analysis and results

"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 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 negative 0 10 0 0
Reals Core positive 0 2 0 0
Randoms Core positive 0 10 0 0
Reals Proximal negative 0 2 0 0
Randoms Proximal negative 0 10 0 0
Reals Proximal positive 0 2 0 0
Randoms Proximal positive 0 10 0 0
Reals Distal negative 1 2 0.5 0.5
Randoms Distal negative 1 10 0.1 0.05
Reals Distal positive 1 2 0.5 0.5
Randoms Distal positive 0 10 0 0.05

Comparison:

The occurrences of real responsive element consensus sequences are larger than the randoms. This suggests that the real responsive element consensus sequences 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 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