Androgen response element gene transcriptions: Difference between revisions

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{{AE}} Henry A. Hoff
{{AE}} Henry A. Hoff


"Androgen receptors (ARs) (NR3C4; nuclear receptor subfamily 3,group C, member 4) have a crucial role in the development,function and homeostasis of PCa cells. ARs can be activated as atranscription factor via binding to androgen hormones (eithertestosterone or dihydrotestosterone). This receptor has two mainfunctional domains: ligand-binding and DNA-binding (DBD).<sup>8</sup>"<ref name=Kouhpayeh/>
"Androgen receptors (ARs) (NR3C4; nuclear receptor subfamily 3, group C, member 4) have a crucial role in the development, function and homeostasis of PCa cells. ARs can be activated as a transcription factor via binding to androgen hormones (either testosterone or dihydrotestosterone). This receptor has two mainfunctional domains: ligand-binding and DNA-binding (DBD).<sup>8</sup>"<ref name=Kouhpayeh/>


"Androgen response elements structurally consist of a short DNAmotif with  base  sequence  specificity  within  the  promoterupstream of the androgen-responsive genes. The HRE contains apair of conserved sequences, which are separated by a three-nucleotide spacer. This sequence is determined as 5'-GGTACAnnnTGTTCT-3'<sup>10, 11</sup> with 5'-CGG-3' as the spacer in the androgen response element."<ref name=Kouhpayeh/>
"Androgen response elements structurally consist of a short DNA motif with  base  sequence  specificity  within  the  promoter upstream of the androgen-responsive genes. The HRE contains apair of conserved sequences, which are separated by a three-nucleotide spacer. This sequence is determined as 5'-GGTACAnnnTGTTCT-3'<sup>10, 11</sup> with 5'-CGG-3' as the spacer in the androgen response element."<ref name=Kouhpayeh/>


"The androgen response element sequence, 5'-GGTACACGGTGTTCT-3', was obtained  from  the  National  Center  of  Biotechnology  Information (NCBI)."<ref name=Kouhpayeh/>
"The androgen response element sequence, 5'-GGTACACGGTGTTCT-3', was obtained  from  the  National  Center  of  Biotechnology  Information (NCBI)."<ref name=Kouhpayeh/>
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==Hypotheses==
==Hypotheses==
{{main|Hypotheses}}
{{main|Hypotheses}}
# A1BG has no A boxes in either promoter.
# A1BG has no Androgen response elements in either promoter.
# A1BG is not transcribed by an ATA box.
# A1BG is not transcribed by an Androgen response element.
# AGCE1 does not participate in the transcription of A1BG.
# Androgen response element does not participate in the transcription of A1BG.


==Androgen response element (Kouhpayeh) samplings==
==Androgen response element (Kouhpayeh) samplings==
Line 64: Line 64:
Copying a responsive elements consensus sequence 5'-GGTACA-3' 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 5'-GGTACA-3' 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 5'-AAAAAAAA-3' (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 5'-GGTACA-3' (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:
# negative strand, negative direction, looking for 5'-AAAAAAAA-3', 0.
# negative strand, negative direction, looking for 5'-GGTACA-3', 0.
# negative strand, positive direction, looking for 5'-AAAAAAAA-3', 0.
# negative strand, positive direction, looking for 5'-GGTACA-3', 0.
# positive strand, negative direction, looking for 5'-AAAAAAAA-3', 0.
# positive strand, negative direction, looking for 5'-GGTACA-3', 0.
# positive strand, positive direction, looking for 5'-AAAAAAAA-3', 0.
# positive strand, positive direction, looking for 5'-GGTACA-3', 3, 5'-GGTACA-3' at 3901, 5'-GGTACA-3' at 3336, 5'-GGTACA-3' at 2474 and complements.
# complement, negative strand, negative direction, looking for 5'-TTTTTTTT-3', 0.
# complement, negative strand, negative direction, looking for 5'-CCATGT-3', 0.
# complement, negative strand, positive direction, looking for 5'-TTTTTTTT-3', 0.
# complement, negative strand, positive direction, looking for 5'-CCATGT-3', 3, 5'-CCATGT-3' at 3901, 5'-CCATGT-3' at 3336, 5'-CCATGT-3' at 2474.
# complement, positive strand, negative direction, looking for 5'-TTTTTTTT-3', 0.
# complement, positive strand, negative direction, looking for 5'-CCATGT-3', 0.
# complement, positive strand, positive direction, looking for 5'-TTTTTTTT-3', 0.
# complement, positive strand, positive direction, looking for 5'-CCATGT-3', 0.
# inverse complement, negative strand, negative direction, looking for 5'-TTTTTTTT-3', 0.
# inverse complement, negative strand, negative direction, looking for 5'-TGTACC-3', 3, TGTACC-3' at 2614, 5'-TGTACC-3' at 2152, 5'-TGTACC-3' at 1207 and complements.
# inverse complement, negative strand, positive direction, looking for 5'-TTTTTTTT-3', 0.
# inverse complement, negative strand, positive direction, looking for 5'-TGTACC-3', 0.
# inverse complement, positive strand, negative direction, looking for 5'-TTTTTTTT-3', 0.
# inverse complement, positive strand, negative direction, looking for 5'-TGTACC-3', 1, 5'-TGTACC-3' at 798 and complement.
# inverse complement, positive strand, positive direction, looking for 5'-TTTTTTTT-3', 0.
# inverse complement, positive strand, positive direction, looking for 5'-TGTACC-3', 1, 5'-TGTACC-3' at 2032.
# inverse negative strand, negative direction, looking for 5'-AAAAAAAA-3', 0.
# inverse negative strand, negative direction, looking for 5'-ACATGG-3', 1, 5'-ACATGG-3' at 798.
# inverse negative strand, positive direction, looking for 5'-AAAAAAAA-3', 0.
# inverse negative strand, positive direction, looking for 5'-ACATGG-3', 1, 5'-ACATGG-3' at 2032.
# inverse positive strand, negative direction, looking for 5'-AAAAAAAA-3', 0.
# inverse positive strand, negative direction, looking for 5'-ACATGG-3', 3, 5'-ACATGG-3' at 2614, 5'-ACATGG-3' at 2152, 5'-ACATGG-3' at 1207.
# inverse positive strand, positive direction, looking for 5'-AAAAAAAA-3', 0.
# inverse positive strand, positive direction, looking for 5'-ACATGG-3', 0.


===AAA (Kouhpayeh) core promoters===
===AnRE (Kouhpayeh) distal promoters===
{{main|Core promoter gene transcriptions}}
{{main|Distal promoter gene transcriptions}}
Negative strand, negative direction: TGTACC-3' at 2614, 5'-TGTACC-3' at 2152, 5'-TGTACC-3' at 1207, 5'-ACATGG-3' at 798 and complements.


===AAA (Kouhpayeh) proximal promoters===
Positive strand, positive direction: 5'-GGTACA-3' at 3901, 5'-GGTACA-3' at 3336, 5'-GGTACA-3' at 2474, 5'-TGTACC-3' at 2032 and complements.
{{main|Proximal promoter gene transcriptions}}
 
===AAA (Kouhpayeh) distal promoters===
{{main|Distal promoter gene transcriptions}}


==Androgen response element (Wilson) samplings==
==Androgen response element (Wilson) samplings==

Revision as of 05:38, 2 November 2020

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

"Androgen receptors (ARs) (NR3C4; nuclear receptor subfamily 3, group C, member 4) have a crucial role in the development, function and homeostasis of PCa cells. ARs can be activated as a transcription factor via binding to androgen hormones (either testosterone or dihydrotestosterone). This receptor has two mainfunctional domains: ligand-binding and DNA-binding (DBD).8"[1]

"Androgen response elements structurally consist of a short DNA motif with base sequence specificity within the promoter upstream of the androgen-responsive genes. The HRE contains apair of conserved sequences, which are separated by a three-nucleotide spacer. This sequence is determined as 5'-GGTACAnnnTGTTCT-3'10, 11 with 5'-CGG-3' as the spacer in the androgen response element."[1]

"The androgen response element sequence, 5'-GGTACACGGTGTTCT-3', was obtained from the National Center of Biotechnology Information (NCBI)."[1]

Human genes

Main article: Human genes

Gene ID: 367 is AR androgen receptor aka NR3C4 on Xq12: "The androgen receptor gene is more than 90 kb long and codes for a protein that has 3 major functional domains: the N-terminal domain, DNA-binding domain, and androgen-binding domain. The protein functions as a steroid-hormone activated transcription factor. Upon binding the hormone ligand, the receptor dissociates from accessory proteins, translocates into the nucleus, dimerizes, and then stimulates transcription of androgen responsive genes. This gene contains 2 polymorphic trinucleotide repeat segments that encode polyglutamine and polyglycine tracts in the N-terminal transactivation domain of its protein. Expansion of the polyglutamine tract from the normal 9-34 repeats to the pathogenic 38-62 repeats causes spinal bulbar muscular atrophy (SBMA, also known as Kennedy's disease). Mutations in this gene are also associated with complete androgen insensitivity (CAIS). Alternative splicing results in multiple transcript variants encoding different isoforms."[2]

Gene expressions

Main article: Gene expressions

"Biased expression in liver (RPKM 12.9), endometrium (RPKM 10.8) and 13 other tissues."[2]

Consensus sequences

Main article: Consensus sequence gene transcriptions

5′-GGTACACGGTGTTCT-3′[1]

5'-(A/T)(A/G)(A/C/G)(C/T)(C/G/T)(A/C/G)(C/G)(A/C/T)(A/C/G)(A/T)G(A/G/T)(A/G)(C/G)(A/C/T)-3'[3]

Hypotheses

Main article: Hypotheses
  1. A1BG has no Androgen response elements in either promoter.
  2. A1BG is not transcribed by an Androgen response element.
  3. Androgen response element does not participate in the transcription of A1BG.

Androgen response element (Kouhpayeh) samplings

Main article: Model samplings

Copying a responsive elements consensus sequence 5'-GGTACA-3' 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 5'-GGTACA-3' (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:

  1. negative strand, negative direction, looking for 5'-GGTACA-3', 0.
  2. negative strand, positive direction, looking for 5'-GGTACA-3', 0.
  3. positive strand, negative direction, looking for 5'-GGTACA-3', 0.
  4. positive strand, positive direction, looking for 5'-GGTACA-3', 3, 5'-GGTACA-3' at 3901, 5'-GGTACA-3' at 3336, 5'-GGTACA-3' at 2474 and complements.
  5. complement, negative strand, negative direction, looking for 5'-CCATGT-3', 0.
  6. complement, negative strand, positive direction, looking for 5'-CCATGT-3', 3, 5'-CCATGT-3' at 3901, 5'-CCATGT-3' at 3336, 5'-CCATGT-3' at 2474.
  7. complement, positive strand, negative direction, looking for 5'-CCATGT-3', 0.
  8. complement, positive strand, positive direction, looking for 5'-CCATGT-3', 0.
  9. inverse complement, negative strand, negative direction, looking for 5'-TGTACC-3', 3, TGTACC-3' at 2614, 5'-TGTACC-3' at 2152, 5'-TGTACC-3' at 1207 and complements.
  10. inverse complement, negative strand, positive direction, looking for 5'-TGTACC-3', 0.
  11. inverse complement, positive strand, negative direction, looking for 5'-TGTACC-3', 1, 5'-TGTACC-3' at 798 and complement.
  12. inverse complement, positive strand, positive direction, looking for 5'-TGTACC-3', 1, 5'-TGTACC-3' at 2032.
  13. inverse negative strand, negative direction, looking for 5'-ACATGG-3', 1, 5'-ACATGG-3' at 798.
  14. inverse negative strand, positive direction, looking for 5'-ACATGG-3', 1, 5'-ACATGG-3' at 2032.
  15. inverse positive strand, negative direction, looking for 5'-ACATGG-3', 3, 5'-ACATGG-3' at 2614, 5'-ACATGG-3' at 2152, 5'-ACATGG-3' at 1207.
  16. inverse positive strand, positive direction, looking for 5'-ACATGG-3', 0.

AnRE (Kouhpayeh) distal promoters

Main article: Distal promoter gene transcriptions

Negative strand, negative direction: TGTACC-3' at 2614, 5'-TGTACC-3' at 2152, 5'-TGTACC-3' at 1207, 5'-ACATGG-3' at 798 and complements.

Positive strand, positive direction: 5'-GGTACA-3' at 3901, 5'-GGTACA-3' at 3336, 5'-GGTACA-3' at 2474, 5'-TGTACC-3' at 2032 and complements.

Androgen response element (Wilson) samplings

Main article: Model samplings

Copying a responsive elements consensus sequence 5'-TGATTCGTGAG-3' 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 5'-AAAAAAAA-3' (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:

  1. negative strand, negative direction, looking for 5'-AAAAAAAA-3', 0.
  2. negative strand, positive direction, looking for 5'-AAAAAAAA-3', 0.
  3. positive strand, negative direction, looking for 5'-AAAAAAAA-3', 0.
  4. positive strand, positive direction, looking for 5'-AAAAAAAA-3', 0.
  5. complement, negative strand, negative direction, looking for 5'-TTTTTTTT-3', 0.
  6. complement, negative strand, positive direction, looking for 5'-TTTTTTTT-3', 0.
  7. complement, positive strand, negative direction, looking for 5'-TTTTTTTT-3', 0.
  8. complement, positive strand, positive direction, looking for 5'-TTTTTTTT-3', 0.
  9. inverse complement, negative strand, negative direction, looking for 5'-TTTTTTTT-3', 0.
  10. inverse complement, negative strand, positive direction, looking for 5'-TTTTTTTT-3', 0.
  11. inverse complement, positive strand, negative direction, looking for 5'-TTTTTTTT-3', 0.
  12. inverse complement, positive strand, positive direction, looking for 5'-TTTTTTTT-3', 0.
  13. inverse negative strand, negative direction, looking for 5'-AAAAAAAA-3', 0.
  14. inverse negative strand, positive direction, looking for 5'-AAAAAAAA-3', 0.
  15. inverse positive strand, negative direction, looking for 5'-AAAAAAAA-3', 0.
  16. inverse positive strand, positive direction, looking for 5'-AAAAAAAA-3', 0.

AAA (Wilson) core promoters

Main article: Core promoter gene transcriptions

AAA (Wilson) proximal promoters

Main article: Proximal promoter gene transcriptions

AAA (Wilson) distal promoters

Main article: Distal promoter gene transcriptions

Acknowledgements

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

See also

References

  1. ↑ 1.0 1.1 1.2 1.3 S Kouhpayeh, AR Einizadeh, Z Hejazi, M Boshtam, L Shariati, M Mirian, L Darzi, M Sojoudi, H Khanahmad and A Rezaei (1 July 2016). "Antiproliferative effect of a synthetic aptamer mimicking androgen response elements in the LNCaP cell line" (PDF). Cancer Gene Therapy. 23: 254–257. doi:10.1038/cgt.2016.26. Retrieved 3 October 2020.
  2. ↑ 2.0 2.1 RefSeq (January 2017). "AR androgen receptor [ Homo sapiens (human) ]". 8600 Rockville Pike, Bethesda MD, 20894 USA: National Center for Biotechnology Information, U.S. National Library of Medicine. Retrieved 1 November 2020.
  3. ↑ Stephen Wilson, Jianfei Qi & Fabian V. Filipp (14 September 2016). "Refinement of the androgen response element based on ChIP-Seq in androgen-insensitive and androgen-responsive prostate cancer cell lines". Scientific Reports. 6: 32611. doi:10.1038/srep32611. Retrieved 3 October 2020.

External links

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