P53 response element gene transcriptions: Difference between revisions
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{{AE}} Henry A. Hoff | {{AE}} Henry A. Hoff | ||
"A p53 consensus DNA RE is composed of a tandem of two decameric palindromic sequences (half-sites) 5′-RRRCWWGYYY-3′, where R = purine, Y = pyrimidine and W is either A or T. There is a variability in composition of p53 REs, thus two half-sites can be separated by a spacer DNA, typically 0–13 bp in length and many p53 DNA REs have varying numbers of half-sites (19,20,22,33–37)."<ref name=Kearns>{{ cite journal | |||
|author=Sinéad Kearns, Rudi Lurz, Elena V. Orlova, Andrei L. Okorokov | |||
|title=Two p53 tetramers bind one consensus DNA response element | |||
|journal=Nucleic Acid Research | |||
|date=27 July 2016 | |||
|volume=44 | |||
|issue=13 | |||
|pages=6185–6199 | |||
|url=https://academic.oup.com/nar/article/44/13/6185/2457565 | |||
|arxiv= | |||
|bibcode= | |||
|doi=10.1093/nar/gkw215 | |||
|pmid= | |||
|accessdate=6 October 2020 }}</ref> | |||
"The p53 REs are defined by two closely spaced decameric half-sites [consensus sequence: 5′-(RRRCWWGYYY)n(RRRCWWGYYY)-3′; R = A,G; W = A,T; Y = C,T; n = spacer of length 0–20 base pairs (bp)], and hundreds of them have been validated in human and mouse (1)."<ref name=XZhang2014>{{ cite journal | "The p53 REs are defined by two closely spaced decameric half-sites [consensus sequence: 5′-(RRRCWWGYYY)n(RRRCWWGYYY)-3′; R = A,G; W = A,T; Y = C,T; n = spacer of length 0–20 base pairs (bp)], and hundreds of them have been validated in human and mouse (1)."<ref name=XZhang2014>{{ cite journal | ||
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==Human genes== | ==Human genes== | ||
p53 response elements found in the promoter of TUG1: 5'-CAGGCCC-3' and 5'-GGGCGTG-3'.<ref name=Long>{{ cite journal | |||
|author=Jianyin Long | |||
|author2=Daniel L. Galvan | |||
|author3=Koki Mise | |||
|author4=Yashpal S. Kanwar | |||
|author5=Li Li | |||
|author6=Naravat Poungavrin | |||
|author7=Paul A. Overbeek | |||
|author8=Benny H. Chang | |||
|author9=Farhad R. Danesh | |||
|title=Role for carbohydrate response element-binding protein (ChREBP) in high glucose-mediated repression of long noncoding RNA Tug1 | |||
|journal=Journal of Biological Chemistry | |||
|date=28 May 2020 | |||
|volume=5 | |||
|issue=28 | |||
|pages= | |||
|url=https://www.jbc.org/content/early/2020/05/28/jbc.RA120.013228.full.pdf | |||
|arxiv= | |||
|bibcode= | |||
|doi=10.1074/jbc.RA120.013228 | |||
|pmid= | |||
|accessdate=6 October 2020 }}</ref> | |||
==Consensus sequences== | ==Consensus sequences== | ||
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# complement, positive strand, negative direction is SuccessablesPREc+-.bas, looking for 3'-(C/T)(C/T)(C/T)G(A/T)(A/T)C(A/G)(A/G)(A/G)-5', 0. | # complement, positive strand, negative direction is SuccessablesPREc+-.bas, looking for 3'-(C/T)(C/T)(C/T)G(A/T)(A/T)C(A/G)(A/G)(A/G)-5', 0. | ||
# complement, positive strand, positive direction is SuccessablesPREc++.bas, looking for 3'-(C/T)(C/T)(C/T)G(A/T)(A/T)C(A/G)(A/G)(A/G)-5', 0. | # complement, positive strand, positive direction is SuccessablesPREc++.bas, looking for 3'-(C/T)(C/T)(C/T)G(A/T)(A/T)C(A/G)(A/G)(A/G)-5', 0. | ||
===p53 response element UTRs=== | |||
Positive strand, negative direction: AGGCAAGCCT at 457, AGACTTGCCT at 1621, and AGACAAGCTT at 4186. | |||
===p53 response element distal promoters=== | |||
Positive strand, negative direction: AGACTTGCCT at 1621, AGGCAAGCCT at 457. | |||
==Acknowledgements== | |||
The content on this page was first contributed by: Henry A. Hoff. | |||
==See also== | ==See also== | ||
{{div col|colwidth=20em}} | {{div col|colwidth=20em}} | ||
* [[A1BG gene transcription core promoters]] | |||
* [[A1BG gene transcriptions]] | |||
* [[A1BG regulatory elements and regions]] | |||
* [[A1BG response element negative results]] | |||
* [[A1BG response element positive results]] | |||
* [[Complex locus A1BG and ZNF497]] | * [[Complex locus A1BG and ZNF497]] | ||
{{Div col end}} | {{Div col end}} | ||
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==External links== | ==External links== | ||
* [http://www.genome.jp/ GenomeNet KEGG database] | |||
* [http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene Home - Gene - NCBI] | |||
* [http://www.ncbi.nlm.nih.gov/sites/gquery NCBI All Databases Search] | |||
* [http://www.ncbi.nlm.nih.gov/ncbisearch/ NCBI Site Search] | |||
* [http://www.ncbi.nlm.nih.gov/pccompound PubChem Public Chemical Database] | |||
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[[Category:Resources last modified in | [[Category:Resources last modified in February 2021]] | ||
Revision as of 17:33, 13 February 2021
Associate Editor(s)-in-Chief: Henry A. Hoff
"A p53 consensus DNA RE is composed of a tandem of two decameric palindromic sequences (half-sites) 5′-RRRCWWGYYY-3′, where R = purine, Y = pyrimidine and W is either A or T. There is a variability in composition of p53 REs, thus two half-sites can be separated by a spacer DNA, typically 0–13 bp in length and many p53 DNA REs have varying numbers of half-sites (19,20,22,33–37)."[1]
"The p53 REs are defined by two closely spaced decameric half-sites [consensus sequence: 5′-(RRRCWWGYYY)n(RRRCWWGYYY)-3′; R = A,G; W = A,T; Y = C,T; n = spacer of length 0–20 base pairs (bp)], and hundreds of them have been validated in human and mouse (1)."[2]
"According to EMSA binding experiments, all core sequences CAGG and CGTG and their palindrome sequences CCTG and CACG can be bound by p63 [18]. TAACATGTTT or TAACTTGTAT or TAACCTGTAT or TAACGTGTAT bound to p63 much more strongly than AGGCATGATG or GAGCTTGATT or GACCCTGACC or CCCCGTGCAC in EMSA experiments [21]. Therefore, p63 prefers AT-rich flanking sequences rather than general GC rich in purine (Pu) and pyrimidine (Py) bases that comprise the flanking sequence for p53 or p73 [...] [21]."[3]
Human genes
p53 response elements found in the promoter of TUG1: 5'-CAGGCCC-3' and 5'-GGGCGTG-3'.[4]
Consensus sequences
An apparent consensus sequence for the p53RE is (A/G)(A/G)(A/G)C(A/T)(A/T)G(C/T)(C/T)(C/T).
Samplings
Copying an apparent consensus sequence for the p53RE (GGGCATGCCT) and putting it in "⌘F" finds none located between ZSCAN22 and none between ZNF497 and A1BG as can be found by the computer programs.
Copying an apparent core consensus sequence for the p53RE (CAGG) and putting it in "⌘F" finds three located between ZSCAN22 and 49 between ZNF497 and A1BG as can be found by the computer programs.
Copying an apparent core consensus sequence for the p53RE (CGTG) and putting it in "⌘F" finds 27 located between ZSCAN22 and eleven between ZNF497 and A1BG as can be found by the computer programs.
Copying an apparent consensus sequence for the p53RE (TAACATGTTT) and putting it in "⌘F" finds none located between ZSCAN22 and none between ZNF497 and A1BG as can be found by the computer programs.
Copying an apparent consensus sequence for the p53RE (TAACTTGTAT) and putting it in "⌘F" finds none located between ZSCAN22 and none between ZNF497 and A1BG as can be found by the computer programs.
Copying an apparent consensus sequence for the p53RE (TAACCTGTAT) and putting it in "⌘F" finds none located between ZSCAN22 and none between ZNF497 and A1BG as can be found by the computer programs.
Copying an apparent consensus sequence for the p53RE (TAACGTGTAT) and putting it in "⌘F" finds none located between ZSCAN22 and none between ZNF497 and A1BG as can be found by the computer programs.
Copying an apparent consensus sequence for the p53RE (AGGCATGATG) and putting it in "⌘F" finds none located between ZSCAN22 and none between ZNF497 and A1BG as can be found by the computer programs.
Copying an apparent consensus sequence for the p53RE (GAGCTTGATT) and putting it in "⌘F" finds none located between ZSCAN22 and none between ZNF497 and A1BG as can be found by the computer programs.
Copying an apparent consensus sequence for the p53RE (GACCCTGACC) and putting it in "⌘F" finds none located between ZSCAN22 and none between ZNF497 and A1BG as can be found by the computer programs.
Copying an apparent consensus sequence for the p53RE (CCCCGTGCAC) and putting it in "⌘F" finds none located between ZSCAN22 and none between ZNF497 and A1BG as can be found by the computer programs.
For the Basic programs (starting with SuccessablesPbox.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 in the negative direction (from ZSCAN22 to A1BG) is SuccessablesPRE--.bas, looking for 3'-(A/G)(A/G)(A/G)C(A/T)(A/T)G(C/T)(C/T)(C/T)-5', 0.
- negative strand in the positive direction (from ZNF497 to A1BG) is SuccessablesPRE-+.bas, looking for 3'-(A/G)(A/G)(A/G)C(A/T)(A/T)G(C/T)(C/T)(C/T)-5', 0.
- positive strand in the negative direction is SuccessablesPRE+-.bas, looking for 3'-(A/G)(A/G)(A/G)C(A/T)(A/T)G(C/T)(C/T)(C/T)-5', 3, 3'-AGGCAAGCCT-5', 457, 3'-AGACTTGCCT-5', 1621, 3'-AGACAAGCTT-5', 4186.
- positive strand in the positive direction is SuccessablesPRE++.bas, looking for 3'-(A/G)(A/G)(A/G)C(A/T)(A/T)G(C/T)(C/T)(C/T)-5', 0.
- complement, negative strand, negative direction is SuccessablesPREc--.bas, looking for 3'-(C/T)(C/T)(C/T)G(A/T)(A/T)C(A/G)(A/G)(A/G)-5', 3, 3'-TCCGTTCGGA-5', 457, 3'-TCTGAACGGA-5', 1621, 3'-TCTGTTCGAA-5', 4186.
- complement, negative strand, positive direction is SuccessablesPREc-+.bas, looking for 3'-(C/T)(C/T)(C/T)G(A/T)(A/T)C(A/G)(A/G)(A/G)-5', 0.
- complement, positive strand, negative direction is SuccessablesPREc+-.bas, looking for 3'-(C/T)(C/T)(C/T)G(A/T)(A/T)C(A/G)(A/G)(A/G)-5', 0.
- complement, positive strand, positive direction is SuccessablesPREc++.bas, looking for 3'-(C/T)(C/T)(C/T)G(A/T)(A/T)C(A/G)(A/G)(A/G)-5', 0.
p53 response element UTRs
Positive strand, negative direction: AGGCAAGCCT at 457, AGACTTGCCT at 1621, and AGACAAGCTT at 4186.
p53 response element distal promoters
Positive strand, negative direction: AGACTTGCCT at 1621, AGGCAAGCCT at 457.
Acknowledgements
The content on this page was first contributed by: Henry A. Hoff.
See also
References
- ↑ Sinéad Kearns, Rudi Lurz, Elena V. Orlova, Andrei L. Okorokov (27 July 2016). "Two p53 tetramers bind one consensus DNA response element". Nucleic Acid Research. 44 (13): 6185–6199. doi:10.1093/nar/gkw215. Retrieved 6 October 2020.
- ↑ Xiaojun Zhang, Ana Carolina Dantas Machado, Yuan Ding, Yongheng Chen, Yan Lu, Yankun Duan, Kenneth W. Tham, Lin Chen, Remo Rohs, Peter Z. Qin (1 February 2014). "Conformations of p53 response elements in solution deduced using site-directed spin labeling and Monte Carlo sampling". Nucleic Acids Research. 42 (4): 2789–2797. doi:10.1093/nar/gkt1219. PMID 24293651. Retrieved 28 August 2020.
- ↑ Bi-He Cai, Chung-Faye Chao, Hsiang-Chi Huang, Hsueh-Yi Lee, Reiji Kannagi, and Jang-Yi Chen (27 July 2019). "Roles of p53 Family Structure and Function in Non-Canonical Response Element Binding and Activation". International Journal of Molecular Sciences. 20 (15): 3681–3700. doi:10.3390/ijms20153681. Retrieved 5 October 2020.
- ↑ Jianyin Long; Daniel L. Galvan; Koki Mise; Yashpal S. Kanwar; Li Li; Naravat Poungavrin; Paul A. Overbeek; Benny H. Chang; Farhad R. Danesh (28 May 2020). "Role for carbohydrate response element-binding protein (ChREBP) in high glucose-mediated repression of long noncoding RNA Tug1" (PDF). Journal of Biological Chemistry. 5 (28). doi:10.1074/jbc.RA120.013228. Retrieved 6 October 2020.