A box gene transcriptions: Difference between revisions
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"A<sup>S/T</sup>, serine/threonine-rich subdomain within the A box".<ref name=Jin/> "A<sup>Q</sup>, glutamine-rich subdomain within the A box".<ref name=Jin/> | "A<sup>S/T</sup>, serine/threonine-rich subdomain within the A box".<ref name=Jin/> "A<sup>Q</sup>, glutamine-rich subdomain within the A box".<ref name=Jin/> | ||
==Consensus sequences== | |||
{{main|Consensus sequence gene transcriptions}} | |||
"The human [Transforming growth factor b1] TGFB1 promoter region contains two binding sequences for [Activator protein-1] AP-1, designated AP-1 box A (TGACTCT) and box B (TGTCTCA), which mediate the upregulation of promoter activity via a PKC-dependent pathway after exposure of cells to a high-glucose environment (Refs 37, 38)."<ref name=Paratore>{{ cite journal | "The human [Transforming growth factor b1] TGFB1 promoter region contains two binding sequences for [Activator protein-1] AP-1, designated AP-1 box A (TGACTCT) and box B (TGTCTCA), which mediate the upregulation of promoter activity via a PKC-dependent pathway after exposure of cells to a high-glucose environment (Refs 37, 38)."<ref name=Paratore>{{ cite journal | ||
|author=Amber Paratore Sanchez and Kumar Sharma | |author=Amber Paratore Sanchez and Kumar Sharma | ||
| Line 31: | Line 33: | ||
|pmid= | |pmid= | ||
|accessdate=1 October 2018 }}</ref> | |accessdate=1 October 2018 }}</ref> | ||
Most bZIP proteins show high binding affinity for the ACGT motifs, which include [...] TACGTA (A box) [...].<ref name=Landschulz>{{ cite journal | |||
| vauthors = Landschulz WH, Johnson PF, McKnight SL | title = The leucine zipper: a hypothetical structure common to a new class of DNA binding proteins | journal = Science | volume = 240 | issue = 4860 | pages = 1759–64 | date = June 1988 | pmid = 3289117 | |||
| doi = 10.1126/science.3289117 | bibcode = 1988Sci...240.1759L | |||
| url = https://semanticscholar.org/paper/3a61c172ddfa79ce9f4909ca6bea2f6f40f7893e }}</ref><ref name=Zhang2014>{{ cite journal | |||
| vauthors = Z G E, Zhang YP, Zhou JH, Wang L | |||
| title = Mini review roles of the bZIP gene family in rice | |||
| journal = Genetics and Molecular Research | |||
| volume = 13 | |||
| issue = 2 | |||
| pages = 3025–36 | |||
| date = April 2014 | |||
| pmid = 24782137 | |||
| doi = 10.4238/2014.April.16.11 }}</ref><ref name=Nijhawan>{{ cite journal | vauthors = Nijhawan A, Jain M, Tyagi AK, Khurana JP | |||
| title = Genomic survey and gene expression analysis of the basic leucine zipper transcription factor family in rice | |||
| journal = Plant Physiology | |||
| volume = 146 | |||
| issue = 2 | |||
| pages = 333–50 | |||
| date = February 2008 | |||
| pmid = 18065552 | |||
| doi = 10.1104/pp.107.112821 }}</ref> | |||
"The human TGF-β1 promoter region contains two binding sequences for AP-1, designated AP-1 box A (TGACTCT) and box B (TGTCTCA), which mediate the up-regulation of promoter activity after [High glucose] HG stimulation."<ref name=Kokoroishi>{{ cite journal | |||
|author=Keiko Kokoroishi, Ayumu Nakashima, Shigehiro Doi, Toshinori Ueno, Toshiki Doi, Yukio Yokoyama, Kiyomasa Honda, Masami Kanawa, Yukio Kato, Nobuoki Kohno & Takao Masaki | |||
|title=High glucose promotes TGF-β1 production by inducing FOS expression in human peritoneal mesothelial cells | |||
|journal=Clinical and Experimental Nephrology | |||
|date=28 May 2015 | |||
|volume=20 | |||
|issue=1 | |||
|pages=30-8 | |||
|url=https://link.springer.com/article/10.1007/s10157-015-1128-9 | |||
|arxiv= | |||
|bibcode= | |||
|doi=10.1007/s10157-015-1128-9 | |||
|pmid=26018137 | |||
|accessdate=14 August 2020 }}</ref> | |||
==Hypotheses== | ==Hypotheses== | ||
# A1BG has no A boxes in either promoter. | # A1BG has no A boxes in either promoter. | ||
# A1BG is not transcribed by an A box. | |||
# An A box does not participate in the transcription of A1BG. | |||
==Samplings== | ==Samplings== | ||
| Line 61: | Line 102: | ||
# inverse positive strand in the negative direction (from ZSCAN22 to A1BG) is SuccessablesAboxi+-.bas, looking for 3'-TCTCAGT-5', 0. | # inverse positive strand in the negative direction (from ZSCAN22 to A1BG) is SuccessablesAboxi+-.bas, looking for 3'-TCTCAGT-5', 0. | ||
# inverse positive strand in the positive direction (from ZNF497 to A1BG) is SuccessablesAboxi++.bas, looking for 3'-TCTCAGT-5', 1, 3'-TCTCAGT-5' at 2613. | # inverse positive strand in the positive direction (from ZNF497 to A1BG) is SuccessablesAboxi++.bas, looking for 3'-TCTCAGT-5', 1, 3'-TCTCAGT-5' at 2613. | ||
==Core promoters== | |||
{{main|Core promoter gene transcriptions}} | |||
==Proximal promoters== | |||
{{main|Proximal promoter gene transcriptions}} | |||
==Distal promoters== | |||
{{main|Distal promoter gene transcriptions}} | |||
Negative direction: 3'-TGACTCT-5' at 2788 and complement. | |||
Positive direction: 3'-TCTCAGT-5' at 2613 and complement. | |||
==Acknowledgements== | ==Acknowledgements== | ||
Revision as of 21:24, 7 October 2020
Associate Editor(s)-in-Chief: Henry A. Hoff
The GC boxes are not apparently associated with the A box, B box, C box, and D box.[1]
"AS/T, serine/threonine-rich subdomain within the A box".[1] "AQ, glutamine-rich subdomain within the A box".[1]
Consensus sequences
"The human [Transforming growth factor b1] TGFB1 promoter region contains two binding sequences for [Activator protein-1] AP-1, designated AP-1 box A (TGACTCT) and box B (TGTCTCA), which mediate the upregulation of promoter activity via a PKC-dependent pathway after exposure of cells to a high-glucose environment (Refs 37, 38)."[2]
Most bZIP proteins show high binding affinity for the ACGT motifs, which include [...] TACGTA (A box) [...].[3][4][5]
"The human TGF-β1 promoter region contains two binding sequences for AP-1, designated AP-1 box A (TGACTCT) and box B (TGTCTCA), which mediate the up-regulation of promoter activity after [High glucose] HG stimulation."[6]
Hypotheses
- A1BG has no A boxes in either promoter.
- A1BG is not transcribed by an A box.
- An A box does not participate in the transcription of A1BG.
Samplings
3-TGACTCT-5' was not found using "⌘F" to locate any consensus sequences.
Regarding hypothesis 1
Hypothesis 1: A1BG is not transcribed by an A box.
For the Basic programs testing consensus sequence 3'-TGACTCT-5' (starting with SuccessablesAbox.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 SuccessablesAbox--.bas, looking for 3'-TGACTCT-5', 0.
- negative strand in the positive direction (from ZNF497 to A1BG) is SuccessablesAbox-+.bas, looking for 3'-TGACTCT-5', 0.
- positive strand in the negative direction (from ZSCAN22 to A1BG) is SuccessablesAbox+-.bas, looking for 3'-TGACTCT-5', 1, 3'-TGACTCT-5' at 2788.
- positive strand in the positive direction (from ZNF497 to A1BG) is SuccessablesAbox++.bas, looking for 3'-TGACTCT-5', 0.
- complement, negative strand, negative direction is SuccessablesAboxc--.bas, looking for 3'-ACTGAGA-5', 1, 3'-ACTGAGA-5' at 2788.
- complement, negative strand in the positive direction (from ZNF497 to A1BG) is SuccessablesAboxc-+.bas, looking for 3'-ACTGAGA-5', 0.
- complement, positive strand in the negative direction (from ZSCAN22 to A1BG) is SuccessablesAboxc+-.bas, looking for 3'-ACTGAGA-5', 0.
- complement, positive strand in the positive direction (from ZNF497 to A1BG) is SuccessablesAboxc++.bas, looking for 3'-ACTGAGA-5', 0.
- inverse complement, negative strand, negative direction is SuccessablesAboxci--.bas, looking for 3'-AGAGTCA-5', 0.
- inverse complement, negative strand in the positive direction (from ZNF497 to A1BG) is SuccessablesAboxci-+.bas, looking for 3'-AGAGTCA-5', 1, 3'-AGAGTCA-5' at 2613.
- inverse complement, positive strand in the negative direction (from ZSCAN22 to A1BG) is SuccessablesAboxci+-.bas, looking for 3'-AGAGTCA-5', 0.
- inverse complement, positive strand in the positive direction (from ZNF497 to A1BG) is SuccessablesAboxci++.bas, looking for 3'-AGAGTCA-5', 0.
- inverse negative strand in the negative direction (from ZSCAN22 to A1BG) is SuccessablesAboxi--.bas, looking for 3'-TCTCAGT-5', 0.
- inverse negative strand in the positive direction (from ZNF497 to A1BG) is SuccessablesAboxi-+.bas, looking for 3'-TCTCAGT-5', 0.
- inverse positive strand in the negative direction (from ZSCAN22 to A1BG) is SuccessablesAboxi+-.bas, looking for 3'-TCTCAGT-5', 0.
- inverse positive strand in the positive direction (from ZNF497 to A1BG) is SuccessablesAboxi++.bas, looking for 3'-TCTCAGT-5', 1, 3'-TCTCAGT-5' at 2613.
Core promoters
Proximal promoters
Distal promoters
Negative direction: 3'-TGACTCT-5' at 2788 and complement.
Positive direction: 3'-TCTCAGT-5' at 2613 and complement.
Acknowledgements
The content on this page was first contributed by: Henry A. Hoff.
See also
References
- ↑ 1.0 1.1 1.2 Huajun Jin, Arthi Kanthasamy, Dilshan S. Harischandra, Naveen Kondru, Anamitra Ghosh, Nikhil Panicker, Vellareddy Anantharam, Ajay Rana, and Anumantha G. Kanthasamy (December 12, 2014). "Histone Hyperacetylation Up-regulates Protein Kinase C in Dopaminergic Neurons to Induce Cell Death RELEVANCE TO EPIGENETIC MECHANISMS OF NEURODEGENERATION IN PARKINSON DISEASE" (PDF). 289 (50): 34743–34767. doi:10.1074/jbc.M114.576702. Retrieved 10 April 2019.
- ↑ Amber Paratore Sanchez and Kumar Sharma (July 2009). "Transcription factors in the pathogenesis of diabetic nephropathy". Expert Reviews in Molecular Medicine. 11: e13. doi:10.1017/S1462399409001057. Retrieved 1 October 2018.
- ↑ Landschulz WH, Johnson PF, McKnight SL (June 1988). "The leucine zipper: a hypothetical structure common to a new class of DNA binding proteins". Science. 240 (4860): 1759–64. Bibcode:1988Sci...240.1759L. doi:10.1126/science.3289117. PMID 3289117.
- ↑ Z G E, Zhang YP, Zhou JH, Wang L (April 2014). "Mini review roles of the bZIP gene family in rice". Genetics and Molecular Research. 13 (2): 3025–36. doi:10.4238/2014.April.16.11. PMID 24782137. Vancouver style error: name (help)
- ↑ Nijhawan A, Jain M, Tyagi AK, Khurana JP (February 2008). "Genomic survey and gene expression analysis of the basic leucine zipper transcription factor family in rice". Plant Physiology. 146 (2): 333–50. doi:10.1104/pp.107.112821. PMID 18065552.
- ↑ Keiko Kokoroishi, Ayumu Nakashima, Shigehiro Doi, Toshinori Ueno, Toshiki Doi, Yukio Yokoyama, Kiyomasa Honda, Masami Kanawa, Yukio Kato, Nobuoki Kohno & Takao Masaki (28 May 2015). "High glucose promotes TGF-β1 production by inducing FOS expression in human peritoneal mesothelial cells". Clinical and Experimental Nephrology. 20 (1): 30–8. doi:10.1007/s10157-015-1128-9. PMID 26018137. Retrieved 14 August 2020.
External links