Gcn4p gene transcriptions: Difference between revisions
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{{AE}} Henry A. Hoff | {{AE}} Henry A. Hoff | ||
"The saturation mutagenesis of the transcription factor Gcn4p’s binding site (5′-ATGACTCTT-3′) within the ''HIS3'' promoter found that almost all mismatch mutants reduced the PHIS3 activity significantly and only one mutant with the sequence 5′-ATGACTCAT-3′ increased the binding affinity of Gcn4p and improved the P<sub>HIS3</sub> activity [82]. It has been shown that regulatory regions containing multiple UAS or URS sites for binding the same transcription factor could enhance their activation or repression of transcription. In a test of 15 transcription factors, such as Gal4p, Gcn4p, Bas1p, increasing the number of their UAS sites improved promoter activities; similarly, promoters with multiple URS sites showed a stronger repression, such as Matα2p-Mcm1p."<ref name=Tang/> | "The saturation mutagenesis of the transcription factor [general control nonderepressible gene protein] Gcn4p’s binding site (5′-ATGACTCTT-3′) within the ''HIS3'' promoter found that almost all mismatch mutants reduced the PHIS3 activity significantly and only one mutant with the sequence 5′-ATGACTCAT-3′ increased the binding affinity of Gcn4p and improved the P<sub>HIS3</sub> activity [82]. It has been shown that regulatory regions containing multiple UAS or URS sites for binding the same transcription factor could enhance their activation or repression of transcription. In a test of 15 transcription factors, such as Gal4p, Gcn4p, Bas1p, increasing the number of their UAS sites improved promoter activities; similarly, promoters with multiple URS sites showed a stronger repression, such as Matα2p-Mcm1p."<ref name=Tang/> | ||
==Human genes== | ==Human genes== | ||
| Line 25: | Line 25: | ||
|pmid=32781665 | |pmid=32781665 | ||
|accessdate=18 September 2020 }}</ref> | |accessdate=18 September 2020 }}</ref> | ||
"The program DNA-Pattern was used to search for and catalogue occurrences of consensus GCRE (TGABTVW) [TGA(C/G/T)T(A/C/G)(A/T)] and GATA (GATAAG, GATAAH, GATTA) motifs in yeast promoters."<ref name=Staschke>{{ cite journal | |||
|author=Kirk A. Staschke, Souvik Dey, John M. Zaborske, Lakshmi Reddy Palam, Jeanette N. McClintick, Tao Pan, Howard J. Edenberg, and Ronald C. Wek | |||
|title=Integration of General Amino Acid Control and Target of Rapamycin (TOR) Regulatory Pathways in Nitrogen | |||
Assimilation in Yeast | |||
|journal=The Journal of Biological Chemistry | |||
|date=May 28, 2010 | |||
|volume=285 | |||
|issue=22 | |||
|pages=16893–16911 | |||
|url=https://www.jbc.org/content/285/22/16893.full.pdf | |||
|arxiv= | |||
|bibcode= | |||
|doi=10.1074/jbc.M110.121947 | |||
|pmid= | |||
|accessdate=4 January 2021 }}</ref> | |||
"The predicted Gln3p and Gcn4p binding sites in the UGA3 promoter are [...] the consensus Gln3p (GATA) [CTTATG] and Gcn4p (GCRE) [TGAGTCA] binding sites present in the minimal UGA3 promoter at -206 and -112, respectively, [...]."<ref name=Staschke/> | |||
==Samplings== | ==Samplings== | ||
| Line 30: | Line 48: | ||
Copying 5'-ATGACTCTT-3' in "⌘F" yields none between ZSCAN22 and A1BG and none between ZNF497 and A1BG as can be found by the computer programs. | Copying 5'-ATGACTCTT-3' in "⌘F" yields none between ZSCAN22 and A1BG and none between ZNF497 and A1BG as can be found by the computer programs. | ||
For the Basic programs testing consensus sequence | For the Basic programs testing consensus sequence TGA(C/G/T)T(A/C/G)(A/T) (starting with SuccessablesGcn4.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 | # negative strand, negative direction, looking for TGA(C/G/T)T(A/C/G)(A/T), 2, TGAGTCT at 3644, TGACTAT at 3544, and complements. | ||
# negative strand, positive direction, looking for | # negative strand, positive direction, looking for TGA(C/G/T)T(A/C/G)(A/T), 5, TGATTAT at 4165, TGATTAT at 4158, TGAGTGA at 3712, TGAGTGT at 3592, TGATTGT at 2678, and complements. | ||
# positive strand, negative direction, looking for | # positive strand, negative direction, looking for TGA(C/G/T)T(A/C/G)(A/T), 3, TGAGTAT at 3829, TGACTCT at 2788, TGAGTCT at 278, and complements. | ||
# positive strand, positive direction, looking for | # positive strand, positive direction, looking for TGA(C/G/T)T(A/C/G)(A/T), 2, TGAGTGA at 4338, TGACTAA at 2676, and complements. | ||
# complement, negative strand, negative direction, looking for | # complement, negative strand, negative direction, looking for ACT(A/C/G)A(C/G/T)(A/T), 3, ACTCATA at 3829, ACTGAGA at 2788, ACTCAGA at 278. | ||
# complement, negative strand, positive direction, looking for | # complement, negative strand, positive direction, looking for ACT(A/C/G)A(C/G/T)(A/T), 2, ACTCACT at 4338, ACTGATT at 2676. | ||
# complement, positive strand, negative direction, looking for | # complement, positive strand, negative direction, looking for ACT(A/C/G)A(C/G/T)(A/T), 2, ACTCAGA at 3644, ACTGATA at 3544. | ||
# complement, positive strand, positive direction, looking for | # complement, positive strand, positive direction, looking for ACT(A/C/G)A(C/G/T)(A/T), 5, ACTAATA at 4165, ACTAATA at 4158, ACTCACT at 3712, ACTCACA at 3592, ACTAACA at 2678. | ||
# inverse complement, negative strand, negative direction, looking for | # inverse complement, negative strand, negative direction, looking for (A/T)(C/G/T)A(A/C/G)TCA, 2, ACACTCA at 4094, ATACTCA at 276, and complements. | ||
# inverse complement, negative strand, positive direction, looking for | # inverse complement, negative strand, positive direction, looking for (A/T)(C/G/T)A(A/C/G)TCA, 4, ACACTCA at 4336, TTAATCA at 4147, AGAGTCA at 2613, TCAGTCA at 2100, and complements. | ||
# inverse complement, positive strand, negative direction, looking for | # inverse complement, positive strand, negative direction, looking for (A/T)(C/G/T)A(A/C/G)TCA, 5, AGACTCA at 4055, AGAATCA at 3237, AGACTCA at 1404, AGAATCA at 293, AGAATCA at 198, and complements. | ||
# inverse complement, positive strand, positive direction, looking for | # inverse complement, positive strand, positive direction, looking for (A/T)(C/G/T)A(A/C/G)TCA, 3, TTACTCA at 3447, AGACTCA at 3008, AGACTCA at 2952, and complements. | ||
# inverse negative strand, negative direction, looking for | # inverse negative strand, negative direction, looking for (A/T)(A/C/G)T(C/G/T)AGT, 5, TCTGAGT at 4055, TCTTAGT at 3237, TCTGAGT at 1404, TCTTAGT at 293, TCTTAGT at 198. | ||
# inverse negative strand, positive direction, looking for | # inverse negative strand, positive direction, looking for (A/T)(A/C/G)T(C/G/T)AGT, 3, AATGAGT at 3447, TCTGAGT at 3008, TCTGAGT at 2952. | ||
# inverse positive strand, negative direction, looking for | # inverse positive strand, negative direction, looking for (A/T)(A/C/G)T(C/G/T)AGT, 2, TGTGAGT at 4094, TATGAGT at 276. | ||
# inverse positive strand, positive direction, looking for | # inverse positive strand, positive direction, looking for (A/T)(A/C/G)T(C/G/T)AGT, 4, TGTGAGT at 4336, AATTAGT at 4147, TCTCAGT at 2613, AGTCAGT at 2100. | ||
===AAA core promoters=== | ===AAA core promoters=== | ||
Revision as of 20:35, 4 January 2021
Associate Editor(s)-in-Chief: Henry A. Hoff
"The saturation mutagenesis of the transcription factor [general control nonderepressible gene protein] Gcn4p’s binding site (5′-ATGACTCTT-3′) within the HIS3 promoter found that almost all mismatch mutants reduced the PHIS3 activity significantly and only one mutant with the sequence 5′-ATGACTCAT-3′ increased the binding affinity of Gcn4p and improved the PHIS3 activity [82]. It has been shown that regulatory regions containing multiple UAS or URS sites for binding the same transcription factor could enhance their activation or repression of transcription. In a test of 15 transcription factors, such as Gal4p, Gcn4p, Bas1p, increasing the number of their UAS sites improved promoter activities; similarly, promoters with multiple URS sites showed a stronger repression, such as Matα2p-Mcm1p."[1]
Human genes
Interactions
The "transcription factor Rap1p not only depleted the nucleosome from its own binding site of the HIS4 promoter, but also reduced a nearby nucleosome to increase the accessibility of other transcription factors, including Gcn4p, Bas1p, Bas2p [102]."[1]
Consensus sequences
UAS Sequence for the transcription factor Gcn4p is 5'-ATGACTCTT-3'.[1]
"The program DNA-Pattern was used to search for and catalogue occurrences of consensus GCRE (TGABTVW) [TGA(C/G/T)T(A/C/G)(A/T)] and GATA (GATAAG, GATAAH, GATTA) motifs in yeast promoters."[2]
"The predicted Gln3p and Gcn4p binding sites in the UGA3 promoter are [...] the consensus Gln3p (GATA) [CTTATG] and Gcn4p (GCRE) [TGAGTCA] binding sites present in the minimal UGA3 promoter at -206 and -112, respectively, [...]."[2]
Samplings
Copying 5'-ATGACTCTT-3' in "⌘F" yields none between ZSCAN22 and A1BG and none between ZNF497 and A1BG as can be found by the computer programs.
For the Basic programs testing consensus sequence TGA(C/G/T)T(A/C/G)(A/T) (starting with SuccessablesGcn4.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 TGA(C/G/T)T(A/C/G)(A/T), 2, TGAGTCT at 3644, TGACTAT at 3544, and complements.
- negative strand, positive direction, looking for TGA(C/G/T)T(A/C/G)(A/T), 5, TGATTAT at 4165, TGATTAT at 4158, TGAGTGA at 3712, TGAGTGT at 3592, TGATTGT at 2678, and complements.
- positive strand, negative direction, looking for TGA(C/G/T)T(A/C/G)(A/T), 3, TGAGTAT at 3829, TGACTCT at 2788, TGAGTCT at 278, and complements.
- positive strand, positive direction, looking for TGA(C/G/T)T(A/C/G)(A/T), 2, TGAGTGA at 4338, TGACTAA at 2676, and complements.
- complement, negative strand, negative direction, looking for ACT(A/C/G)A(C/G/T)(A/T), 3, ACTCATA at 3829, ACTGAGA at 2788, ACTCAGA at 278.
- complement, negative strand, positive direction, looking for ACT(A/C/G)A(C/G/T)(A/T), 2, ACTCACT at 4338, ACTGATT at 2676.
- complement, positive strand, negative direction, looking for ACT(A/C/G)A(C/G/T)(A/T), 2, ACTCAGA at 3644, ACTGATA at 3544.
- complement, positive strand, positive direction, looking for ACT(A/C/G)A(C/G/T)(A/T), 5, ACTAATA at 4165, ACTAATA at 4158, ACTCACT at 3712, ACTCACA at 3592, ACTAACA at 2678.
- inverse complement, negative strand, negative direction, looking for (A/T)(C/G/T)A(A/C/G)TCA, 2, ACACTCA at 4094, ATACTCA at 276, and complements.
- inverse complement, negative strand, positive direction, looking for (A/T)(C/G/T)A(A/C/G)TCA, 4, ACACTCA at 4336, TTAATCA at 4147, AGAGTCA at 2613, TCAGTCA at 2100, and complements.
- inverse complement, positive strand, negative direction, looking for (A/T)(C/G/T)A(A/C/G)TCA, 5, AGACTCA at 4055, AGAATCA at 3237, AGACTCA at 1404, AGAATCA at 293, AGAATCA at 198, and complements.
- inverse complement, positive strand, positive direction, looking for (A/T)(C/G/T)A(A/C/G)TCA, 3, TTACTCA at 3447, AGACTCA at 3008, AGACTCA at 2952, and complements.
- inverse negative strand, negative direction, looking for (A/T)(A/C/G)T(C/G/T)AGT, 5, TCTGAGT at 4055, TCTTAGT at 3237, TCTGAGT at 1404, TCTTAGT at 293, TCTTAGT at 198.
- inverse negative strand, positive direction, looking for (A/T)(A/C/G)T(C/G/T)AGT, 3, AATGAGT at 3447, TCTGAGT at 3008, TCTGAGT at 2952.
- inverse positive strand, negative direction, looking for (A/T)(A/C/G)T(C/G/T)AGT, 2, TGTGAGT at 4094, TATGAGT at 276.
- inverse positive strand, positive direction, looking for (A/T)(A/C/G)T(C/G/T)AGT, 4, TGTGAGT at 4336, AATTAGT at 4147, TCTCAGT at 2613, AGTCAGT at 2100.
AAA core promoters
AAA proximal promoters
AAA distal promoters
See also
References
- ↑ 1.0 1.1 1.2 Hongting Tang, Yanling Wu, Jiliang Deng, Nanzhu Chen, Zhaohui Zheng, Yongjun Wei, Xiaozhou Luo, and Jay D. Keasling (6 August 2020). "Promoter Architecture and Promoter Engineering in Saccharomyces cerevisiae". Metabolites. 10 (8): 320–39. doi:10.3390/metabo10080320. PMID 32781665 Check
|pmid=value (help). Retrieved 18 September 2020. - ↑ 2.0 2.1 Kirk A. Staschke, Souvik Dey, John M. Zaborske, Lakshmi Reddy Palam, Jeanette N. McClintick, Tao Pan, Howard J. Edenberg, and Ronald C. Wek (May 28, 2010). "Integration of General Amino Acid Control and Target of Rapamycin (TOR) Regulatory Pathways in Nitrogen Assimilation in Yeast" (PDF). The Journal of Biological Chemistry. 285 (22): 16893–16911. doi:10.1074/jbc.M110.121947. Retrieved 4 January 2021. line feed character in
|title=at position 104 (help)