Gcn4p gene transcriptions: Difference between revisions

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# Gcn4r3: 2, TGACTCT at 4481, TGACTCT at 2451.
# Gcn4r3: 2, TGACTCT at 4481, TGACTCT at 2451.
# Gcn4r4: 6, TGATTGT at 3795, TGAGTAA at 3403, TGACTCA at 2963, TGAGTGT at 2573, TGAGTCA at 2248, TGAGTGA at 1000.
# Gcn4r4: 6, TGATTGT at 3795, TGAGTAA at 3403, TGACTCA at 2963, TGAGTGT at 2573, TGAGTCA at 2248, TGAGTGA at 1000.
# Gcn4r5: 0.
# Gcn4r5: 2, TGAGTCA at 4249, TGATTAA at 4204.
# Gcn4r6: 0.
# Gcn4r6: 4, TGATTCT at 3178, TGACTCA at 2045, TGATTCA at 283, TGATTCT at 260.
# Gcn4r7: 0.
# Gcn4r7: 1, TGACTAA at 4046.
# Gcn4r8: 0.
# Gcn4r8: 0.
# Gcn4r9: 0.
# Gcn4r9: 0.

Revision as of 05:42, 10 August 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) 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:

  1. 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.
  2. 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.
  3. 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.
  4. 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.
  5. 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.
  6. complement, negative strand, positive direction, looking for ACT(A/C/G)A(C/G/T)(A/T), 2, ACTCACT at 4338, ACTGATT at 2676.
  7. complement, positive strand, negative direction, looking for ACT(A/C/G)A(C/G/T)(A/T), 2, ACTCAGA at 3644, ACTGATA at 3544.
  8. 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.
  9. 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.
  10. 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.
  11. 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.
  12. 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.
  13. 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.
  14. 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.
  15. inverse positive strand, negative direction, looking for (A/T)(A/C/G)T(C/G/T)AGT, 2, TGTGAGT at 4094, TATGAGT at 276.
  16. 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.

Gcn4 core promoters

Main article: Core promoter gene transcriptions

Negative strand, positive direction: ACACTCA at 4336, and complement.

Positive strand, positive direction: TGAGTGA at 4338, and complement.

Gcn4 proximal promoters

Main article: Proximal promoter gene transcriptions

Negative strand, positive direction: TGATTAT at 4165, TGATTAT at 4158, TTAATCA at 4147, and complements.

Gcn4 distal promoters

Main article: Distal promoter gene transcriptions

Negative strand, negative direction: ACACTCA at 4094, TGAGTCT at 3644, TGACTAT at 3544, ATACTCA at 276, and complements.

Positive strand, negative direction: AGACTCA at 4055, TGAGTAT at 3829, AGAATCA at 3237, TGACTCT at 2788, AGACTCA at 1404, AGAATCA at 293, TGAGTCT at 278, AGAATCA at 198, and complements.

Negative strand, positive direction: TGAGTGA at 3712, TGAGTGT at 3592, TGATTGT at 2678, AGAGTCA at 2613, TCAGTCA at 2100, and complements.

Positive strand, positive direction: TTACTCA at 3447, AGACTCA at 3008, AGACTCA at 2952, TGACTAA at 2676, and complement.

Tang random dataset samplings

  1. Gcn4r0: 2, TGAGTGA at 743, TGACTAT at 706.
  2. Gcn4r1: 1, TGATTAA at 2851.
  3. Gcn4r2: 2, TGAGTAA at 3017, TGATTCA at 489.
  4. Gcn4r3: 2, TGACTCT at 4481, TGACTCT at 2451.
  5. Gcn4r4: 6, TGATTGT at 3795, TGAGTAA at 3403, TGACTCA at 2963, TGAGTGT at 2573, TGAGTCA at 2248, TGAGTGA at 1000.
  6. Gcn4r5: 2, TGAGTCA at 4249, TGATTAA at 4204.
  7. Gcn4r6: 4, TGATTCT at 3178, TGACTCA at 2045, TGATTCA at 283, TGATTCT at 260.
  8. Gcn4r7: 1, TGACTAA at 4046.
  9. Gcn4r8: 0.
  10. Gcn4r9: 0.
  11. Gcn4r0ci: 0.
  12. Gcn4r1ci: 0.
  13. Gcn4r2ci: 0.
  14. Gcn4r3ci: 0.
  15. Gcn4r4ci: 0.
  16. Gcn4r5ci: 0.
  17. Gcn4r6ci: 0.
  18. Gcn4r7ci: 0.
  19. Gcn4r8ci: 0.
  20. Gcn4r9ci: 0.

Gcn4r UTRs

Main article: UTR promoter gene transcriptions

Gcn4r core promoters

Main article: Core promoter gene transcriptions

Gcn4r proximal promoters

Main article: Proximal promoter gene transcriptions

Gcn4r distal promoters

Main article: Distal promoter gene transcriptions

See also

References

  1. ↑ 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. ↑ 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.

External links

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