Gcn4p gene transcriptions: Difference between revisions

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Copying ATGACTCA in "⌘F" yields none between ZSCAN22 and A1BG on the positive strand.
Copying ATGACTCA in "⌘F" yields none between ZSCAN22 and A1BG on the positive strand.


Copying ATGACTC(A/T)T in "⌘F" yields none between ZSCAN22 and A1BG and none between ZNF497 and A1BG as can be found by the computer programs.
Copying ATGACTC(A/T)T in "⌘F" yields none between ZSCAN22 and A1BG and none between ZNF497 and A1BG as can be found by the computer programs:
 
# Negative strand, negative direction: 0.
# Positive strand, negative direction: 0.
# Negative strand, positive direction: 0.
# Positive strand, positive direction: 0.
# ci Negative strand, negative direction: 0.
# ci Positive strand, negative direction: 0.
# ci Negative strand, positive direction: 0.
# ci Positive strand, positive direction: 0.


==Consensus sequences (Staschke)==
==Consensus sequences (Staschke)==

Revision as of 22:17, 15 November 2022

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 (Tang)

UAS Sequence for the transcription factor Gcn4p binding site is ATGACTCTT.[1]

Gcn4p binding site (Tang) samplings

Copying ATGACTC in "⌘F" yields none between ZNF497 and A1BG on the negative strand.

Copying ATGACTCT in "⌘F" yields none between ZNF497 and A1BG on the positive strand.

Copying ATGACTCA in "⌘F" yields none between ZNF497 and A1BG on the positive strand.

Copying ATGACTC in "⌘F" yields none between ZSCAN22 and A1BG on the negative strand.

Copying ATGACTCTT in "⌘F" yields none between ZSCAN22 and A1BG on the positive strand.

Copying ATGACTCA in "⌘F" yields none between ZSCAN22 and A1BG on the positive strand.

Copying ATGACTC(A/T)T in "⌘F" yields none between ZSCAN22 and A1BG and none between ZNF497 and A1BG as can be found by the computer programs:

  1. Negative strand, negative direction: 0.
  2. Positive strand, negative direction: 0.
  3. Negative strand, positive direction: 0.
  4. Positive strand, positive direction: 0.
  5. ci Negative strand, negative direction: 0.
  6. ci Positive strand, negative direction: 0.
  7. ci Negative strand, positive direction: 0.
  8. ci Positive strand, positive direction: 0.

Consensus sequences (Staschke)

"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]

GCRE samplings

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.

GCRE UTRs

  1. Negative strand, negative direction: ACACTCA at 4094, TGAGTCT at 3644, TGACTAT at 3544.
  2. Positive strand, negative direction: AGACTCA at 4055, TGAGTAT at 3829, AGAATCA at 3237.

GCRE core promoters

Main article: Core promoter gene transcriptions
  1. Negative strand, positive direction: ACACTCA at 4336.
  2. Positive strand, positive direction: TGAGTGA at 4338.

GCRE proximal promoters

Main article: Proximal promoter gene transcriptions
  1. Positive strand, negative direction: TGACTCT at 2788.


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

GCRE distal promoters

Main article: Distal promoter gene transcriptions
  1. Negative strand, negative direction: ATACTCA at 276.
  2. Positive strand, negative direction: AGACTCA at 1404, AGAATCA at 293, TGAGTCT at 278, AGAATCA at 198.
  1. Negative strand, positive direction: TGAGTGA at 3712, TGAGTGT at 3592, TGATTGT at 2678, AGAGTCA at 2613, TCAGTCA at 2100.
  2. Positive strand, positive direction: TTACTCA at 3447, AGACTCA at 3008, AGACTCA at 2952, TGACTAA at 2676.

GCRE 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: 2, TGAGTAA at 1966, TGATTGA at 1177.
  10. Gcn4r9: 7, TGACTAA at 4474, TGAGTAT at 4268, TGATTGA at 4264, TGACTGA at 4207, TGACTAA at 3706, TGACTCT at 3523, TGACTCA at 2082.
  11. Gcn4r0ci: 2, TTAGTCA at 3188, TCACTCA at 2589.
  12. Gcn4r1ci: 1, TTAATCA at 3460.
  13. Gcn4r2ci: 3, TTACTCA at 4306, TTAGTCA at 2899, TCAATCA at 71.
  14. Gcn4r3ci: 6, ATACTCA at 4179, TCAATCA at 1655, TGAATCA at 1555, TTAATCA at 1352, AGAGTCA at 477, AGACTCA at 216.
  15. Gcn4r4ci: 7, ATAGTCA at 4258, ATAATCA at 4118, TGACTCA at 2963, TTACTCA at 2650, TGAGTCA at 2248, TTACTCA at 1137, ACACTCA at 626.
  16. Gcn4r5ci: 4, TGAGTCA at 4249, ACACTCA at 4026, ATAATCA at 3215, TTAGTCA at 1354.
  17. Gcn4r6ci: 7, AGAGTCA at 4503, AGAGTCA at 4449, TGACTCA at 2045, ACACTCA at 1842, TCAATCA at 1836, AGAGTCA at 1109, TTAATCA at 35.
  18. Gcn4r7ci: 4, AGACTCA at 3443, TCAATCA at 1137, ACAGTCA at 1014, ACAGTCA at 202.
  19. Gcn4r8ci: 2, TTACTCA at 2158, ATAATCA at 1749.
  20. Gcn4r9ci: 5, TTAATCA at 3367, ATACTCA at 3248, TGACTCA at 2082, ATACTCA at 1195, TCAGTCA at 106.

GCREr UTRs

Main article: UTR promoter gene transcriptions
  1. Gcn4r2: TGAGTAA at 3017.
  2. Gcn4r4: TGATTGT at 3795, TGAGTAA at 3403, TGACTCA at 2963.
  3. Gcn4r6: TGATTCT at 3178.
  4. Gcn4r0ci: TTAGTCA at 3188.
  5. Gcn4r2ci: TTACTCA at 4306, TTAGTCA at 2899.
  6. Gcn4r4ci: ATAGTCA at 4258, ATAATCA at 4118, TGACTCA at 2963.
  7. Gcn4r6ci: AGAGTCA at 4503, AGAGTCA at 4449.

GCREr core promoters

Main article: Core promoter gene transcriptions
  1. Gcn4r3: TGACTCT at 4481.
  2. Gcn4r9: TGACTAA at 4474, TGAGTAT at 4268.

GCREr proximal promoters

Main article: Proximal promoter gene transcriptions
  1. Gcn4r4ci: TTACTCA at 2650.


  1. Gcn4r5: TGAGTCA at 4249, TGATTAA at 4204.
  2. Gcn4r7: TGACTAA at 4046.
  3. Gcn4r9: TGATTGA at 4264, TGACTGA at 4207.
  4. Gcn4r3ci: ATACTCA at 4179.
  5. Gcn4r5ci: TGAGTCA at 4249.

GCREr distal promoters

Main article: Distal promoter gene transcriptions
  1. Gcn4r0: TGAGTGA at 743, TGACTAT at 706.
  2. Gcn4r2: TGATTCA at 489.
  3. Gcn4r4: TGAGTGT at 2573, TGAGTCA at 2248, TGAGTGA at 1000.
  4. Gcn4r6: TGACTCA at 2045, TGATTCA at 283, TGATTCT at 260.
  5. Gcn4r8: TGAGTAA at 1966, TGATTGA at 1177.
  6. Gcn4r0ci: TCACTCA at 2589.
  7. Gcn4r2ci: TCAATCA at 71.
  8. Gcn4r4ci: TGAGTCA at 2248, TTACTCA at 1137, ACACTCA at 626.
  9. Gcn4r6ci: TGACTCA at 2045, ACACTCA at 1842, TCAATCA at 1836, AGAGTCA at 1109, TTAATCA at 35.
  10. Gcn4r8ci: TTACTCA at 2158, ATAATCA at 1749.


  1. Gcn4r1: TGATTAA at 2851.
  2. Gcn4r3: TGACTCT at 2451.
  3. Gcn4r7: TGACTAA at 4046.
  4. Gcn4r9: TGACTAA at 3706, TGACTCT at 3523, TGACTCA at 2082.
  5. Gcn4r1ci: TTAATCA at 3460.
  6. Gcn4r3ci: TCAATCA at 1655, TGAATCA at 1555, TTAATCA at 1352, AGAGTCA at 477, AGACTCA at 216.
  7. Gcn4r5ci: ACACTCA at 4026, ATAATCA at 3215, TTAGTCA at 1354.
  8. Gcn4r7ci: TCAATCA at 1137, ACAGTCA at 1014, ACAGTCA at 202.
  9. Gcn4r9ci: TTAATCA at 3367, ATACTCA at 3248, TGACTCA at 2082, ATACTCA at 1195, TCAGTCA at 106.

GCRE analyses and results

Main article: Complex locus A1BG and ZNF497 § GCN4 motif

"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]

For TGA(C/G/T)T(A/C/G)(A/T) there are three UTRs for each strand (3.0), one core promoter for each strand in the positive direction only (1.0), one proximal promoter in the negative direction (0.5) and three in the positive direction (1.5), with five distal promoters on the negative direction (2.5) and seventeen in the positive direction (8.5).

The random datasets have thirteen UTRs for ten datasets (1.3), three core promoters in the positive direction only for ten datasets (0.3), one proximal promoter in the negative direction for ten datasets (0.1) and seven proximal promoters in the positive direction for ten datasets (0.7), and twenty-three distal promoters for ten datasets in the negative direction (2.3) and twenty-three distal promoters in the positive direction for ten datasets (2.3).

GCRE (Staschke) results and analysis
Promoters Datasets Frequency Occurrences Reals, Randoms random, likely active or activable
UTRs 2 6 3.0 Reals likely active or activable
UTRs 10 13 1.3 Randoms
Cores, negative 0 0 0 Reals likely active or activable
Cores, negative 10 0 0 Randoms
Cores, positive 2 2 1.0 Reals likely active or activable
Cores, positive 10 1 0.1 Randoms
Proximals, negative 2 1 0.5 Reals likely active or activable
Proximals, negative 10 1 0.1 Randoms
Proximals, positive 2 3 1.5 Reals likely active or activable
Proximals, positive 10 7 0.7 Randoms
Distals, negative 2 5 2.5 Reals maybe active or activable
Distals, negative 10 23 2.3 Randoms
Distals, positive 2 17 8.5 Reals likely active or activable
Distals, positive 10 23 2.3 Randoms

Generally, these GCREs are likely active or activable.

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 2.2 2.3 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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