Phosphate starvation-response transcription factor gene transcriptions

Jump to navigation Jump to search

Associate Editor(s)-in-Chief: Henry A. Hoff

One phosphate starvation-response transcription factor is Pho4.

Human genes

Main article: Human genes

Consensus sequences

Main article: Consensus sequence gene transcriptions

"The [palindromic E-box motif (CACGTG)] motif is bound by the transcription factor Pho4, [and has the] class of basic helix-loop-helix DNA binding domain and core recognition sequence (Zhou and O'Shea 2011)."[1]

"Pho4 bound to virtually all E-boxes in vitro (96%) [...]. That was not the case in vivo, where only 5% were bound by Pho4, under activating conditions as determined by ChIP-seq [Zhou and O'Shea 2011]."[1]

"Pho4 possesses the intrinsic ability to bind every E-box, but in vivo is prevented from binding by chromatin unless assisted by chromatin remodelers (Svaren et al. 1994) that are targeted at promoter regions."[1]

"On one end of that spectrum, typical transcription factors like Pho4 do not appear to compete with nucleosomes and instead predominantly sample motifs that already exist in the [nucleosome-free promoter regions] NFRs generated by other factors. In vitro (PB-exo), Pho4 bound nearly every instance of an E-box motif across the yeast genome. However, in vivo, Pho4 is a low-abundance protein that is recruited to the nucleus upon phosphate starvation by other factors, to act at a few dozen genes (Komeili and O'Shea 1999; Zhou and O'Shea 2011). Since Pho4 appears unable to compete with nucleosomes, competent sites that are occluded by nucleosomes are invisible to Pho4."[1]

The Pho4 homodimer binds to DNA sequences containing the bHLH binding site 5'-CACGTG-3'.[2]

The upstream activating sequence (UAS) for Pho4p is 5'-CAC(A/G)T(T/G)-3' in the promoters of HIS4 and PHO5 regarding phosphate limitation with respect to regulation of the purine and histidine biosynthesis pathways [66].[3]

Hypotheses

Main article: Hypotheses
  1. A1BG has no Phosphate starvation-response transcription factors in either promoter.
  2. A1BG is not transcribed by a Phosphate starvation-response transcription factor (Pho4).
  3. Pho4 does not participate in the transcription of A1BG.

Pho samplings

Main articles: Model samplings and Samplings

Copying the apparent consensus sequence for the Pho (CACGTG) and putting it in "⌘F" finds none located between ZSCAN22 or one between ZNF497 and A1BG as can be found by the computer programs.

For the Basic programs (starting with SuccessablesPho.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 looking for, and found:

  1. negative strand, negative direction is SuccessablesPho--.bas, looking for CACGTG, 0.
  2. negative strand, positive direction is SuccessablesPho-+.bas, looking for CACGTG, 1, CACGTG, 570.
  3. positive strand, negative direction is SuccessablesPho+-.bas, looking for CACGTG, 0.
  4. positive strand, positive direction is SuccessablesPho++.bas, looking for CACGTG, 4, CACGTG, 547, CACGTG, 1219, CACGTG, 2961, CACGTG, 3884.

Inverse complement is the same as above.

Pho4 distal promoters

Main article: Distal promoter gene transcriptions

Negative strand, positive direction: CACGTG at 570.

Positive strand, positive direction: CACGTG at 3884, CACGTG at 2961, CACGTG at 1219, and CACGTG at 547.

Pho random dataset samplings

  1. Phor0: 1, CACGTG at 4343.
  2. Phor1: 0.
  3. Phor2: 0.
  4. Phor3: 1, CACGTG at 3769.
  5. Phor4: 1, CACGTG at 2287.
  6. Phor5: 1, CACGTG at 59.
  7. Phor6: 2, CACGTG at 2905, CACGTG at 654.
  8. Phor7: 1, CACGTG at 1856.
  9. Phor8: 0.
  10. Phor9: 1, CACGTG at 1187.

Phor UTRs

Main article: UTR promoter gene transcriptions
  1. Phor0: CACGTG at 4343.
  2. Phor6: CACGTG at 2905.

Phor distal promoters

Main article: Distal promoter gene transcriptions
  1. Phor4: CACGTG at 2287.
  2. Phor6: CACGTG at 654.
  1. Phor3: CACGTG at 3769.
  2. Phor5: CACGTG at 59.
  3. Phor7: CACGTG at 1856.
  4. Phor9: CACGTG at 1187.

Phor analysis and results

Main article: Complex locus A1BG and ZNF497 § Phors

"The [palindromic E-box motif (CACGTG)] motif is bound by the transcription factor Pho4, [and has the] class of basic helix-loop-helix DNA binding domain and core recognition sequence (Zhou and O'Shea 2011)."[1]

Reals or randoms Promoters direction Numbers Strands Occurrences Averages (± 0.1)
Reals UTR negative 0 2 0 0
Randoms UTR arbitrary negative 2 10 0.2 0.15
Randoms UTR alternate negative 1 10 0.1 0.15
Reals Core negative 0 2 0 0
Randoms Core arbitrary negative 0 10 0 0
Randoms Core alternate negative 0 10 0 0
Reals Core positive 0 2 0 0
Randoms Core arbitrary positive 0 10 0 0.05
Randoms Core alternate positive 1 10 0.1 0.05
Reals Proximal negative 0 2 0 0
Randoms Proximal arbitrary negative 0 10 0 0
Randoms Proximal alternate negative 0 10 0 0
Reals Proximal positive 0 2 0 0
Randoms Proximal arbitrary positive 0 10 0 0
Randoms Proximal alternate positive 0 10 0 0
Reals Distal negative 0 2 0 0
Randoms Distal arbitrary negative 2 10 0.2 0.25
Randoms Distal alternate negative 3 10 0.3 0.25
Reals Distal positive 5 2 2.5 2.5 ± 1.5 (-+1,++4)
Randoms Distal arbitrary positive 4 10 0.4 0.3
Randoms Distal alternate positive 2 10 0.2 0.3

Comparison:

The occurrences of real E-box motif are greater than the randoms. This suggests that the real E-box motifs are likely active or activable.

Phop samplings

Main articles: Model samplings and Samplings

For the Basic programs testing consensus sequence CAC(A/G)T(T/G) (starting with SuccessablesPhop.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 (from ZSCAN22 to A1BG) is SuccessablesPhop--.bas, looking for CAC(A/G)T(T/G), 6, CACATG, 324, CACATT, 612, CACATG, 797, CACGTT, 1536, CACATT, 2087, CACGTT, 2864.
  2. negative strand in the positive direction (from ZNF497 to A1BG) is SuccessablesPhop-+.bas, looking for CAC(A/G)T(T/G), 5, CACGTG, 570, CACATG, 2031, CACATG, 3707, CACATG, 3742, CACATG, 3956.
  3. positive strand, negative direction is SuccessablesPhop+-.bas, looking for CAC(A/G)T(T/G), 3, CACGTT, 343, CACATG, 2667, CACATT, 4533.
  4. positive strand, positive direction is SuccessablesPhop++.bas, looking for CAC(A/G)T(T/G), 6, CACGTG at 547, CACGTG at 1219, CACGTT at 2335, CACGTT at 2801, CACGTG at 2961, CACGTG at 3884.
  5. complement, negative strand, negative direction is SuccessablesPhopc--.bas, looking for GTG(C/T)A(A/C), 3, GTGCAA at 343, GTGTAC at 2667, GTGTAA at 4533.
  6. complement, negative strand, positive direction is SuccessablesPhopc-+.bas, looking for GTG(C/T)A(A/C), 6, GTGCAC at 547, GTGCAC at 1219, GTGCAA at 2335, GTGCAA at 2801, GTGCAC at 2961, GTGCAC at 3884.
  7. complement, positive strand, negative direction is SuccessablesPhopc+-.bas, looking for GTG(C/T)A(A/C), 6, GTGTAC at 324, GTGTAA at 612, GTGTAC at 797, GTGCAA at 1536, GTGTAA at 2087, GTGCAA at 2864.
  8. complement, positive strand, positive direction is SuccessablesPhopc++.bas, looking for GTG(C/T)A(A/C), 5, GTGCAC at 570, GTGTAC at 2031, GTGTAC at 3707, GTGTAC at 3742, GTGTAC at 3956.
  9. inverse complement, negative strand, negative direction is SuccessablesPhopci--.bas, looking for (A/C)A(C/T)GTG, 4, AACGTG at 1338, AACGTG at 1346, AACGTG at 1718, AACGTG at 3288.
  10. inverse complement, negative strand, positive direction is SuccessablesPhopci-+.bas, looking for (A/C)A(C/T)GTG, 4, AATGTG at 229, CACGTG at 570, CATGTG at 3902, CATGTG at 3958.
  11. inverse complement, positive strand, negative direction is SuccessablesPhopci+-.bas, looking for (A/C)A(C/T)GTG, 2, AATGTG at 2064, AATGTG at 4091.
  12. inverse complement, positive strand, positive direction is SuccessablesPhopci++.bas, looking for (A/C)A(C/T)GTG, 6, CACGTG at 547, CATGTG at 567, CACGTG at 1219, CACGTG at 2961, AACGTG at 3342, CACGTG at 3884.
  13. inverse negative strand, negative direction is SuccessablesPhopi--.bas, looking for (G/T)T(A/G)CAC, 2, TTACAC at 2064, TTACAC at 4091.
  14. inverse negative strand, positive direction is SuccessablesPhopi-+.bas, looking for (G/T)T(A/G)CAC, 6, GTGCAC at 547, GTACAC at 567, GTGCAC at 1219, GTGCAC at 2961, TTGCAC at 3342, GTGCAC at 3884.
  15. inverse positive strand, negative direction is SuccessablesPhopi+-.bas, looking for (G/T)T(A/G)CAC, 4, TTGCAC at 1338, TTGCAC at 1346, TTGCAC at 1718, TTGCAC at 3288.
  16. inverse positive strand, positive direction is SuccessablesPhopi++.bas, looking for (G/T)T(A/G)CAC, 4, TTACAC at 229, GTGCAC at 570, GTACAC at 3902, GTACAC at 3958.

Phop UTR promoters

Main article: UTR promoter gene transcriptions

Negative strand, negative direction: TTACAC at 4091, AACGTG at 3288, CACGTT at 2864.

Positive strand, negative direction: CACATT at 4533.

Phop proximal promoters

Main article: Proximal promoter gene transcriptions

Positive strand, negative direction: CACATG at 2667.

Phop distal promoters

Main article: Distal promoter gene transcriptions

Negative strand, negative direction: CACATT at 2087, TTACAC at 2064, AACGTG at 1718, CACGTT at 1536, AACGTG at 1346, AACGTG at 1338, CACATG at 797, CACATT at 612, and CACATG at 324.

Positive strand, negative direction: CACGTT at 343.

Negative strand, positive direction: CATGTG at 3958, CACATG at 3956, CATGTG at 3902, CACATG at 3742, CACATG at 3707, CACATG at 2031, CACGTG at 570, AATGTG at 229.

Positive strand, positive direction: CACGTG at 3884, CACGTG at 2961, CACGTT at 2801, CACGTT at 2335, CACGTG at 1219, CACGTG at 547.

Phop random dataset samplings

  1. Phopr0: 4, CACGTG at 4343, CACGTT at 1357, CACATT at 1165, CACATT at 889.
  2. Phopr1: 2, CACGTT at 192, CACATT at 180.
  3. Phopr2: 2, CACATT at 4068, CACATG at 3734.
  4. Phopr3: 3, CACATT at 4285, CACGTG at 3769, CACGTT at 2751.
  5. Phopr4: 3, CACGTT at 4411, CACGTG at 2287, CACATG at 909.
  6. Phopr5: 3, CACGTT at 4068, CACGTT at 844, CACGTG at 59.
  7. Phopr6: 5, CACGTT at 3434, CACGTG at 2905, CACATG at 2601, CACATT at 1299, CACGTG at 654.
  8. Phopr7: 2, CACGTG at 1856, CACGTT at 1392.
  9. Phopr8: 3, CACGTT at 2985, CACATT at 1505, CACGTT at 898.
  10. Phopr9: 3, CACATG at 4071, CACGTG at 1187, CACGTT at 875.
  11. Phopr0ci: 6, CACGTG at 4343, CATGTG at 3956, AACGTG at 3209, AACGTG at 2399, AACGTG at 1935, CATGTG at 1059.
  12. Phopr1ci: 3, AACGTG at 4030, CATGTG at 3891, AATGTG at 2528.
  13. Phopr2ci: 3, AATGTG at 2764, AACGTG at 1697, CATGTG at 166.
  14. Phopr3ci: 5, AATGTG at 4318, CACGTG at 3769, AACGTG at 1437, CATGTG at 1134, CATGTG at 93.
  15. Phopr4ci: 6, AATGTG at 4054, CACGTG at 2287, CATGTG at 2243, CATGTG at 2224, AATGTG at 1316, AATGTG at 286.
  16. Phopr5ci: 2, AATGTG at 1129, CACGTG at 59.
  17. Phopr6ci: 5, CACGTG at 2905, CATGTG at 2330, AATGTG at 2004, CATGTG at 1342, CACGTG at 654.
  18. Phopr7ci: 3, AACGTG at 3534, CACGTG at 1856, AATGTG at 1509.
  19. Phopr8ci: 0.
  20. Phopr9ci: 3, CATGTG at 1975, CACGTG at 1187, AACGTG at 797.

Phopr arbitrary UTRs

  1. Phopr0: CACGTG at 4343.
  2. Phopr2: CACATT at 4068, CACATG at 3734.
  3. Phopr4: CACGTT at 4411.
  4. Phopr6: CACGTT at 3434, CACGTG at 2905.
  5. Phopr8: CACGTT at 2985.
  6. Phopr0ci: CACGTG at 4343, CATGTG at 3956, AACGTG at 3209.
  7. Phopr4ci: AATGTG at 4054.
  8. Phopr6ci: CACGTG at 2905.

Phopr alternate UTRs

  1. Phopr3: CACATT at 4285, CACGTG at 3769.
  2. Phopr5: CACGTT at 4068.
  3. Phopr9: CACATG at 4071.
  4. Phopr1ci: AACGTG at 4030, CATGTG at 3891.
  5. Phopr3ci: AATGTG at 4318, CACGTG at 3769.
  6. Phopr7ci: AACGTG at 3534.

Phopr arbitrary positive direction core promoters

  1. Phopr3: CACATT at 4285.
  2. Phopr3ci: AATGTG at 4318.

Phopr alternate positive direction core promoters

  1. Phopr0: CACGTG at 4343.
  2. Phopr4: CACGTT at 4411.
  3. Phopr0ci: CACGTG at 4343.

Phopr arbitrary negative direction proximal promoters

  1. Phopr6: CACATG at 2601.
  2. Phopr2ci: AATGTG at 2764.

Phopr alternate negative direction proximal promoters

  1. Phopr3: CACGTT at 2751.

Phopr arbitrary positive direction proximal promoters

  1. Phopr5: CACGTT at 4068.
  2. Phopr9: CACATG at 4071.

Phopr alternate positive direction proximal promoters

  1. Phopr2: CACATT at 4068.
  2. Phopr4ci: AATGTG at 4054.

Phopr arbitrary negative direction distal promoters

  1. Phopr0: CACGTT at 1357, CACATT at 1165, CACATT at 889.
  2. Phopr4: CACGTG at 2287, CACATG at 909.
  3. Phopr6: CACATT at 1299, CACGTG at 654.
  4. Phopr8: CACATT at 1505, CACGTT at 898.
  5. Phopr0ci: AACGTG at 2399, AACGTG at 1935, CATGTG at 1059.
  6. Phopr2ci: AACGTG at 1697, CATGTG at 166.
  7. Phopr4ci: CACGTG at 2287, CATGTG at 2243, CATGTG at 2224, AATGTG at 1316, AATGTG at 286.
  8. Phopr6ci: CATGTG at 2330, AATGTG at 2004, CATGTG at 1342, CACGTG at 654.

Phopr alternate negative direction distal promoters

  1. Phopr1: CACGTT at 192, CACATT at 180.
  2. Phopr5: CACGTT at 844, CACGTG at 59.
  3. Phopr7: CACGTG at 1856, CACGTT at 1392.
  4. Phopr9: CACGTG at 1187, CACGTT at 875.
  5. Phopr1ci: AATGTG at 2528.
  6. Phopr3ci: AACGTG at 1437, CATGTG at 1134, CATGTG at 93.
  7. Phopr5ci: AATGTG at 1129, CACGTG at 59.
  8. Phopr7ci: CACGTG at 1856, AATGTG at 1509.
  9. Phopr9ci: CATGTG at 1975, CACGTG at 1187, AACGTG at 797.

Phopr arbitrary positive direction distal promoters

  1. Phopr1: CACGTT at 192, CACATT at 180.
  2. Phopr3: CACGTG at 3769, CACGTT at 2751.
  3. Phopr5: CACGTT at 844, CACGTG at 59.
  4. Phopr7: CACGTG at 1856, CACGTT at 1392.
  5. Phopr9: CACGTG at 1187, CACGTT at 875.
  6. Phopr1ci: AACGTG at 4030, CATGTG at 3891, AATGTG at 2528.
  7. Phopr3ci: CACGTG at 3769, AACGTG at 1437, CATGTG at 1134, CATGTG at 93.
  8. Phopr5ci: AATGTG at 1129, CACGTG at 59.
  9. Phopr7ci: AACGTG at 3534, CACGTG at 1856, AATGTG at 1509.
  10. Phopr9ci: CATGTG at 1975, CACGTG at 1187, AACGTG at 797.

Phopr alternate positive direction distal promoters

  1. Phopr0: CACGTT at 1357, CACATT at 1165, CACATT at 889.
  2. Phopr2: CACATG at 3734.
  3. Phopr4: CACGTG at 2287, CACATG at 909.
  4. Phopr6: CACGTT at 3434, CACGTG at 2905, CACATG at 2601, CACATT at 1299, CACGTG at 654.
  5. Phopr8: CACGTT at 2985, CACATT at 1505, CACGTT at 898.
  6. Phopr0ci: CATGTG at 3956, AACGTG at 3209, AACGTG at 2399, AACGTG at 1935, CATGTG at 1059.
  7. Phopr2ci: AATGTG at 2764, AACGTG at 1697, CATGTG at 166.
  8. Phopr4ci: CACGTG at 2287, CATGTG at 2243, CATGTG at 2224, AATGTG at 1316, AATGTG at 286.
  9. Phopr6ci: CACGTG at 2905, CATGTG at 2330, AATGTG at 2004, CATGTG at 1342, CACGTG at 654.

Phop analysis and results

Main article: Complex locus A1BG and ZNF497 § Pho4

The upstream activating sequence (UAS) for Pho4p is CAC(A/G)T(T/G) in the promoters of HIS4 and PHO5 regarding phosphate limitation with respect to regulation of the purine and histidine biosynthesis pathways [66].[3]

Reals or randoms Promoters direction Numbers Strands Occurrences Averages (± 0.1)
Reals UTR negative 4 2 2 2 ± 1 (+-1,--3)
Randoms UTR arbitrary negative 12 10 1.2 1.05
Randoms UTR alternate negative 9 10 0.9 1.05
Reals Core negative 0 2 0 0
Randoms Core arbitrary negative 0 10 0 0
Randoms Core alternate negative 0 10 0 0
Reals Core positive 0 2 0 0
Randoms Core arbitrary positive 2 10 0.2 0.25
Randoms Core alternate positive 3 10 0.2 0.25
Reals Proximal negative 1 2 0.5 0.5 ± 0.5 (--0,+-1)
Randoms Proximal arbitrary negative 2 10 0.2 0.15
Randoms Proximal alternate negative 1 10 0.1 0.15
Reals Proximal positive 0 2 0 0
Randoms Proximal arbitrary positive 2 10 0.2 0.2
Randoms Proximal alternate positive 2 10 0.2 0.2
Reals Distal negative 10 2 5 5 ± 4 (+-1,--9)
Randoms Distal arbitrary negative 23 10 2.3 2.1
Randoms Distal alternate negative 19 10 1.9 2.1
Reals Distal positive 14 2 7 7 ± 1 (++6,-+8)
Randoms Distal arbitrary positive 25 10 2.5 2.85
Randoms Distal alternate positive 32 10 3.2 2.85

Comparison:

The occurrences of real Pho4p UTRs overlap the high randoms, the negative proximals, and positive distals are greater than the randoms, negative distals are outside the randoms. This suggests that the real Pho4ps are likely active or activable.

Discussion

For the Pho consensus sequence (CACGTG) which is an enhancer box, the five occurrences are all in the distal promoter on the ZNF497 side of A1BG. The random datasets have one to two occurrences of CACGTG in the UTR on the negative side to one to two in the distal promoters. The real occurrences are more numerous and all in the distal promoter in the positive direction.

See also

References

  1. ↑ 1.0 1.1 1.2 1.3 1.4 Matthew J. Rossi, William K.M. Lai and B. Franklin Pugh (21 March 2018). "Genome-wide determinants of sequence-specific DNA binding of general regulatory factors". Genome Research. 28: 497–508. doi:10.1101/gr.229518.117. PMID 29563167. Retrieved 31 August 2020.
  2. ↑ Dalei Shao, Caretha L. Creasy, Lawrence W. Bergman (1 February 1998). "A cysteine residue in helixII of the bHLH domain is essential for homodimerization of the yeast transcription factor Pho4p". Nucleic Acids Research. 26 (3): 710–4. doi:10.1093/nar/26.3.710. PMC 147311. PMID 9443961.
  3. ↑ 3.0 3.1 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.

External links

Retrieved from "https://www.wikidoc.org/index.php?title=Phosphate_starvation-response_transcription_factor_gene_transcriptions&oldid=1736008"