Phosphate starvation-response transcription factor gene transcriptions

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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 5'-CACGTG-3', 0.
  2. negative strand, positive direction is SuccessablesPho-+.bas, looking for 5'-CACGTG-3', 1, 5'-CACGTG-3', 570.
  3. positive strand, negative direction is SuccessablesPho+-.bas, looking for 5'-CACGTG-3', 0.
  4. positive strand, positive direction is SuccessablesPho++.bas, looking for 5'-CACGTG-3', 4, 5'-CACGTG-3', 547, 5'-CACGTG-3', 1219, 5'-CACGTG-3', 2961, 5'-CACGTG-3', 3884.
  5. complement, negative strand, negative direction is SuccessablesPhoc--.bas, looking for 5'-GTGCAC-3', 0.
  6. complement, negative strand, positive direction is SuccessablesPhoc-+.bas, looking for 5'-GTGCAC-3', 4, 5'-GTGCAC-3', 547, 5'-GTGCAC-3', 1219, 5'-GTGCAC-3', 2961, 5'-GTGCAC-3', 3884.
  7. complement, positive strand, negative direction is SuccessablesPhoc+-.bas, looking for 5'-GTGCAC-3', 0.
  8. complement, positive strand, positive direction is SuccessablesPhoc++.bas, looking for 5'-GTGCAC-3', 1, 5'-GTGCAC-3', 570.

Pho4 distal promoters

Main article: Distal promoter gene transcriptions

Negative strand, positive direction: CACGTG at 570 and complement.

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

Random dataset samplings

  1. RDr0: 0.
  2. RDr1: 0.
  3. RDr2: 0.
  4. RDr3: 0.
  5. RDr4: 0.
  6. RDr5: 0.
  7. RDr6: 0.
  8. RDr7: 0.
  9. RDr8: 0.
  10. RDr9: 0.
  11. RDr0ci: 0.
  12. RDr1ci: 0.
  13. RDr2ci: 0.
  14. RDr3ci: 0.
  15. RDr4ci: 0.
  16. RDr5ci: 0.
  17. RDr6ci: 0.
  18. RDr7ci: 0.
  19. RDr8ci: 0.
  20. RDr9ci: 0.

RDr UTRs

Main article: UTR promoter gene transcriptions

RDr core promoters

Main article: Core promoter gene transcriptions

RDr proximal promoters

Main article: Proximal promoter gene transcriptions

RDr distal promoters

Main article: Distal promoter gene transcriptions

Phop samplings

Main articles: Model samplings and Samplings

For the Basic programs testing consensus sequence 5'-CAC(A/G)T(T/G)-3' (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 5'-CAC(A/G)T(T/G)-3', 6, 3'-CACATG-5', 324, 3'-CACATT-5', 612, 3'-CACATG-5', 797, 3'-CACGTT-5', 1536, 3'-CACATT-5', 2087, 3'-CACGTT-5', 2864.
  2. negative strand in the positive direction (from ZNF497 to A1BG) is SuccessablesPhop-+.bas, looking for 5'-CAC(A/G)T(T/G)-3', 5, 5'-CACGTG-3', 570, 5'-CACATG-3', 2031, 5'-CACATG-3', 3707, 5'-CACATG-3', 3742, 5'-CACATG-3', 3956.
  3. positive strand, negative direction is SuccessablesPhop+-.bas, looking for 5'-CAC(A/G)T(T/G)-3', 3, 5'-CACGTT-3', 343, 5'-CACATG-3', 2667, 5'-CACATT-3', 4533.
  4. positive strand, positive direction is SuccessablesPhop++.bas, looking for 5'-CAC(A/G)T(T/G)-3', 6, 5'-CACGTG-3' at 547, 5'-CACGTG-3' at 1219, 5'-CACGTT-3' at 2335, 5'-CACGTT-3' at 2801, 5'-CACGTG-3' at 2961, 5'-CACGTG-3' at 3884.
  5. complement, negative strand, negative direction is SuccessablesPhopc--.bas, looking for 5'-GTG(C/T)A(A/C)-3', 3, 5'-GTGCAA-3' at 343, 5'-GTGTAC-3' at 2667, 5'-GTGTAA-3' at 4533.
  6. complement, negative strand, positive direction is SuccessablesPhopc-+.bas, looking for 5'-GTG(C/T)A(A/C)-3', 6, 5'-GTGCAC-3' at 547, 5'-GTGCAC-3' at 1219, 5'-GTGCAA-3' at 2335, 5'-GTGCAA-3' at 2801, 5'-GTGCAC-3' at 2961, 5'-GTGCAC-3' at 3884.
  7. complement, positive strand, negative direction is SuccessablesPhopc+-.bas, looking for 5'-GTG(C/T)A(A/C)-3', 6, 5'-GTGTAC-3' at 324, 5'-GTGTAA-3' at 612, 5'-GTGTAC-3' at 797, 5'-GTGCAA-3' at 1536, 5'-GTGTAA-3' at 2087, 5'-GTGCAA-3' at 2864.
  8. complement, positive strand, positive direction is SuccessablesPhopc++.bas, looking for 5'-GTG(C/T)A(A/C)-3', 5, 5'-GTGCAC-3' at 570, 5'-GTGTAC-3' at 2031, 5'-GTGTAC-3' at 3707, 5'-GTGTAC-3' at 3742, 5'-GTGTAC-3' at 3956.
  9. inverse complement, negative strand, negative direction is SuccessablesPhopci--.bas, looking for 5'-(A/C)A(C/T)GTG-3', 4, 5'-AACGTG-3' at 1338, 5'-AACGTG-3' at 1346, 5'-AACGTG-3' at 1718, 5'-AACGTG-3' at 3288.
  10. inverse complement, negative strand, positive direction is SuccessablesPhopci-+.bas, looking for 5'-(A/C)A(C/T)GTG-3', 4, 5'-AATGTG-3' at 229, 5'-CACGTG-3' at 570, 5'-CATGTG-3' at 3902, 5'-CATGTG-3' at 3958.
  11. inverse complement, positive strand, negative direction is SuccessablesPhopci+-.bas, looking for 5'-(A/C)A(C/T)GTG-3', 2, 5'-AATGTG-3' at 2064, 5'-AATGTG-3' at 4091.
  12. inverse complement, positive strand, positive direction is SuccessablesPhopci++.bas, looking for 5'-(A/C)A(C/T)GTG-3', 6, 5'-CACGTG-3' at 547, 5'-CATGTG-3' at 567, 5'-CACGTG-3' at 1219, 5'-CACGTG-3' at 2961, 5'-AACGTG-3' at 3342, 5'-CACGTG-3' at 3884.
  13. inverse negative strand, negative direction is SuccessablesPhopi--.bas, looking for 5'-(G/T)T(A/G)CAC-3', 2, 5'-TTACAC-3' at 2064, 5'-TTACAC-3' at 4091.
  14. inverse negative strand, positive direction is SuccessablesPhopi-+.bas, looking for 5'-(G/T)T(A/G)CAC-3', 6, 5'-GTGCAC-3' at 547, 5'-GTACAC-3' at 567, 5'-GTGCAC-3' at 1219, 5'-GTGCAC-3' at 2961, 5'-TTGCAC-3' at 3342, 5'-GTGCAC-3' at 3884.
  15. inverse positive strand, negative direction is SuccessablesPhopi+-.bas, looking for 5'-(G/T)T(A/G)CAC-3', 4, 5'-TTGCAC-3' at 1338, 5'-TTGCAC-3' at 1346, 5'-TTGCAC-3' at 1718, 5'-TTGCAC-3' at 3288.
  16. inverse positive strand, positive direction is SuccessablesPhopi++.bas, looking for 5'-(G/T)T(A/G)CAC-3', 4, 5'-TTACAC-3' at 229, 5'-GTGCAC-3' at 570, 5'-GTACAC-3' at 3902, 5'-GTACAC-3' 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.

See also

References

  1. ↑ 1.0 1.1 1.2 1.3 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. ↑ 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

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