Pdr1,3p gene transcriptions

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

Human genes

Interactions

Consensus sequences

The upstream activating sequence (UAS) for the Pdr1p/Pdr3p is 5'-TCCGCGGA-3'.^[1]

Pdr1p binds to sequence TCCGYGGR (TCCG(C/T)GG(A/G)) of PDRE, which is located within the promoter sequences of its target genes.^[2]^[3]

Pdr samplings

Copying TCCGCGGA 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 TCCGCGGA (starting with SuccessablesPdr.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 TCCGCGGA, 0.
positive strand, negative direction, looking for TCCGCGGA, 0.
positive strand, positive direction, looking for TCCGCGGA, 0.
negative strand, positive direction, looking for TCCGCGGA, 0.
complement, negative strand, negative direction, looking for AGGCGCCT, 0.
complement, positive strand, negative direction, looking for AGGCGCCT, 0.
complement, positive strand, positive direction, looking for AGGCGCCT, 0.
complement, negative strand, positive direction, looking for AGGCGCCT, 0.
inverse complement, negative strand, negative direction, looking for TCCGCGGA, 0.
inverse complement, positive strand, negative direction, looking for TCCGCGGA, 0.
inverse complement, positive strand, positive direction, looking for TCCGCGGA, 0.
inverse complement, negative strand, positive direction, looking for TCCGCGGA, 0.
inverse negative strand, negative direction, looking for AGGCGCCT, 0.
inverse positive strand, negative direction, looking for AGGCGCCT, 0.
inverse positive strand, positive direction, looking for AGGCGCCT, 0.
inverse negative strand, positive direction, looking for AGGCGCCT, 0.

Pdr1 (Salin) samplings

Copying a responsive elements consensus sequence TCCG(C/T)GG(A/G) and putting the sequence in "⌘F" finds none between ZNF497 and A1BG or none between ZSCAN22 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence TCCG(C/T)GG(A/G) (starting with SuccessablesPdrS.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: 0.
Positive strand, negative direction: 0.
Negative strand, positive direction: 0.
Positive strand, positive direction: 0.
inverse complement, negative strand, negative direction: 3, CCCACGGA at 3198, CCCACGGA at 2335, CCCACGGA at 1256.
inverse complement, positive strand, negative direction: 0.
inverse complement, negative strand, positive direction: 1, TCCACGGA at 300.
inverse complement, positive strand, positive direction: 0.

PdrS (4560-2846) UTRs

Negative strand, negative direction: CCCACGGA at 3198.

PdrS negative direction (2596-1) distal promoters

Negative strand, negative direction: CCCACGGA at 2335, CCCACGGA at 1256.

PdrS positive direction (4050-1) distal promoters

Negative strand, positive direction: TCCACGGA at 300.

Pdr (Salin 2008) random dataset samplings

PdrSr0: 0.
PdrSr1: 1, TCCGTGGG at 661.
PdrSr2: 2, TCCGCGGA at 3565, TCCGCGGA at 3371.
PdrSr3: 0.
PdrSr4: 0.
PdrSr5: 0.
PdrSr6: 0.
PdrSr7: 0.
PdrSr8: 0.
PdrSr9: 0.
PdrSr0ci: 1, CCCGCGGA at 1894.
PdrSr1ci: 0.
PdrSr2ci: 3, CCCGCGGA at 3875.
PdrSr3ci: 0.
PdrSr4ci: 0.
PdrSr5ci: 0.
PdrSr6ci: 0.
PdrSr7ci: 0.
PdrSr8ci: 0.
PdrSr9ci: 0.

PdrSr arbitrary (evens) (4560-2846) UTRs

PdrSr2: TCCGCGGA at 3565, TCCGCGGA at 3371.
PdrSr2ci: CCCGCGGA at 3875.

PdrSr arbitrary negative direction (evens) (2596-1) distal promoters

PdrSr0ci: CCCGCGGA at 1894.

PdrSr alternate negative direction (odds) (2596-1) distal promoters

PdrSr1: TCCGTGGG at 661.

PdrSr arbitrary positive direction (odds) (4050-1) distal promoters

PdrSr1: TCCGTGGG at 661.

PdrSr alternate positive direction (evens) (4050-1) distal promoters

PdrSr2: TCCGCGGA at 3565, TCCGCGGA at 3371.
PdrSr0ci: CCCGCGGA at 1894.
PdrSr2ci: CCCGCGGA at 3875.

PdrS analysis and results

Pdr1p binds to sequence TCCGYGGR (TCCG(C/T)GG(A/G)) of PDRE, which is located within the promoter sequences of its target genes.^[2]^[3]

Reals or randoms	Promoters	direction	Numbers	Strands	Occurrences	Averages (± 0.1)
Reals	UTR	negative	1	2	0.5	0.5 ± 0.5 (--1,+-0)
Randoms	UTR	arbitrary negative	3	10	0.3	0.15
Randoms	UTR	alternate negative	0	10	0	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
Randoms	Core	alternate positive	0	10	0	0
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	2	2	1	1 ± 1 (--2,+-0)
Randoms	Distal	arbitrary negative	1	10	0.1	0.1
Randoms	Distal	alternate negative	1	10	0.1	0.1
Reals	Distal	positive	1	2	0.5	0.5 ± 0.5 (-+1,++0)
Randoms	Distal	arbitrary positive	1	10	0.1	0.25
Randoms	Distal	alternate positive	4	10	0.4	0.25

Comparison:

The occurrences of real PdrS UTRs and distals are greater than the randoms. This suggests that the real PdrSs are likely active or activable.

Acknowledgements

The content on this page was first contributed by: Henry A. Hoff.

References

↑ 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 Salin H, Fardeau V, Piccini E, Lelandais G, Tanty V, Lemoine S, Jacq C, Devaux F (July 2008). "Structure and properties of transcriptional networks driving selenite stress response in yeasts". BMC Genomics. 9: 333. doi:10.1186/1471-2164-9-333. PMC 2515152. PMID 18627600.
↑ ^3.0 ^3.1 Katzmann DJ, Burnett PE, Golin J, Mahé Y, Moye-Rowley WS (July 1994). "Transcriptional control of the yeast PDR5 gene by the PDR3 gene product". Molecular and Cellular Biology. 14 (7): 4653–61. doi:10.1128/MCB.14.7.4653. PMC 358838. PMID 8007969.

External links

[Tang-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.

[Salin-2] 2.0 ^2.1 Salin H, Fardeau V, Piccini E, Lelandais G, Tanty V, Lemoine S, Jacq C, Devaux F (July 2008). "Structure and properties of transcriptional networks driving selenite stress response in yeasts". BMC Genomics. 9: 333. doi:10.1186/1471-2164-9-333. PMC 2515152. PMID 18627600.

[Katzmann-3] 3.0 ^3.1 Katzmann DJ, Burnett PE, Golin J, Mahé Y, Moye-Rowley WS (July 1994). "Transcriptional control of the yeast PDR5 gene by the PDR3 gene product". Molecular and Cellular Biology. 14 (7): 4653–61. doi:10.1128/MCB.14.7.4653. PMC 358838. PMID 8007969.

[1]

[2]

[3]

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