Unfolded protein response element gene transcriptions

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

X-box binding protein 1s "XBP1s binds to the [unfolded protein response] UPR element (UPRE) containing the consensus sequence TGACGTGG/A and regulates the transcription of target genes in a cell type- and condition-specific manner (Yamamoto et al., 2004)."^[1]

Human genes

Consensus sequences

The consensus sequence for UPRE is 5'-TGACGTG(G/A)-3'.^[1]

UPRE samplings

Copying the consensus UPRE: TGACGTG(G/A) and putting the sequence in "⌘F" finds no locations between ZNF497 and A1BG or between ZSCAN22 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence TGACGTG(G/A) (starting with SuccessablesUPR.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 TGACGTG(G/A), 4, TGACGTGA at 4340, TGACGTGG at 2761, TGACGTGA at 2426, TGACGTGA at 2000.
positive strand, negative direction, looking for TGACGTG(G/A), 0.
positive strand, positive direction, looking for TGACGTG(G/A), 2, TGACGTGG at 4343, TGACGTGG at 3322.
negative strand, positive direction, looking for TGACGTG(G/A), 0.
complement, negative strand, negative direction, looking for ACTGCAC(C/T), 0.
complement, positive strand, negative direction, looking for ACTGCAC(C/T), 4, ACTGCACT at 4340, ACTGCACC at 2761, ACTGCACT at 2426, ACTGCACT at 2000.
complement, positive strand, positive direction, looking for ACTGCAC(C/T), 0.
complement, negative strand, positive direction, looking for ACTGCAC(C/T), 2, ACTGCACC at 4343, ACTGCACC at 3322.
inverse complement, negative strand, negative direction, looking for (C/T)CACGTCA, 2, CCACGTCA at 2083, TCACGTCA at 1472.
inverse complement, positive strand, negative direction, looking for (C/T)CACGTCA, 0.
inverse complement, positive strand, positive direction, looking for (C/T)CACGTCA, 2, TCACGTCA at 2328, TCACGTCA at 2065.
inverse complement, negative strand, positive direction, looking for (C/T)CACGTCA, 0.
inverse negative strand, negative direction, looking for (A/G)GTGCAGT, 0.
inverse positive strand, negative direction, looking for (A/G)GTGCAGT, 2, GGTGCAGT at 2083, AGTGCAGT at 1472.
inverse positive strand, positive direction, looking for (A/G)GTGCAGT, 0.
inverse negative strand, positive direction, looking for (A/G)GTGCAGT, 2, AGTGCAGT at 2328, AGTGCAGT at 2065.

UPR (4560-2846) UTRs

Negative strand, negative direction: TGACGTGA at 4340.

UPR positive direction (4445-4265) core promoters

Positive strand, positive direction: TGACGTGG at 4343.

UPR negative direction (2811-2596) proximal promoters

Negative strand, negative direction: TGACGTGG at 2761.

UPR negative direction (2596-1) distal promoters

Negative strand, negative direction: TGACGTGA at 2426, TGACGTGA at 2000.
Negative strand, negative direction: CCACGTCA at 2083, TCACGTCA at 1472.

UPR positive direction (4050-1) distal promoters

Positive strand, positive direction: TGACGTGG at 3322.
Positive strand, positive direction: TCACGTCA at 2328, TCACGTCA at 2065.

UPRE random dataset samplings

UPREr0: 0.
UPREr1: 0.
UPREr2: 0.
UPREr3: 0.
UPREr4: 0.
UPREr5: 0.
UPREr6: 0.
UPREr7: 0.
UPREr8: 0.
UPREr9: 0.
UPREr0ci: 0.
UPREr1ci: 0.
UPREr2ci: 0.
UPREr3ci: 0.
UPREr4ci: 0.
UPREr5ci: 0.
UPREr6ci: 0.
UPREr7ci: 0.
UPREr8ci: 0.
UPREr9ci: 1, TCACGTCA at 1860.

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

UPREr9ci: TCACGTCA at 1860.

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

UPREr9ci: TCACGTCA at 1860.

UPRE analysis and results

X-box binding protein 1s "XBP1s binds to the [unfolded protein response] UPR element (UPRE) containing the consensus sequence TGACGTGG/A and regulates the transcription of target genes in a cell type- and condition-specific manner (Yamamoto et al., 2004)."^[1]

Reals or randoms	Promoters	direction	Numbers	Strands	Occurrences	Averages (± 0.1)
Reals	UTR	negative	1	2	0.5	0.5
Randoms	UTR	arbitrary negative	0	10	0	0
Randoms	UTR	alternate negative	0	10	0	0
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	1	2	0.5	0.5 ± 0.5 (-+0,++1)
Randoms	Core	arbitrary positive	0	10	0	0
Randoms	Core	alternate positive	0	10	0	0
Reals	Proximal	negative	1	2	0.5	0.5 ± 0.5 (+-0,--1)
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	4	2	2	2 ± 2 (+-0,--4)
Randoms	Distal	arbitrary negative	0	10	0	0.05
Randoms	Distal	alternate negative	1	10	0.1	0.05
Reals	Distal	positive	3	2	1.5	1.5 ± 0.5 (-+0,++3)
Randoms	Distal	arbitrary positive	1	10	0.1	0.05
Randoms	Distal	alternate positive	0	10	0	0.05

Comparison:

The occurrences of real UPREs are larger than the randoms. This suggests that the real UPREs are likely active or activable.

Acknowledgements

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

References

↑ ^1.0 ^1.1 ^1.2 Jae-Seon So (31 August 2018). "Roles of Endoplasmic Reticulum Stress in Immune Responses". Molecules and Cells. 41 (8): 705–16. doi:10.14348/molcells.2018.0241. PMID 30078231. Retrieved 5 September 2020.

External links

[So-1] 1.0 ^1.1 ^1.2 Jae-Seon So (31 August 2018). "Roles of Endoplasmic Reticulum Stress in Immune Responses". Molecules and Cells. 41 (8): 705–16. doi:10.14348/molcells.2018.0241. PMID 30078231. Retrieved 5 September 2020.

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