Nutrient-sensing response element gene transcriptions

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

There is only one nucleotide difference between the SESN2 CARE and the ATF4-inducible asparagine synthase gene ASNS consensus sequence (GTTTCATCA).^[1]

Human genes

Consensus sequences

An apparent consensus sequence for the nutrient-sensing response element 1 is 5'-GTTTCATCA-3'.^[1]

Samplings

Copying an apparent consensus sequence for the nutrient-sensing response element 1 (GTTTCATCA) and putting it in "⌘F" finds none located between ZSCAN22 and none between ZNF497 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence GTTTCATCA (starting with SuccessablesNSRE.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 GTTTCATCA, 0.
positive strand, negative direction, looking for GTTTCATCA, 0.
positive strand, positive direction, looking for GTTTCATCA, 0.
negative strand, positive direction, looking for GTTTCATCA, 0.
complement, negative strand, negative direction, looking for CAAAGTAGT, 0.
complement, positive strand, negative direction, looking for CAAAGTAGT, 0.
complement, positive strand, positive direction, looking for CAAAGTAGT, 0.
complement, negative strand, positive direction, looking for CAAAGTAGT, 0.
inverse complement, negative strand, negative direction, looking for TGATGAAAC, 0.
inverse complement, positive strand, negative direction, looking for TGATGAAAC, 0.
inverse complement, positive strand, positive direction, looking for TGATGAAAC, 0.
inverse complement, negative strand, positive direction, looking for TGATGAAAC, 1, TGATGAAAC at 2147.
inverse negative strand, negative direction, looking for ACTACTTTG, 0.
inverse positive strand, negative direction, looking for ACTACTTTG, 0.
inverse positive strand, positive direction, looking for ACTACTTTG, 1, ACTACTTTG at 2147.
inverse negative strand, positive direction, looking for ACTACTTTG, 0.

NSRE positive direction (4050-1) distal promoters

Negative strand, positive direction: TGATGAAAC at 2147.

NSRE random dataset samplings

NSREr0: 0.
NSREr1: 0.
NSREr2: 0.
NSREr3: 0.
NSREr4: 0.
NSREr5: 0.
NSREr6: 0.
NSREr7: 0.
NSREr8: 0.
NSREr9: 1, GTTTCATCA at 1242.
NSREr0ci: 1, TGATGAAAC at 1932.
NSREr1ci: 0.
NSREr2ci: 0.
NSREr3ci: 0.
NSREr4ci: 0.
NSREr5ci: 0.
NSREr6ci: 0.
NSREr7ci: 0.
NSREr8ci: 0.
NSREr9ci: 0.

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

NSREr0ci: TGATGAAAC at 1932.

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

NSREr9: GTTTCATCA at 1242.

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

NSREr9: GTTTCATCA at 1242.

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

NSREr0ci: TGATGAAAC at 1932.

NSRE analysis and results

There is only one nucleotide difference between the SESN2 CARE and the ATF4-inducible asparagine synthase gene ASNS consensus sequence (GTTTCATCA).^[1]

Reals or randoms	Promoters	direction	Numbers	Strands	Occurrences	Averages (± 0.1)
Reals	UTR	negative	0	2	0	0
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	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	0	2	0	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	0.1
Randoms	Distal	alternate positive	1	10	0.1	0.1

Comparison:

The occurrences of real NSRE is greater than the randoms. This suggests that the real NSRE is likely active or activable.

References

↑ ^1.0 ^1.1 ^1.2 Alisa A. Garaeva, Irina E. Kovaleva, Peter M. Chumakov & Alexandra G. Evstafieva (15 January 2016). "Mitochondrial dysfunction induces SESN2 gene expression through Activating Transcription Factor 4". Cell Cycle. 15 (1): 64–71. doi:10.1080/15384101.2015.1120929. PMID 26771712. Retrieved 5 September 2020.

External links

[Garaeva-1] 1.0 ^1.1 ^1.2 Alisa A. Garaeva, Irina E. Kovaleva, Peter M. Chumakov & Alexandra G. Evstafieva (15 January 2016). "Mitochondrial dysfunction induces SESN2 gene expression through Activating Transcription Factor 4". Cell Cycle. 15 (1): 64–71. doi:10.1080/15384101.2015.1120929. PMID 26771712. Retrieved 5 September 2020.

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