EIN3 binding site gene transcriptions

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

"We scanned the ORE1 promoter and found a putative EIN3 binding site (EBS), ATGAACCT, located 1056~1064 bp upstream from the start codon (ATG) of the gene [...]."^[1]

Human genes

Gene expressions

EIN3 mat affect the gene expression of ORE1.^[1]

Interactions

Consensus sequences

"EIN3/EIL1 transcription factors were reported to bind to a consensus DNA sequence of A[CT]G[AT]A[CT]CT [34,35]."^[1]

Binding site for

A binding site for EIN3 occurs in the ORE1 promoter.^[1]

Promoter occurrences

ORE1 promoter has a putative EIN3 binding site.^[1]

Hypotheses

A1BG has no EIN3 binding sites in either promoter.
A1BG is not transcribed by an EIN3 binding site.
EIN3 binding site does not participate in the transcription of A1BG.

Samplings

Copying a responsive elements consensus sequence 5'-ACGTACC-3' 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 5'-A(C/T)G(A/T)A(C/T)CT-3' (starting with SuccessablesEIN.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 5'-A(C/T)G(A/T)A(C/T)CT-3', 1, 5'-ATGAACCT-3' at 329, and complement.
negative strand, positive direction, looking for 5'-A(C/T)G(A/T)A(C/T)CT-3', 0.
positive strand, negative direction, looking for 5'-A(C/T)G(A/T)A(C/T)CT-3', 1, 5'-ATGAACCT-3' at 1957, and complement.
positive strand, positive direction, looking for 5'-A(C/T)G(A/T)A(C/T)CT-3', 0.
complement, negative strand, negative direction, looking for 5'-T(A/G)C(A/T)T(A/G)GA-3', 1, 5'-TACTTGGA-3' at 1957.
complement, negative strand, positive direction, looking for 5'-T(A/G)C(A/T)T(A/G)GA-3', 0.
complement, positive strand, negative direction, looking for 5'-T(A/G)C(A/T)T(A/G)GA-3', 1, 5'-TACTTGGA-3' at 329.
complement, positive strand, positive direction, looking for 5'-T(A/G)C(A/T)T(A/G)GA-3', 0.
inverse complement, negative strand, negative direction, looking for 5'-AG(A/G)T(A/T)C(A/G)T-3', 0.
inverse complement, negative strand, positive direction, looking for 5'-AG(A/G)T(A/T)C(A/G)T-3', 1, 5'-AGGTTCGT-3' at 1928, and complement.
inverse complement, positive strand, negative direction, looking for 5'-AG(A/G)T(A/T)C(A/G)T-3', 0.
inverse complement, positive strand, positive direction, looking for 5'-AG(A/G)T(A/T)C(A/G)T-3', 1, 5'-AGGTACGT-3' at 1935, and complement.
inverse negative strand, negative direction, looking for 5'-TC(C/T)A(A/T)G(C/T)A-3', 0.
inverse negative strand, positive direction, looking for 5'-TC(C/T)A(A/T)G(C/T)A-3', 1, 5'-TCCATGCA-3' at 1935.
inverse positive strand, negative direction, looking for 5'-TC(C/T)A(A/T)G(C/T)A-3', 0.
inverse positive strand, positive direction, looking for 5'-TC(C/T)A(A/T)G(C/T)A-3', 1, 5'-TCCAAGCA-3' at 1928.

EIN distal promoters

Negative strand, negative direction: ATGAACCT at 329.
Positive strand, negative direction: ATGAACCT at 1957.

Negative strand, positive direction: AGGTTCGT at 1928.
Positive strand, positive direction: AGGTACGT at 1935.

EIN3r UTRs

EIN3r2: ATGAACCT at 3145.
EIN3r4: ATGTACCT at 4544.

EIN3r core promoters

EIN3r5: ATGTACCT at 4396.
EIN3r3ci: AGGTTCGT at 4467.

EIN3r proximal promoters

EIN3r8: ATGTACCT at 2781.

EIN3r5ci: AGATTCGT at 4092.

EIN3r distal promoters

EIN3r6ci: AGGTTCGT at 1273.

EIN3r5: ACGTACCT at 3129.
EIN3r1ci: AGGTACAT at 1128.

Response element analysis and results

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	0.3
Randoms	UTR	alternate negative	4	10	0.4	0.3
Reals	Core	negative	0	2	0	0
Randoms	Core	negative	0	10	0	0.05
Reals	Core	positive	0	2	0	0
Randoms	Core	positive	1	10	0.1	0.05
Reals	Proximal	negative	0	2	0	0
Randoms	Proximal	negative	1	10	0.1	0.1
Reals	Proximal	positive	0	2	0	0
Randoms	Proximal	positive	1	10	0.1	0.1
Reals	Distal	negative	2	2	1.0	1.0
Randoms	Distal	negative	1	10	0.1	0.15
Reals	Distal	positive	2	2	1.0	1.0
Randoms	Distal	positive	2	10	0.2	0.15

Comparison: Reals occur only in the distal promoters in both directions where the occurrences are much larger than the randoms suggesting that the reals 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 ^1.3 ^1.4 Kai Qiu, Zhongpeng Li, Zhen Yang, Junyi Chen, Shouxin Wu, Xiaoyu Zhu, Shan Gao, Jiong Gao, Guodong Ren, Benke Kuai, and Xin Zhou (July 2015). "EIN3 and ORE1 Accelerate Degreening during Ethylene-Mediated Leaf Senescence by Directly Activating Chlorophyll Catabolic Genes in Arabidopsis". PLoS Genetics. 11 (7): e1005399. doi:10.1371/journal.pgen.1005399. PMID 26218222. Retrieved 4 October 2020.

External links

[Qiu-1] 1.0 ^1.1 ^1.2 ^1.3 ^1.4 Kai Qiu, Zhongpeng Li, Zhen Yang, Junyi Chen, Shouxin Wu, Xiaoyu Zhu, Shan Gao, Jiong Gao, Guodong Ren, Benke Kuai, and Xin Zhou (July 2015). "EIN3 and ORE1 Accelerate Degreening during Ethylene-Mediated Leaf Senescence by Directly Activating Chlorophyll Catabolic Genes in Arabidopsis". PLoS Genetics. 11 (7): e1005399. doi:10.1371/journal.pgen.1005399. PMID 26218222. Retrieved 4 October 2020.

[1]

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