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 ethylene insensitive (EIN) 3 (EIN3) occurs in the oresara1 (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.

EIN3 samplings

Copying a responsive elements consensus sequence ACGTACC 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 A(C/T)G(A/T)A(C/T)CT (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 A(C/T)G(A/T)A(C/T)CT, 1, ATGAACCT at 329, and complement.
negative strand, positive direction, looking for A(C/T)G(A/T)A(C/T)CT, 0.
positive strand, negative direction, looking for A(C/T)G(A/T)A(C/T)CT, 1, ATGAACCT at 1957, and complement.
positive strand, positive direction, looking for A(C/T)G(A/T)A(C/T)CT, 0.
complement, negative strand, negative direction, looking for T(A/G)C(A/T)T(A/G)GA, 1, TACTTGGA at 1957.
complement, negative strand, positive direction, looking for T(A/G)C(A/T)T(A/G)GA, 0.
complement, positive strand, negative direction, looking for T(A/G)C(A/T)T(A/G)GA, 1, TACTTGGA at 329.
complement, positive strand, positive direction, looking for T(A/G)C(A/T)T(A/G)GA, 0.
inverse complement, negative strand, negative direction, looking for AG(A/G)T(A/T)C(A/G)T, 0.
inverse complement, negative strand, positive direction, looking for AG(A/G)T(A/T)C(A/G)T, 1, AGGTTCGT at 1928, and complement.
inverse complement, positive strand, negative direction, looking for AG(A/G)T(A/T)C(A/G)T, 0.
inverse complement, positive strand, positive direction, looking for AG(A/G)T(A/T)C(A/G)T, 1, AGGTACGT at 1935, and complement.
inverse negative strand, negative direction, looking for TC(C/T)A(A/T)G(C/T)A, 0.
inverse negative strand, positive direction, looking for TC(C/T)A(A/T)G(C/T)A, 1, TCCATGCA at 1935.
inverse positive strand, negative direction, looking for TC(C/T)A(A/T)G(C/T)A, 0.
inverse positive strand, positive direction, looking for TC(C/T)A(A/T)G(C/T)A, 1, TCCAAGCA at 1928.

EIN3 negative direction (2596-1) distal promoters

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

EIN3 positive direction (4050-1) distal promoters

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

EIN3r arbitrary (evens) (4560-2846) UTRs

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

EIN3r alternate (odds) (4560-2846) UTRs

EIN3r5: ATGTACCT at 4396, ACGTACCT at 3129.
EIN3r3ci: AGGTTCGT at 4467.
EIN3r5ci: AGATTCGT at 4092.

EIN3r arbitrary positive direction (odds) (4445-4265) core promoters

EIN3r5: ATGTACCT at 4396.

EIN3r arbitrary negative direction (evens) (2811-2596) proximal promoters

EIN3r8: ATGTACCT at 2781.

EIN3r arbitrary positive direction (odds) (4265-4050) proximal promoters

EIN3r5ci: AGATTCGT at 4092.

EIN3r arbitrary negative direction (evens) (2596-1) distal promoters

EIN3r6ci: AGGTTCGT at 1273.

EIN3r alternate negative direction (odds) (2596-1) distal promoters

EIN3r1ci: AGGTACAT at 1128.

EIN3r arbitrary positive direction (odds) (4050-1) distal promoters

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

EIN3r alternate positive direction (evens) (4050-1) distal promoters

EIN3r2: ATGAACCT at 3145.
EIN3r8: ATGTACCT at 2781.
EIN3r6ci: AGGTTCGT at 1273.

EIN3 analysis and results

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

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	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	1	10	0.1	0.05
Randoms	Core	alternate positive	0	10	0	0.05
Reals	Proximal	negative	0	2	0	0
Randoms	Proximal	arbitrary negative	1	10	0.1	0.05
Randoms	Proximal	alternate negative	0	10	0	0.05
Reals	Proximal	positive	0	2	0	0
Randoms	Proximal	arbitrary positive	1	10	0.1	0.05
Randoms	Proximal	alternate positive	0	10	0	0.05
Reals	Distal	negative	2	2	1	1
Randoms	Distal	arbitrary negative	1	10	0.1	0.1
Randoms	Distal	alternate negative	1	10	0.1	0.1
Reals	Distal	positive	2	2	1	1
Randoms	Distal	arbitrary positive	2	10	0.2	0.25
Randoms	Distal	alternate positive	3	10	0.3	0.25

Comparison:

The occurrences of real EIN3 distals are greater than the randoms. This suggests that the real EIN3s 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 ^1.5 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 ^1.5 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.

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