Ethylene responsive element gene transcriptions

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

"In vitro DNA binding assays associate [Ethylene Response Factor] ERF family members with GCC-box motifs (5’-AGCCGCC-3’) (Ohme-Takagi and Shinshi, 1995; Hao et al., 1998), which have been traced out in many genes induced by ethylene, pathogenesis, wounding, or jasmonate (Brown et al., 2003; Zarei et al., 2011)."^[1]

Human genes

Consensus sequences

Ethylene responsive elements (ATTTCAAA).^[2]

Hypotheses

A1BG has no ethylene responsive elements in either promoter.
A1BG is not transcribed by an ethylene responsive element.
An ethylene responsive element does not participate in the transcription of A1BG.

ERE samplings

Copying an apparent consensus sequence of ATTTCAAA and putting it in "⌘F" finds none located between ZSCAN22 and A1BG and one between ZNF497 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence ATTTCAAA (starting with SuccessablesEth.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'-ATTTCAAA-3', 0.
negative strand, positive direction, looking for 5'-ATTTCAAA-3', 1, ATTTCAAA at 2648.
positive strand, negative direction, looking for 5'-ATTTCAAA-3', 1, ATTTCAAA at 1383.
positive strand, positive direction, looking for 5'-ATTTCAAA-3', 0.
complement, negative strand, negative direction, looking for 5'-TAAAGTTT-3', 1, 5'-TAAAGTTT-3' at 1383.
complement, negative strand, positive direction, looking for 5'-TAAAGTTT-3', 0.
complement, positive strand, negative direction, looking for 5'-TAAAGTTT-3', 0.
complement, positive strand, positive direction, looking for 5'-TAAAGTTT-3', 1, 5'-TAAAGTTT-3' at 2648.
inverse complement, negative strand, negative direction, looking for 5'-TTTGAAAT-3', 0.
inverse complement, negative strand, positive direction, looking for 5'-TTTGAAAT-3', 0.
inverse complement, positive strand, negative direction, looking for 5'-TTTGAAAT-3', 0.
inverse complement, positive strand, positive direction, looking for 5'-TTTGAAAT-3', 0.
inverse negative strand, negative direction, looking for 5'-AAACTTTA-3', 0.
inverse negative strand, positive direction, looking for 5'-AAACTTTA-3', 0.
inverse positive strand, negative direction, looking for 5'-AAACTTTA-3', 0.
inverse positive strand, positive direction, looking for 5'-AAACTTTA-3', 0.

Eth negative direction (2596-1) distal promoters

Positive strand, negative direction: ATTTCAAA at 1383.

Eth positive direction (4050-1) distal promoters

Negative strand, positive direction: ATTTCAAA at 2648.

Random ERE samplings

EREr0: 0.
EREr1: 0.
EREr2: 0.
EREr3: 0.
EREr4: 0.
EREr5: 0.
EREr6: 0.
EREr7: 0.
EREr8: 1, ATTTCAAA at 934.
EREr9: 0.
EREr0ci: 0.
EREr1ci: 0.
EREr2ci: 0.
EREr3ci: 0.
EREr4ci: 0.
EREr5ci: 0.
EREr6ci: 0.
EREr7ci: 0.
EREr8ci: 0.
EREr9ci: 0.

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

EREr8: ATTTCAAA at 934.

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

EREr8: ATTTCAAA at 934.

Response element analysis and results

Ethylene responsive elements (ATTTCAAA).^[2]

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	negative	0	10	0	0
Reals	Core	positive	0	2	0	0
Randoms	Core	positive	0	10	0	0
Reals	Proximal	negative	0	2	0	0
Randoms	Proximal	negative	0	10	0	0
Reals	Proximal	positive	0	2	0	0
Randoms	Proximal	positive	0	10	0	0
Reals	Distal	negative	1	2	0.5	0.5
Randoms	Distal	negative	1	10	0.1	0.05
Reals	Distal	positive	1	2	0.5	0.5
Randoms	Distal	positive	0	10	0	0.05

Comparison:

The occurrences of real ethylene responsive element consensus sequences are larger than the randoms. This suggests that the ethylene responsive element consensus sequences are likely active or activable.

Acknowledgements

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

References

↑ Beatrice Giuntoli and Pierdomenico Perata (February 2018). "Group VII Ethylene Response Factors in Arabidopsis: regulation and physiological roles" (PDF). Plant Physiology. 176 (2): 1143–1155. doi:10.1104/pp.17.01225. PMID 29269576. Retrieved 6 May 2021.
↑ ^2.0 ^2.1 Bhaskar Sharma; Joemar Taganna (12 June 2020). "Genome-wide analysis of the U-box E3 ubiquitin ligase enzyme gene family in tomato". Scientific Reports. 10 (9581). doi:10.1038/s41598-020-66553-1. PMID 32533036 Check |pmid= value (help). Retrieved 27 August 2020.

External links

[Giuntoli-1] Beatrice Giuntoli and Pierdomenico Perata (February 2018). "Group VII Ethylene Response Factors in Arabidopsis: regulation and physiological roles" (PDF). Plant Physiology. 176 (2): 1143–1155. doi:10.1104/pp.17.01225. PMID 29269576. Retrieved 6 May 2021.

[Sharma-2] 2.0 ^2.1 Bhaskar Sharma; Joemar Taganna (12 June 2020). "Genome-wide analysis of the U-box E3 ubiquitin ligase enzyme gene family in tomato". Scientific Reports. 10 (9581). doi:10.1038/s41598-020-66553-1. PMID 32533036 Check |pmid= value (help). Retrieved 27 August 2020.

[1]

[2]

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