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.

ERE random 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.

ERE analysis and results

Ethylene responsive elements (ATTTCAAA).^[2]

Two ethylene response factors or ethylene responsive elements occur in the promoters of A1BG: positive strand, negative direction: ATTTCAAA at 1383 and negative strand, positive direction: ATTTCAAA at 2648. Both of these occur in the distal promoters on either side of A1BG. Sampling of ten random datasets looking for the ERE and its inverse complement found only one: ATTTCAAA at 934. Half way between ZSCAN22 and A1BG is about 2300 nucleotides and between ZNF497 and A1BG is about 2200. One is closer to ZSCAN22 and the other is closer to A1BG. The random occurrence is closer to the zinc finger than A1BG. The response element closer to A1BG is likely real even if inactive. As the real occurrences are more frequent and nearer mid points than the random result, it is likely that the EREs are not random but real and perhaps active.

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	1	2	0.5	0.5
Randoms	Distal	arbitrary negative	1	10	0.1	0.05
Randoms	Distal	alternate negative	0	10	0	0.05
Reals	Distal	positive	1	2	0.5	0.5
Randoms	Distal	arbitrary positive	0	10	0	0.05
Randoms	Distal	alternate positive	1	10	0.1	0.05

Comparison:

The occurrences of real EREs are greater than the randoms. This suggests that the real EREs 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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transcriptions Polycomb response element gene transcriptions Preinitiation complex Preinitiation complex gene transcriptions Pribnow box gene transcriptions Prolamin box gene transcriptions Promoter gene transcriptions Proximal promoter gene transcriptions Promoter occurrence gene transcriptions Pyrimidine box gene transcriptions Q element gene transcriptions Rap1 regulatory factor gene transcriptions Reb1 general regulatory factor gene transcriptions Retinoblastoma control element gene transcriptions Retinoic acid response element gene transcriptions Rgt1p gene transcriptions Rlm1p gene transcriptions RNA polymerase II gene transcriptions RNA polymerase II holoenzyme complex Root specific element gene transcriptions ROR-response element gene transcriptions Rox1p gene transcriptions Rpn4p gene transcriptions R response element gene transcriptions SARE gene transcriptions Seed-specific element gene transcriptions Serum response element gene transcriptions Servenius sequence gene transcriptions Shoot specific element gene transcriptions Sip4p gene transcriptions Smp1p gene transcriptions Sp1 gene transcriptions Spaceflight gene expressions Specificity protein gene transcriptions STAT gene transcriptions Ste12p gene transcriptions Sterol response element gene transcriptions Sucrose box gene transcriptions Synaptic Activity-Responsive Elements TACTAAC box gene transcriptions TAGteam gene transcriptions Tapetum box gene transcriptions TATA binding protein associated factor gene transcriptions TATA binding protein gene transcriptions TATA box actin/cytoskeleton/contractile family TATA box albumin family TATA box aldolase family TATA box alkaline phosphatase family TATA box annexin family TATA box cytochrome superfamily TATA box gene transcriptions TATA box heat shock family TATA box histone family TATA box human genes TATA box keratin family TATA box lipase family TATA box peptidase family TATA box platelet-derived growth factor family TATA box selenium-binding family TATA box serine protease family TATA box serpin superfamily TATA box transforming growth factor superfamily TATA box trefoil family TATA box tumor necrosis factor superfamily TATA box zinc metalloenzyme family TAT box gene transcriptions TATC box gene transcriptions Tbf1 regulatory factor gene transcriptions T box gene transcriptions TCCACCATA element gene transcriptions TC element gene transcriptions TCT gene transcriptions TEA consensus sequence gene transcriptions Tec1p gene transcriptions Telomeric repeat DNA-binding factor gene transcriptions Tetradecanoylphorbol-13-acetate response element gene transcriptions TGF-β control elements (TCEs) TGF-β inhibitory elements (TIEs) Thyroid hormone response element gene transcriptions Transcriptional regulation Transcription bubble gene transcriptions Transcription factor gene transcriptions Transcription factor 3 gene transcriptions Transcription factory gene transcriptions Transcription start site gene transcriptions Translational 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