ORE1 binding site gene transcriptions: Difference between revisions

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Positive strand, positive direction: GCGTAGAGGGTACA at 3336.
Positive strand, positive direction: GCGTAGAGGGTACA at 3336.


==ORE1-2 samplings==
==ORE1 (Olsen) samplings==
{{main|Model samplings}}
{{main|Model samplings}}
Copying 5'-TTACGTG-3' in "⌘F" yields none between ZSCAN22 and A1BG and none between ZNF497 and A1BG as can be found by the computer programs.
Copying 5'-TTACGTG-3' in "⌘F" yields none between ZSCAN22 and A1BG and none between ZNF497 and A1BG as can be found by the computer programs.
Line 159: Line 159:
# inverse negative strand, positive direction, looking for AAAAAAAA, 0.
# inverse negative strand, positive direction, looking for AAAAAAAA, 0.


===ORE1-2 UTR gene transcriptions===
===ORE1 (Olsen) UTR gene transcriptions===
{{main|UTR promoter gene transcriptions}}
{{main|UTR promoter gene transcriptions}}


===ORE1-2 core promoters===
===ORE1 (Olsen) core promoters===
{{main|Core promoter gene transcriptions}}
{{main|Core promoter gene transcriptions}}


===ORE1-2 proximal promoters===
===ORE1 (Olsen) proximal promoters===
{{main|Proximal promoter gene transcriptions}}
{{main|Proximal promoter gene transcriptions}}


===ORE1-2 distal promoters===
===ORE1 (Olsen) distal promoters===
{{main|Distal promoter gene transcriptions}}
{{main|Distal promoter gene transcriptions}}


Revision as of 16:41, 12 February 2021

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

"The Arabidopsis oresara1-1 (ore1-1, oresara means “long-living” in Korean) mutant was initially identified as a delayed leaf senescence mutant (4)."[1]

"ORE1, which is a NAC (NAM, ATAF, and CUC) transcription factor, positively regulates aging-induced cell death in Arabidopsis leaves. ORE1 expression is up-regulated concurrently with leaf aging by EIN2 but is negatively regulated by miR164. miR164 expression gradually decreases with aging through negative regulation by EIN2, which leads to the elaborate up-regulation of ORE1 expression. However, EIN2 still contributes to aging-induced cell death in the absence of ORE1. The trifurcate feed-forward pathway involving ORE1, miR164, and EIN2 provides a highly robust regulation to ensure that aging induces cell death in Arabidopsis leaves."[1]

"Nitrogen deficiency (−N) in plants triggers leaf senescence which is regulated by the transcription factor ORE1."[2]

"As a transcription factor, ORE1 was reported to bind to consensus DNA sequences of [ACG][CA]GT[AG]N{5,6}[CT]AC[AG][3] or T[TAG][GA]CGT[GA][TCA][TAG][4]."[5]

Human genes

Main article: Human genes

Consensus sequences

Main article: Consensus sequence gene transcriptions

Consensus sequences are 5'-(A/C/G)(A/C)GT(A/G)N5,6(C/T)AC(A/G)-3' or 5'-T(A/G/T)(A/G)CGT(A/G)(A/C/T)(A/G/T)-3'.[5]

ORE1-1 samplings

Main article: Model samplings

Copying CAGTGCAGTGT in "⌘F" yields none between ZSCAN22 and A1BG and none between ZNF497 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence (A/C/G)(A/C)GT(A/G)N5,6(C/T)AC(A/G) (starting with SuccessablesORE.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:

  1. negative strand, negative direction, looking for (A/C/G)(A/C)GT(A/G)NNNNN(C/T)AC(A/G), 2, GCGTAGAAGACACA at 3558, AAGTAGTTTCTACG at 2895.
  2. negative strand, negative direction, looking for (A/C/G)(A/C)GT(A/G)NNNNNN(C/T)AC(A/G), 0.
  3. positive strand, negative direction, looking for (A/C/G)(A/C)GT(A/G)NNNNN(C/T)AC(A/G), 1, CAGTGGATCACACG at 530.
  4. positive strand, negative direction, looking for (A/C/G)(A/C)GT(A/G)NNNNNN(C/T)AC(A/G), 0.
  5. positive strand, positive direction, looking for (A/C/G)(A/C)GT(A/G)NNNNN(C/T)AC(A/G), 1, GCGTAGAGGGTACA at 3336.
  6. positive strand, positive direction, looking for (A/C/G)(A/C)GT(A/G)NNNNNN(C/T)AC(A/G), 0.
  7. negative strand, positive direction, looking for (A/C/G)(A/C)GT(A/G)NNNNN(C/T)AC(A/G), 0.
  8. negative strand, positive direction, looking for (A/C/G)(A/C)GT(A/G)NNNNNN(C/T)AC(A/G), 1, CCGTGGTGGGTCACA at 3822.
  9. complement, negative strand, negative direction, looking for (C/G/T)(G/T)CA(C/T)NNNNN(A/G)TG(C/T), 1, GTCACCTAGTGTGC at 530.
  10. complement, negative strand, negative direction, looking for (C/G/T)(G/T)CA(C/T)NNNNNN(A/G)TG(C/T), 0.
  11. complement, positive strand, negative direction, looking for (C/G/T)(G/T)CA(C/T)NNNNN(A/G)TG(C/T), 2, CGCATCTTCTGTGT at 3558, TTCATCAAAGATGC at 2895.
  12. complement, positive strand, negative direction, looking for (C/G/T)(G/T)CA(C/T)NNNNNN(A/G)TG(C/T), 0.
  13. complement, positive strand, positive direction, looking for (C/G/T)(G/T)CA(C/T)NNNNN(A/G)TG(C/T), 0.
  14. complement, positive strand, positive direction, looking for (C/G/T)(G/T)CA(C/T)NNNNNN(A/G)TG(C/T), 1, GGCACCACCCAGTGT at 3822.
  15. complement, negative strand, positive direction, looking for (C/G/T)(G/T)CA(C/T)NNNNN(A/G)TG(C/T), 1, CGCATCTCCCATGT at 3336.
  16. complement, negative strand, positive direction, looking for (C/G/T)(G/T)CA(C/T)NNNNNN(A/G)TG(C/T), 0.
  17. inverse complement, negative strand, negative direction, looking for (C/T)GT(A/G)NNNNN(C/T)AC(G/T)(C/G/T), 1, CGTGTATTATACTC at 275.
  18. inverse complement, negative strand, negative direction, looking for (C/T)GT(A/G)NNNNNN(C/T)AC(G/T)(C/G/T), 1, ACATCCTCAAATGAA at 1581.
  19. inverse complement, positive strand, negative direction, looking for (C/T)GT(A/G)NNNNN(C/T)AC(G/T)(C/G/T), 0.
  20. inverse complement, positive strand, negative direction, looking for (C/T)GT(A/G)NNNNNN(C/T)AC(G/T)(C/G/T), 0.
  21. inverse complement, positive strand, positive direction, looking for (C/T)GT(A/G)NNNNN(C/T)AC(G/T)(C/G/T), 0.
  22. inverse complement, positive strand, positive direction, looking for (C/T)GT(A/G)NNNNNN(C/T)AC(G/T)(C/G/T), 2, GCACCGGCGCGTGCA at 1218, GCATCGGCGCGTGCA at 546.
  23. inverse complement, negative strand, positive direction, looking for (C/T)GT(A/G)NNNNN(C/T)AC(G/T)(C/G/T), 0.
  24. inverse complement, negative strand, positive direction, looking for (C/T)GT(A/G)NNNNNN(C/T)AC(G/T)(C/G/T), 0.
  25. inverse negative strand, negative direction, looking for (A/G)CA(C/T)NNNNN(A/G)TG(A/C)(A/C/G), 0.
  26. inverse negative strand, negative direction, looking for (A/G)CA(C/T)NNNNNN(A/G)TG(A/C)(A/C/G), 0.
  27. inverse positive strand, negative direction, looking for (A/G)CA(C/T)NNNNN(A/G)TG(A/C)(A/C/G), 1, GCACATAATATGAG at 275.
  28. inverse positive strand, negative direction, looking for (A/G)CA(C/T)NNNNNN(A/G)TG(A/C)(A/C/G), 1, ACATCCTCAAATGAA at 1581.
  29. inverse positive strand, positive direction, looking for (A/G)CA(C/T)NNNNN(A/G)TG(A/C)(A/C/G), 0.
  30. inverse positive strand, positive direction, looking for (A/G)CA(C/T)NNNNNN(A/G)TG(A/C)(A/C/G), 0.
  31. inverse negative strand, positive direction, looking for (A/G)CA(C/T)NNNNN(A/G)TG(A/C)(A/C/G), 0.
  32. inverse negative strand, positive direction, looking for (A/G)CA(C/T)NNNNNN(A/G)TG(A/C)(A/C/G), 2, GCACCGGCGCGTGCA at 1218, GCATCGGCGCGTGCA at 546.

ORE1-1 UTR gene transcriptions

Main article: UTR promoter gene transcriptions

Negative strand, negative direction: GCGTAGAAGACACA at 3558, AAGTAGTTTCTACG at 2895.

ORE1-1 distal promoters

Main article: Distal promoter gene transcriptions

Positive strand, negative direction: ACATCCTCAAATGAA at 1581, CAGTGGATCACACG at 530, GCACATAATATGAG at 275.

Negative strand, positive direction: CCGTGGTGGGTCACA at 3822, GCACCGGCGCGTGCA at 1218, GCATCGGCGCGTGCA at 546.

Positive strand, positive direction: GCGTAGAGGGTACA at 3336.

ORE1 (Olsen) samplings

Main article: Model samplings

Copying 5'-TTACGTG-3' in "⌘F" yields none between ZSCAN22 and A1BG and none between ZNF497 and A1BG as can be found by the computer programs.

Copying 5'-TGACGTGAG-3' in "⌘F" yields three between ZSCAN22 and A1BG and none between ZNF497 and A1BG as can be found by the computer programs.

Copying 5'-TAGCGT-3' in "⌘F" yields none between ZSCAN22 and A1BG and none between ZNF497 and A1BG as can be found by the computer programs.

Copying 5'-TAACGTGAG-3' in "⌘F" yields two between ZSCAN22 and A1BG and none between ZNF497 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence T(A/G/T)(A/G)CGT(A/G)(A/C/T)(A/G/T) (starting with SuccessablesORE2.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:

  1. negative strand, negative direction, looking for AAAAAAAA, 0.
  2. positive strand, negative direction, looking for AAAAAAAA, 0.
  3. positive strand, positive direction, looking for T(A/G/T)(A/G)CGT(A/G)(A/C/T)(A/G/T), 3, TTACGTAAG at 3073, TGACGTAAG at 2207, TGGCGTACG at 2154.
  4. negative strand, positive direction, looking for AAAAAAAA, 0.
  5. complement, negative strand, negative direction, looking for TTTTTTTT, 0.
  6. complement, positive strand, negative direction, looking for TTTTTTTT, 0.
  7. complement, positive strand, positive direction, looking for TTTTTTTT, 0.
  8. complement, negative strand, positive direction, looking for TTTTTTTT, 0.
  9. inverse complement, negative strand, negative direction, looking for TTTTTTTT, 0.
  10. inverse complement, positive strand, negative direction, looking for TTTTTTTT, 0.
  11. inverse complement, positive strand, positive direction, looking for TTTTTTTT, 0.
  12. inverse complement, negative strand, positive direction, looking for TTTTTTTT, 0.
  13. inverse negative strand, negative direction, looking for AAAAAAAA, 0.
  14. inverse positive strand, negative direction, looking for AAAAAAAA, 0.
  15. inverse positive strand, positive direction, looking for AAAAAAAA, 0.
  16. inverse negative strand, positive direction, looking for AAAAAAAA, 0.

ORE1 (Olsen) UTR gene transcriptions

Main article: UTR promoter gene transcriptions

ORE1 (Olsen) core promoters

Main article: Core promoter gene transcriptions

ORE1 (Olsen) proximal promoters

Main article: Proximal promoter gene transcriptions

ORE1 (Olsen) distal promoters

Main article: Distal promoter gene transcriptions

Acknowledgements

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

See also

References

  1. ↑ 1.0 1.1 Jin Hee Kim, Hye Ryun Woo, Jeongsik Kim, Pyung Ok Lim, In Chul Lee, Seung Hee Choi, Daehee Hwang, Hong Gil Nam (20 February 2009). "Trifurcate Feed-Forward Regulation of Age-Dependent Cell Death Involving miR164 in Arabidopsis". Science. 323 (5917): 1053–1057. doi:10.1126/science.1166386. Retrieved 10 February 2021.
  2. ↑ Su‐Hyun Park, Jin Seo Jeong, Jun Sung Seo, Bong Soo Park, Nam‐Hai Chua (3 May 2019). "Arabidopsis ubiquitin‐specific proteases UBP12 and UBP13 shape ORE1 levels during leaf senescence induced by nitrogen deficiency". New Phytologist. 223 (3): 1447–1460. doi:10.1111/nph.15879. Retrieved 10 February 2021.
  3. ↑ Lilian P. Matallana-Ramirez, Mamoona Rauf, Sarit Farage-Barhom, Hakan Dortay, Gang-Ping Xue, Wolfgang Dröge-Laser, Amnon Lers, Salma Balazadeh and Bernd Mueller-Roeber (1 September 2013). "NAC Transcription Factor ORE1 and Senescence-Induced BIFUNCTIONAL NUCLEASE1 (BFN1) Constitute a Regulatory Cascade in Arabidopsis". Molecular Plant. 6 (5): P1438–1452. doi:10.1093/mp/sst012. Retrieved 12 February 2021.
  4. ↑ Addie N. Olsen, Heidi A. Ernst, Leila Lo Leggio, and Karen Skriver (October 2005). "DNA-binding specificity and molecular functions of NAC transcription factors". Plant Science. 169 (4): 785–797. doi:10.1016/j.plantsci.2005.05.035. Retrieved 12 February 2021.
  5. ↑ 5.0 5.1 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

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