ORE1 binding site gene transcriptions

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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 (Matallana) 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 (Matallana) (4560-2846) UTRs

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

ORE1 (Matallana) negative direction (2596-1) distal promoters

  1. Negative strand, negative direction: CGTGTATTATACTC at 275.
  2. Negative strand, negative direction: ACATCCTCAAATGAA at 1581.
  3. Positive strand, negative direction: CAGTGGATCACACG at 530.

ORE1 (Matallana) positive direction (4050-1) distal promoters

  1. Negative strand, positive direction: CCGTGGTGGGTCACA at 3822.
  2. Positive strand, positive direction: GCGTAGAGGGTACA at 3336.
  3. Positive strand, positive direction: GCACCGGCGCGTGCA at 1218, GCATCGGCGCGTGCA at 546.

ORE14 (Matallana) random dataset samplings

  1. ORE14r0: 0.
  2. ORE14r1: 1, CCGTATCGCTCACA at 2696.
  3. ORE14r2: 0.
  4. ORE14r3: 0.
  5. ORE14r4: 1, CAGTAAGGTGCACA at 2197.
  6. ORE14r5: 2, GAGTAGGTCGCACA at 3416, GCGTATGTTTTACG at 2077.
  7. ORE14r6: 1, CAGTACCCGATACG at 3218.
  8. ORE14r7: 0.
  9. ORE14r8: 0.
  10. ORE14r9: 0.
  11. ORE14r0ci: 0.
  12. ORE14r1ci: 1, CGTAAAGGCCACTG at 918.
  13. ORE14r2ci: 0.
  14. ORE14r3ci: 1, CGTAACGCGTACTT at 2222.
  15. ORE14r4ci: 0.
  16. ORE14r5ci: 1, CGTATGTTTTACGG at 2078.
  17. ORE14r6ci: 0.
  18. ORE14r7ci: 1, TGTGTCTTCTACTT at 1363.
  19. ORE14r8ci: 1, TGTACGTTTTACTC at 2157.
  20. ORE14r9ci: 1, TGTAGCCTACACGC at 2116.

ORE15 (Matallana) random dataset samplings

  1. ORE15r0: 1, GAGTGTCAATCCACA at 1163.
  2. ORE15r1: 0.
  3. ORE15r2: 0.
  4. ORE15r3: 0.
  5. ORE15r4: 0.
  6. ORE15r5: 0.
  7. ORE15r6: 1, AAGTAAACCCGCACG at 2193.
  8. RDr7: 0.
  9. RDr8: 0.
  10. RDr9: 0.
  11. RDr0ci: 0.
  12. RDr1ci: 0.
  13. RDr2ci: 0.
  14. RDr3ci: 0.
  15. RDr4ci: 0.
  16. RDr5ci: 0.
  17. RDr6ci: 0.
  18. RDr7ci: 0.
  19. RDr8ci: 0.
  20. RDr9ci: 0.

ORE1r arbitrary (evens) (4560-2846) UTRs

  1. ORE14r6: CAGTACCCGATACG at 3218.

ORE1r alternate (odds) (4560-2846) UTRs

  1. ORE14r1: CCGTATCGCTCACA at 2696.
  2. ORE14r5: GAGTAGGTCGCACA at 3416.

RDr arbitrary negative direction (evens) (2846-2811) core promoters

RDr alternate negative direction (odds) (2846-2811) core promoters

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

RDr alternate positive direction (evens) (4445-4265) core promoters

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

ORE1r alternate negative direction (odds) (2811-2596) proximal promoters

  1. ORE14r1: CCGTATCGCTCACA at 2696.

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

RDr alternate positive direction (evens) (4265-4050) proximal promoters

ORE1r arbitrary negative direction (evens) (2596-1) distal promoters

  1. ORE14r4: CAGTAAGGTGCACA at 2197.
  2. ORE14r8ci: TGTACGTTTTACTC at 2157.
  3. ORE15r0: GAGTGTCAATCCACA at 1163.
  4. ORE15r6: AAGTAAACCCGCACG at 2193.

ORE1r alternate negative direction (odds) (2596-1) distal promoters

  1. ORE14r15: GCGTATGTTTTACG at 2077.
  2. ORE14r1ci: CGTAAAGGCCACTG at 918.
  3. ORE14r3ci: CGTAACGCGTACTT at 2222.
  4. ORE14r5ci: CGTATGTTTTACGG at 2078.
  5. ORE14r7ci: TGTGTCTTCTACTT at 1363.

ORE1r arbitrary positive direction (odds) (4050-1) distal promoters

  1. ORE14r1: CCGTATCGCTCACA at 2696.
  2. ORE14r5: GAGTAGGTCGCACA at 3416, GCGTATGTTTTACG at 2077.
  3. ORE14r1ci: CGTAAAGGCCACTG at 918.
  4. ORE14r3ci: CGTAACGCGTACTT at 2222.
  5. ORE14r5ci: CGTATGTTTTACGG at 2078.
  6. ORE14r7ci: TGTGTCTTCTACTT at 1363.
  7. ORE14r9ci: TGTAGCCTACACGC at 2116.

ORE1r alternate positive direction (evens) (4050-1) distal promoters

  1. ORE14r4: CAGTAAGGTGCACA at 2197.
  2. ORE14r6: CAGTACCCGATACG at 3218.
  3. ORE14r8ci: TGTACGTTTTACTC at 2157.
  4. ORE14r9ci: TGTAGCCTACACGC at 2116.
  5. ORE15r0: GAGTGTCAATCCACA at 1163.
  6. ORE15r6: AAGTAAACCCGCACG at 2193.

ORE1 (Matallana) analysis and results

Main article: Complex locus A1BG and ZNF497 § ORE1 (Matallana)s

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]

Reals or randoms Promoters direction Numbers Strands Occurrences Averages (± 0.1)
Reals UTR negative 2 4 0.5 0.5
Randoms UTR arbitrary negative 0 10 0 0
Randoms UTR alternate negative 0 10 0 0
Reals Core negative 0 4 0 0
Randoms Core arbitrary negative 0 10 0 0
Randoms Core alternate negative 0 10 0 0
Reals Core positive 0 4 0 0
Randoms Core arbitrary positive 0 10 0 0
Randoms Core alternate positive 0 10 0 0
Reals Proximal negative 0 4 0 0
Randoms Proximal arbitrary negative 0 10 0 0
Randoms Proximal alternate negative 0 10 0 0
Reals Proximal positive 0 4 0 0
Randoms Proximal arbitrary positive 0 10 0 0
Randoms Proximal alternate positive 0 10 0 0
Reals Distal negative 3 4 0.75 0.75
Randoms Distal arbitrary negative 0 10 0 0
Randoms Distal alternate negative 0 10 0 0
Reals Distal positive 4 4 1 1
Randoms Distal arbitrary positive 0 10 0 0
Randoms Distal alternate positive 0 10 0 0

Comparison:

The occurrences of real ORE1 (Matallana)s are greater than the randoms. This suggests that the real ORE1 (Matallana)s are likely active or activable.

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 T(A/G/T)(A/G)CGT(A/G)(A/C/T)(A/G/T), 6, TGACGTGAG at 4341, TAACGTGAG at 3290, TGACGTGAG at 2427, TGACGTGAG at 2001, TAACGTGTT at 1720, TAACGTGAG at 1348.
  2. positive strand, negative direction, looking for T(A/G/T)(A/G)CGT(A/G)(A/C/T)(A/G/T), 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 T(A/G/T)(A/G)CGT(A/G)(A/C/T)(A/G/T), 0.
  5. complement, negative strand, negative direction, looking for A(A/C/T)(C/T)GCA(C/T)(A/G/T)(A/C/T), 0.
  6. complement, positive strand, negative direction, looking for A(A/C/T)(C/T)GCA(C/T)(A/G/T)(A/C/T), 6, ACTGCACTC at 4341, ATTGCACTC at 3290, ACTGCACTC at 2427, ACTGCACTC at 2001, ATTGCACAA at 1720, ATTGCACTC at 1348.
  7. complement, positive strand, positive direction, looking for A(A/C/T)(C/T)GCA(C/T)(A/G/T)(A/C/T), 0.
  8. complement, negative strand, positive direction, looking for A(A/C/T)(C/T)GCA(C/T)(A/G/T)(A/C/T), 3, AATGCATTC at 3073, ACTGCATTC at 2207, ACCGCATGC at 2154.
  9. inverse complement, negative strand, negative direction, looking for (A/C/T)(A/G/T)(C/T)ACG(C/T)(A/C/T)A, 1, CTCACGTCA at 1472.
  10. inverse complement, positive strand, negative direction, looking for (A/C/T)(A/G/T)(C/T)ACG(C/T)(A/C/T)A, 4, ATCACGCCA at 3282, CTCACGCCA at 2209, ATCACGCCA at 1993, CACACGTAA at 533.
  11. inverse complement, positive strand, positive direction, looking for (A/C/T)(A/G/T)(C/T)ACG(C/T)(A/C/T)A, 3, TACACGTCA at 3962, CTTACGTAA at 3072, CTCACGTCA at 2328.
  12. inverse complement, negative strand, positive direction, looking for (A/C/T)(A/G/T)(C/T)ACG(C/T)(A/C/T)A, 0.
  13. inverse negative strand, negative direction, looking for (A/G/T)(A/C/T)(A/G)TGC(A/G)(A/G/T)T, 4, TAGTGCGGT at 3282, GAGTGCGGT at 2209, TAGTGCGGT at 1993, GTGTGCATT at 533.
  14. inverse positive strand, negative direction, looking for (A/G/T)(A/C/T)(A/G)TGC(A/G)(A/G/T)T, 1, GAGTGCAGT at 1472.
  15. inverse positive strand, positive direction, looking for (A/G/T)(A/C/T)(A/G)TGC(A/G)(A/G/T)T, 0.
  16. inverse negative strand, positive direction, looking for (A/G/T)(A/C/T)(A/G)TGC(A/G)(A/G/T)T, 3, ATGTGCAGT at 3962, GAATGCATT at 3072, GAGTGCAGT at 2328.

ORE1 (Olsen) UTR gene transcriptions

Main article: UTR promoter gene transcriptions

Negative strand, negative direction: TGACGTGAG at 4341, TAACGTGAG at 3290.

Positive strand, negative direction: ATCACGCCA at 3282.

ORE1 (Olsen) distal promoters

Main article: Distal promoter gene transcriptions

Negative strand, negative direction: TGACGTGAG at 2427, TGACGTGAG at 2001, TAACGTGTT at 1720, CTCACGTCA at 1472, TAACGTGAG at 1348.

Positive strand, negative direction: CTCACGCCA at 2209, ATCACGCCA at 1993, CACACGTAA at 533.

Positive strand, positive direction: TACACGTCA at 3962, TTACGTAAG at 3073, CTTACGTAA at 3072, CTCACGTCA at 2328, TGACGTAAG at 2207, TGGCGTACG at 2154.

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. ↑ 3.0 3.1 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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