ORE1 binding site gene transcriptions: Difference between revisions
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{{AE}} Henry A. Hoff | {{AE}} 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)."<ref name=Kim>{{ cite journal | |||
|author=Jin Hee Kim, Hye Ryun Woo, Jeongsik Kim, Pyung Ok Lim, In Chul Lee, Seung Hee Choi, Daehee Hwang, Hong Gil Nam | |||
|title=Trifurcate Feed-Forward Regulation of Age-Dependent Cell Death Involving ''miR164'' in ''Arabidopsis'' | |||
|journal=Science | |||
|date=20 February 2009 | |||
|volume=323 | |||
|issue=5917 | |||
|pages=1053-1057 | |||
|url=https://science.sciencemag.org/content/323/5917/1053.full?maxtoshow=&hits=10&RESULTFORMAT=&fulltext=oresara+1&searchid=1&FIRSTINDEX=0&resourcetype=HWCIT | |||
|arxiv= | |||
|bibcode= | |||
|doi=10.1126/science.1166386 | |||
|pmid= | |||
|accessdate=10 February 2021 }}</ref> | |||
"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."<ref name=Kim/> | |||
"Nitrogen deficiency (−N) in plants triggers leaf senescence which is regulated by the transcription factor ORE1."<ref name=Park>{{ cite journal | "Nitrogen deficiency (−N) in plants triggers leaf senescence which is regulated by the transcription factor ORE1."<ref name=Park>{{ cite journal | ||
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|accessdate=4 October 2020 }}</ref> | |accessdate=4 October 2020 }}</ref> | ||
== | ==ORE1 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 48: | Line 65: | ||
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. | 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 AAAAAAAA (starting with | For the Basic programs testing consensus sequence AAAAAAAA (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: | ||
# negative strand, negative direction, looking for AAAAAAAA, 0. | # negative strand, negative direction, looking for AAAAAAAA, 0. | ||
# positive strand, negative direction, looking for AAAAAAAA, 0. | # positive strand, negative direction, looking for AAAAAAAA, 0. | ||
| Line 66: | Line 83: | ||
# inverse negative strand, positive direction, looking for AAAAAAAA, 0. | # inverse negative strand, positive direction, looking for AAAAAAAA, 0. | ||
=== | ===ORE UTR gene transcriptions=== | ||
{{main|UTR promoter gene transcriptions}} | {{main|UTR promoter gene transcriptions}} | ||
=== | ===ORE core promoters=== | ||
{{main|Core promoter gene transcriptions}} | {{main|Core promoter gene transcriptions}} | ||
=== | ===ORE proximal promoters=== | ||
{{main|Proximal promoter gene transcriptions}} | {{main|Proximal promoter gene transcriptions}} | ||
=== | ===ORE distal promoters=== | ||
{{main|Distal promoter gene transcriptions}} | {{main|Distal promoter gene transcriptions}} | ||
Revision as of 05:31, 11 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] [29] or T[TAG][GA]CGT[GA][TCA][TAG] [37]."[3]
Human genes
Consensus sequences
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'.[3]
ORE1 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 AAAAAAAA (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:
- negative strand, negative direction, looking for AAAAAAAA, 0.
- positive strand, negative direction, looking for AAAAAAAA, 0.
- positive strand, positive direction, looking for AAAAAAAA, 0.
- negative strand, positive direction, looking for AAAAAAAA, 0.
- complement, negative strand, negative direction, looking for TTTTTTTT, 0.
- complement, positive strand, negative direction, looking for TTTTTTTT, 0.
- complement, positive strand, positive direction, looking for TTTTTTTT, 0.
- complement, negative strand, positive direction, looking for TTTTTTTT, 0.
- inverse complement, negative strand, negative direction, looking for TTTTTTTT, 0.
- inverse complement, positive strand, negative direction, looking for TTTTTTTT, 0.
- inverse complement, positive strand, positive direction, looking for TTTTTTTT, 0.
- inverse complement, negative strand, positive direction, looking for TTTTTTTT, 0.
- inverse negative strand, negative direction, looking for AAAAAAAA, 0.
- inverse positive strand, negative direction, looking for AAAAAAAA, 0.
- inverse positive strand, positive direction, looking for AAAAAAAA, 0.
- inverse negative strand, positive direction, looking for AAAAAAAA, 0.
ORE UTR gene transcriptions
ORE core promoters
ORE proximal promoters
ORE distal promoters
Acknowledgements
The content on this page was first contributed by: Henry A. Hoff.
See also
References
- ↑ 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.
- ↑ 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.
- ↑ 3.0 3.1 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.