Cytokinin response regulator gene transcriptions: Difference between revisions

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===ARRF distal promoters===
===ARRF distal promoters===
{{main|Distal promoter gene transcriptions}}
==ARR (Rashotte1) samplings==
{{main|Model samplings}}
Copying a responsive elements consensus sequence GATCTT and putting the sequence in "⌘F" finds one between ZNF497 and A1BG or three between ZSCAN22 and A1BG as can be found by the computer programs.
For the Basic programs testing consensus sequence GATCTT (starting with SuccessablesARRF.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 GATCTT, 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.
# inverse complement, negative strand, negative direction, looking for TTTTTTTT, 0.
# inverse complement, positive strand, negative direction, looking for AAGATC, 0.
# inverse complement, positive strand, positive direction, looking for TTTTTTTT, 0.
# inverse complement, negative strand, positive direction, looking for TTTTTTTT, 0.
===ARRR1 UTRs===
{{main|UTR promoter gene transcriptions}}
===ARRR1 core promoters===
{{main|Core promoter gene transcriptions}}
===ARRR1 proximal promoters===
{{main|Proximal promoter gene transcriptions}}
===ARRR1 distal promoters===
{{main|Distal promoter gene transcriptions}}
==ARR (Rashotte2) samplings==
{{main|Model samplings}}
Copying a responsive elements consensus sequence (G/A)GAT(T/C) and putting the sequence in "⌘F" finds one between ZNF497 and A1BG or three between ZSCAN22 and A1BG as can be found by the computer programs.
For the Basic programs testing consensus sequence (G/A)GAT(T/C) (starting with SuccessablesARRF.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 (G/A)GAT(T/C), 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.
# inverse complement, negative strand, negative direction, looking for TTTTTTTT, 0.
# inverse complement, positive strand, negative direction, looking for (A/G)ATC(C/T), 0.
# inverse complement, positive strand, positive direction, looking for TTTTTTTT, 0.
# inverse complement, negative strand, positive direction, looking for TTTTTTTT, 0.
===ARRR2 UTRs===
{{main|UTR promoter gene transcriptions}}
===ARRR2 core promoters===
{{main|Core promoter gene transcriptions}}
===ARRR2 proximal promoters===
{{main|Proximal promoter gene transcriptions}}
===ARRR2 distal promoters===
{{main|Distal promoter gene transcriptions}}
{{main|Distal promoter gene transcriptions}}


Revision as of 17:52, 28 April 2021

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

"Cytokinin fulfills its diverse roles in planta through a series of transcriptional responses."[1]

Human genes

Main article: Human genes

Gene expressions

Main article: Gene expressions

Interactions

Main article: Interaction gene transcriptions

"Cytokinin employs a two-component multi-step phosphorelay for its perception and signaling transduction12–14. In Arabidopsis, there are three cytokinin receptors (ARABIDOPSIS HISTIDINE KINASEs; AHK2, 3, 4) and eleven type-B response regulators (ARABIDOSPIS RESPONSE REGULATORs; B-ARRs)8,15."[1]

"The cytokinin transcriptional response centrally affects the family of ARRs. Type-B ARRs (B-ARRs) are transcription factors (TFs) with a GARP-like DNA binding domain at their C-termini and a receiver domain at their N-termini. Type-A ARRs (A-ARRs) are similar to the N-termini receiver domain of B-ARRs but do not possess a DNA binding domain."[1]

Consensus sequences

Main article: Consensus sequence gene transcriptions

ARR1: AGATT(C/T), ARR10: (A/G)GATA(A/C)G, ARR12: (A/G)AGATA.[1]

"Type-B ARRs are transcription factors that localize to the nucleus [9,28,36]. A consensus DNA-binding sequence for type-B ARRs has been delineated (G/A)GGAT(T/C), and this sequence signature is found in the promoters of many of the cytokinin primary response genes [30]."[2]

"We used GeneSpring 5.0 software (Silicon Genetics, Redwood City, CA) to search for common motifs enriched within 1 kb upstream of the translational start site of the 17 genes that are consistently upregulated by cytokinin (those genes induced in six or more of the cytokinin treatments [...]). The sequence GATCTT was identified as a core sequence motif found significantly enriched in the upstream regions of this set of genes. [This] common upstream sequence motif GATCTT [occurs] on the forward strand, and [...] the complement of the motif AAGATC [also occurs]. Upstream regions of the cytokinin-regulated type-A ARRs showed the highest concentration of these motifs, generally clustering in the 500 bp proximal to the coding region. The sequence of this common upstream sequence motif closely matches (G/A)GAT(T/C), the optimal DNA-binding sequence identified in vitro for ARR1 and ARR2, two type-B ARRs (Sakai et al., 2000). Gel shift assays with various derivatives of the optimal type-B ARR-binding site NGAT(T/C) showed a slight preference for A at position 1 and a C at position 5, consistent with part of the common sequence motif we identified (Sakai et al., 2000). The frequency of this common upstream sequence motif in the upstream regions of the type-A ARRs is positively correlated with the level of their induction by cytokinin. The most highly cytokinin-induced genes, ARR5, ARR7, and ARR16, have multiple copies of this motif. Additionally, genes that are either only weakly induced by cytokinin or not expressed at detectable levels, ARR3, ARR4, and ARR17, have one or no motifs [...]. ARR6, which is moderately induced by cytokinin, does not fit this pattern because it has no consensus motif in its upstream region, although two such motifs are found within the fourth intron of this gene. The common upstream sequence motif (GATCTT) should randomly occur approximately 0.32 times per kilobase pair, taking into account the GC content observed in intergenic regions of Arabidopsis (approximately 33%). Our search of all genes present on the Affymetrix GeneChip that are expressed with a raw of at least 500 but not induced by cytokinin (950 genes) revealed that the sequence motif GATCTT is present a total of 358 times in the 1 kb upstream of the translational start site, or approximately 0.38 times per kilobase pair. In contrast, this core sequence motif is present 14 times among the upstream regions of the top 17 cytokinin up-regulated genes and only six times among the upstream regions of the 21 cytokinin down-regulated genes."[3]

Binding site for

Enhancer activity

Main article: Enhancer activity copy gene transcriptions

Promoter occurrences

Main article: Promoter occurrence gene transcriptions

Hypotheses

Main article: Hypotheses
  1. A1BG has no regulatory elements in either promoter.
  2. A1BG is not transcribed by a regulatory element.
  3. No regulatory element participates in the transcription of A1BG.

ARR1 Cytokinin samplings

Main article: Model samplings

Copying a responsive elements consensus sequence AGATT(C/T) and putting the sequence in "⌘F" finds one between ZNF497 and A1BG or one between ZSCAN22 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence AGATT(C/T) (starting with SuccessablesARR1.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 AGATT(C/T), 0.
  2. positive strand, negative direction, looking for AGATT(C/T), 1, AGATTC at 2452.
  3. positive strand, positive direction, looking for AGATT(C/T), 1, AGATTC at 122.
  4. negative strand, positive direction, looking for AGATT(C/T), 1, AGATTT at 2869.
  5. inverse complement, negative strand, negative direction, looking for (A/G)AATCT, 1, AAATCT at 50.
  6. inverse complement, positive strand, negative direction, looking for (A/G)AATCT, 0.
  7. inverse complement, positive strand, positive direction, looking for (A/G)AATCT, 0.
  8. inverse complement, negative strand, positive direction, looking for (A/G)AATCT, 2, GAATCT at 2725, GAATCT at 2243.

ARR1 distal promoters

Main article: Distal promoter gene transcriptions

Negative strand, negative direction: AAATCT at 50.

Positive strand, negative direction: AGATTC at 2452.

Negative strand, positive direction: AGATTT at 2869, GAATCT at 2725, GAATCT at 2243.

Positive strand, positive direction: AGATTC at 122.

ARR10 Cytokinin samplings

Main article: Model samplings

Copying a responsive elements consensus sequence (A/G)GATA(A/C)G and putting the sequence in "⌘F" finds none between ZNF497 and A1BG or none between ZSCAN22 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence (A/G)GATA(A/C)G (starting with SuccessablesARR10.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/G)GATA(A/C)G, 0.
  2. positive strand, negative direction, looking for (A/G)GATA(A/C)G, 0.
  3. positive strand, positive direction, looking for (A/G)GATA(A/C)G, 0.
  4. negative strand, positive direction, looking for (A/G)GATA(A/C)G, 0.
  5. inverse complement, negative strand, negative direction, looking for C(G/T)TATC(C/T), 1, CGTATCC at 3447.
  6. inverse complement, positive strand, negative direction, looking for C(G/T)TATC(C/T), 0.
  7. inverse complement, positive strand, positive direction, looking for C(G/T)TATC(C/T), 0.
  8. inverse complement, negative strand, positive direction, looking for C(G/T)TATC(C/T), 0.

ARR10 UTRs

Main article: UTR promoter gene transcriptions

Negative strand, negative direction: CGTATCC at 3447.

ARR12 Cytokinin samplings

Main article: Model samplings

Copying a responsive elements consensus sequence (A/G)AGATA and putting the sequence in "⌘F" finds none between ZNF497 and A1BG or none between ZSCAN22 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence (A/G)AGATA (starting with SuccessablesARR1.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/G)AGATA, 1, AAGATA at 1525.
  2. positive strand, negative direction, looking for (A/G)AGATA, 3, AAGATA at 2177, AAGATA at 1595, AAGATA at 57.
  3. positive strand, positive direction, looking for (A/G)AGATA, 0.
  4. negative strand, positive direction, looking for (A/G)AGATA, 0.
  5. inverse complement, negative strand, negative direction, looking for TATCT(C/T), 4, TATCTT at 4080, TATCTC at 1711, TATCTT at 356, TATCTT at 101.
  6. inverse complement, positive strand, negative direction, looking for TATCT(C/T), 1, TATCTT at 1732.
  7. inverse complement, positive strand, positive direction, looking for TATCT(C/T), 1, TATCTT at 2628.
  8. inverse complement, negative strand, positive direction, looking for TATCT(C/T), 0.

ARR12 UTRs

Main article: UTR promoter gene transcriptions

Negative strand, negative direction: TATCTT at 4080.

ARR12 distal promoters

Main article: Distal promoter gene transcriptions

Negative strand, negative direction: TATCTC at 1711, AAGATA at 1525, TATCTT at 356, TATCTT at 101.

Positive strand, negative direction: AAGATA at 2177, TATCTT at 1732, AAGATA at 1595, AAGATA at 57.

Positive strand, positive direction: TATCTT at 2628.

ARR (Ferreira) samplings

Main article: Model samplings

Copying a responsive elements consensus sequence (G/A)GGAT(T/C) and putting the sequence in "⌘F" finds one between ZNF497 and A1BG or three between ZSCAN22 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence (G/A)GGAT(T/C) (starting with SuccessablesARRF.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 (G/A)GGAT(T/C), 0.
  2. positive strand, negative direction, looking for AAAAAAAA, 0.
  3. positive strand, positive direction, looking for AAAAAAAA, 0.
  4. negative strand, positive direction, looking for AAAAAAAA, 0.
  5. inverse complement, negative strand, negative direction, looking for (A/G)ATCC(C/T), 0.
  6. inverse complement, positive strand, negative direction, looking for TTTTTTTT, 0.
  7. inverse complement, positive strand, positive direction, looking for TTTTTTTT, 0.
  8. inverse complement, negative strand, positive direction, looking for TTTTTTTT, 0.

ARRF UTRs

Main article: UTR promoter gene transcriptions

ARRF core promoters

Main article: Core promoter gene transcriptions

ARRF proximal promoters

Main article: Proximal promoter gene transcriptions

ARRF distal promoters

Main article: Distal promoter gene transcriptions

ARR (Rashotte1) samplings

Main article: Model samplings

Copying a responsive elements consensus sequence GATCTT and putting the sequence in "⌘F" finds one between ZNF497 and A1BG or three between ZSCAN22 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence GATCTT (starting with SuccessablesARRF.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 GATCTT, 0.
  2. positive strand, negative direction, looking for AAAAAAAA, 0.
  3. positive strand, positive direction, looking for AAAAAAAA, 0.
  4. negative strand, positive direction, looking for AAAAAAAA, 0.
  5. inverse complement, negative strand, negative direction, looking for TTTTTTTT, 0.
  6. inverse complement, positive strand, negative direction, looking for AAGATC, 0.
  7. inverse complement, positive strand, positive direction, looking for TTTTTTTT, 0.
  8. inverse complement, negative strand, positive direction, looking for TTTTTTTT, 0.

ARRR1 UTRs

Main article: UTR promoter gene transcriptions

ARRR1 core promoters

Main article: Core promoter gene transcriptions

ARRR1 proximal promoters

Main article: Proximal promoter gene transcriptions

ARRR1 distal promoters

Main article: Distal promoter gene transcriptions

ARR (Rashotte2) samplings

Main article: Model samplings

Copying a responsive elements consensus sequence (G/A)GAT(T/C) and putting the sequence in "⌘F" finds one between ZNF497 and A1BG or three between ZSCAN22 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence (G/A)GAT(T/C) (starting with SuccessablesARRF.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 (G/A)GAT(T/C), 0.
  2. positive strand, negative direction, looking for AAAAAAAA, 0.
  3. positive strand, positive direction, looking for AAAAAAAA, 0.
  4. negative strand, positive direction, looking for AAAAAAAA, 0.
  5. inverse complement, negative strand, negative direction, looking for TTTTTTTT, 0.
  6. inverse complement, positive strand, negative direction, looking for (A/G)ATC(C/T), 0.
  7. inverse complement, positive strand, positive direction, looking for TTTTTTTT, 0.
  8. inverse complement, negative strand, positive direction, looking for TTTTTTTT, 0.

ARRR2 UTRs

Main article: UTR promoter gene transcriptions

ARRR2 core promoters

Main article: Core promoter gene transcriptions

ARRR2 proximal promoters

Main article: Proximal promoter gene transcriptions

ARRR2 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 1.2 1.3 Mingtang Xie1, Hongyu Chen, Ling Huang, Ryan C. O’Neil1, Maxim N. Shokhirev & Joseph R. Ecker (23 April 2018). "A B-ARR-mediated cytokinin transcriptional network directs hormone cross-regulation and shoot development" (PDF). Nature Communications. 9 (1604): 1–13. doi:10.1038/s41467-018-03921-6. Retrieved 26 April 2021.
  2. ↑ Fernando J Ferreira and Joseph J Kieber (October 2005). "Cytokinin signaling" (PDF). Current Opinion in Plant Biology. 8 (5): 518–525. doi:10.1016/j.pbi.2005.07.013. Retrieved 28 April 2021.
  3. ↑ Aaron M. Rashotte, Susan D.B. Carson, Jennifer P.C. To, and Joseph J. Kieber (August 2003). "Expression Profiling of Cytokinin Action in Arabidopsis" (PDF). Plant Physiology. 132 (4): 1998–2011. doi:10.1104/pp.103.021436. Retrieved 28 April 2021.

External links

Retrieved from "https://www.wikidoc.org/index.php?title=Cytokinin_response_regulator_gene_transcriptions&oldid=1699150"