G box gene transcriptions: Difference between revisions

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Most bZIP proteins show high binding affinity for the ACGT motifs, which include CACGTG (G box) [...].<ref name=Landschulz>{{ cite journal
Most bZIP proteins show high binding affinity for the ACGT motifs, which include CACGTG (G box) [...].<ref name=Landschulz>{{ cite journal
| vauthors = Landschulz WH, Johnson PF, McKnight SL | title = The leucine zipper: a hypothetical structure common to a new class of DNA binding proteins | journal = Science | volume = 240 | issue = 4860 | pages = 1759–64 | date = June 1988 | pmid = 3289117
| author = Landschulz WH, Johnson PF, McKnight SL | title = The leucine zipper: a hypothetical structure common to a new class of DNA binding proteins | journal = Science | volume = 240 | issue = 4860 | pages = 1759–64 | date = June 1988 | pmid = 3289117
| doi = 10.1126/science.3289117 | bibcode = 1988Sci...240.1759L
| doi = 10.1126/science.3289117 | bibcode = 1988Sci...240.1759L
| url = https://semanticscholar.org/paper/3a61c172ddfa79ce9f4909ca6bea2f6f40f7893e }}</ref><ref name=Zhang>{{ cite journal
| url = https://semanticscholar.org/paper/3a61c172ddfa79ce9f4909ca6bea2f6f40f7893e }}</ref><ref name=Zhang>{{ cite journal
| vauthors = Z G E, Zhang YP, Zhou JH, Wang L
| author = Z G E, Zhang YP, Zhou JH, Wang L
| title = Mini review roles of the bZIP gene family in rice
| title = Mini review roles of the bZIP gene family in rice
| journal = Genetics and Molecular Research
| journal = Genetics and Molecular Research
Line 49: Line 49:
| date = April 2014
| date = April 2014
| pmid = 24782137
| pmid = 24782137
| doi = 10.4238/2014.April.16.11 }}</ref><ref name=Nijhawan>{{ cite journal | vauthors = Nijhawan A, Jain M, Tyagi AK, Khurana JP
| doi = 10.4238/2014.April.16.11 }}</ref><ref name=Nijhawan>{{ cite journal | author = Nijhawan A, Jain M, Tyagi AK, Khurana JP
| title = Genomic survey and gene expression analysis of the basic leucine zipper transcription factor family in rice
| title = Genomic survey and gene expression analysis of the basic leucine zipper transcription factor family in rice
| journal = Plant Physiology
| journal = Plant Physiology
Line 79: Line 79:


For the Basic programs (starting with SuccessablesGbox.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 (+), including extending the number of nts from 958 to 4445, the programs are, are looking for, and found:
For the Basic programs (starting with SuccessablesGbox.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 (+), including extending the number of nts from 958 to 4445, the programs are, are looking for, and found:
# negative strand in the negative direction (from ZSCAN22 to A1BG) is SuccessablesGbox--.bas, looking for 3'-GCCACGTGGC-5', 0,
# negative strand in the negative direction (from ZSCAN22 to A1BG) is SuccessablesGbox--.bas, looking for GCCACGTGGC, 0,
# negative strand in the positive direction (from ZNF497 to A1BG) is SuccessablesGbox-+.bas, looking for 3'-GCCACGTGGC-5', 0,
# negative strand in the positive direction (from ZNF497 to A1BG) is SuccessablesGbox-+.bas, looking for GCCACGTGGC, 0,
# positive strand in the negative direction is SuccessablesGbox+-.bas, looking for 3'-GCCACGTGGC-5', 0,
# positive strand in the negative direction is SuccessablesGbox+-.bas, looking for GCCACGTGGC, 0,
# positive strand in the positive direction is SuccessablesGbox++.bas, looking for 3'-GCCACGTGGC-5', 0,
# positive strand in the positive direction is SuccessablesGbox++.bas, looking for GCCACGTGGC, 0,
# complement, negative strand, negative direction is SuccessablesGboxc--.bas, looking for 3'-CGGTGCACCG-5', 0,
# inverse complement, negative strand, negative direction is SuccessablesGboxci--.bas, looking for GCCACGTGGC, 0,
# complement, negative strand, positive direction is SuccessablesGboxc-+.bas, looking for 3'-CGGTGCACCG-5', 0,
# inverse complement, negative strand, positive direction is SuccessablesGboxci-+.bas, looking for GCCACGTGGC, 0,
# complement, positive strand, negative direction is SuccessablesGboxc+-.bas, looking for 3'-CGGTGCACCG-5', 0,
# inverse complement, positive strand, negative direction is SuccessablesGboxci+-.bas, looking for GCCACGTGGC, 0,
# complement, positive strand, positive direction is SuccessablesGboxc++.bas, looking for 3'-CGGTGCACCG-5', 0,
# inverse complement, positive strand, positive direction is SuccessablesGboxci++.bas, looking for GCCACGTGGC, 0,
# inverse complement, negative strand, negative direction is SuccessablesGboxci--.bas, looking for 3'-GCCACGTGGC-5', 0,
 
# inverse complement, negative strand, positive direction is SuccessablesGboxci-+.bas, looking for 3'-GCCACGTGGC-5', 0,
===GObox random dataset samplings===
# inverse complement, positive strand, negative direction is SuccessablesGboxci+-.bas, looking for 3'-GCCACGTGGC-5', 0,
 
# inverse complement, positive strand, positive direction is SuccessablesGboxci++.bas, looking for 3'-GCCACGTGGC-5', 0,
# GOboxr0: 0.
# inverse, negative strand, negative direction, is SuccessablesGboxi--.bas, looking for 3'-CGGTGCACCG-5', 0,
# GOboxr1: 0.
# inverse, negative strand, positive direction, is SuccessablesGboxi-+.bas, looking for 3'-CGGTGCACCG-5', 0,
# GOboxr2: 0.
# inverse, positive strand, negative direction, is SuccessablesGboxi+-.bas, looking for 3'-CGGTGCACCG-5', 0,
# GOboxr3: 0.
# inverse, positive strand, positive direction, is SuccessablesGboxi++.bas, looking for 3'-CGGTGCACCG-5', 0.
# GOboxr4: 0.
# GOboxr5: 0.
# GOboxr6: 0.
# GOboxr7: 0.
# GOboxr8: 0.
# GOboxr9: 0.
 
==Song samplings==
Copying a responsive elements consensus sequence (G/T)CCACGTG(G/T)C 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 (G/T)CCACGTG(G/T)C (starting with SuccessablesGSbox.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/T)CCACGTG(G/T)C, 0.
# positive strand, negative direction, looking for (G/T)CCACGTG(G/T)C, 0.
# positive strand, positive direction, looking for (G/T)CCACGTG(G/T)C, 0.
# negative strand, positive direction, looking for (G/T)CCACGTG(G/T)C, 0.
# inverse complement, negative strand, negative direction, looking for G(A/C)CACGTGG(A/C), 0.
# inverse complement, positive strand, negative direction, looking for G(A/C)CACGTGG(A/C), 0.
# inverse complement, positive strand, positive direction, looking for G(A/C)CACGTGG(A/C), 0.
# inverse complement, negative strand, positive direction, looking for G(A/C)CACGTGG(A/C), 0.
 
===GSbox random dataset samplings===
 
# GSboxr0: 0.
# GSboxr1: 0.
# GSboxr2: 0.
# GSboxr3: 0.
# GSboxr4: 0.
# GSboxr5: 0.
# GSboxr6: 1, TCCACGTGTC at 2907.
# GSboxr7: 0.
# GSboxr8: 0.
# GSboxr9: 0.
# GSboxr0ci: 0.
# GSboxr1ci: 0.
# GSboxr2ci: 0.
# GSboxr3ci: 0.
# GSboxr4ci: 0.
# GSboxr5ci: 0.
# GSboxr6ci: 0.
# GSboxr7ci: 0.
# GSboxr8ci: 0.
# GSboxr9ci: 0.
 
===GSboxr UTRs===
{{main|UTR promoter gene transcriptions}}
# GSboxr6: TCCACGTGTC at 2907.


==Acknowledgements==
==Acknowledgements==
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Latest revision as of 17:26, 15 July 2023

Editor-In-Chief: Henry A. Hoff

"Two distinct sequence elements, the H-box (consensus CCTACC(N)7CT) and the G-box (CACGTG), are required for stimulation of the chsl5 promoter by [p-coumaric acid] 4-CA."[1]

G boxes

The "perfect palindrome 5'-GCCACGTGGC-3' which is also known as the G-box motif."[2]

"TAF-1 can bind to the G-box and related motifs and that it functions as a transcription activator."[2]

"A G-box-related motif, containing the core sequence CACGTG is also present in the 5' regions of two other classes of light-responsive genes".[2]

Most bZIP proteins show high binding affinity for the ACGT motifs, which include CACGTG (G box) [...].[3][4][5]

"Binding to the palindromic G-box (PA G-box, GCCACGTGGC) was moderate. However, binding activity to the G-box of the light-responsive unit 1 (U1) region of the parsley (Petroselinum crispum) CHS promoter (CHS-U1: TCCACGTGGC; Schulze-Lefert et al., 1989) or the G-box of GmAux28 (TCCACGTGTC) was much weaker than to the PA G-box [...]."[6]

(G/T)CCACGTG(G/T)C combines the PA G-box (GCCACGTGGC) with the G-box of GmAux28 (TCCACGTGTC) for testing both.

Oeda samplings

For the Basic programs (starting with SuccessablesGbox.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 (+), including extending the number of nts from 958 to 4445, the programs are, are looking for, and found:

  1. negative strand in the negative direction (from ZSCAN22 to A1BG) is SuccessablesGbox--.bas, looking for GCCACGTGGC, 0,
  2. negative strand in the positive direction (from ZNF497 to A1BG) is SuccessablesGbox-+.bas, looking for GCCACGTGGC, 0,
  3. positive strand in the negative direction is SuccessablesGbox+-.bas, looking for GCCACGTGGC, 0,
  4. positive strand in the positive direction is SuccessablesGbox++.bas, looking for GCCACGTGGC, 0,
  5. inverse complement, negative strand, negative direction is SuccessablesGboxci--.bas, looking for GCCACGTGGC, 0,
  6. inverse complement, negative strand, positive direction is SuccessablesGboxci-+.bas, looking for GCCACGTGGC, 0,
  7. inverse complement, positive strand, negative direction is SuccessablesGboxci+-.bas, looking for GCCACGTGGC, 0,
  8. inverse complement, positive strand, positive direction is SuccessablesGboxci++.bas, looking for GCCACGTGGC, 0,

GObox random dataset samplings

  1. GOboxr0: 0.
  2. GOboxr1: 0.
  3. GOboxr2: 0.
  4. GOboxr3: 0.
  5. GOboxr4: 0.
  6. GOboxr5: 0.
  7. GOboxr6: 0.
  8. GOboxr7: 0.
  9. GOboxr8: 0.
  10. GOboxr9: 0.

Song samplings

Copying a responsive elements consensus sequence (G/T)CCACGTG(G/T)C 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 (G/T)CCACGTG(G/T)C (starting with SuccessablesGSbox.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/T)CCACGTG(G/T)C, 0.
  2. positive strand, negative direction, looking for (G/T)CCACGTG(G/T)C, 0.
  3. positive strand, positive direction, looking for (G/T)CCACGTG(G/T)C, 0.
  4. negative strand, positive direction, looking for (G/T)CCACGTG(G/T)C, 0.
  5. inverse complement, negative strand, negative direction, looking for G(A/C)CACGTGG(A/C), 0.
  6. inverse complement, positive strand, negative direction, looking for G(A/C)CACGTGG(A/C), 0.
  7. inverse complement, positive strand, positive direction, looking for G(A/C)CACGTGG(A/C), 0.
  8. inverse complement, negative strand, positive direction, looking for G(A/C)CACGTGG(A/C), 0.

GSbox random dataset samplings

  1. GSboxr0: 0.
  2. GSboxr1: 0.
  3. GSboxr2: 0.
  4. GSboxr3: 0.
  5. GSboxr4: 0.
  6. GSboxr5: 0.
  7. GSboxr6: 1, TCCACGTGTC at 2907.
  8. GSboxr7: 0.
  9. GSboxr8: 0.
  10. GSboxr9: 0.
  11. GSboxr0ci: 0.
  12. GSboxr1ci: 0.
  13. GSboxr2ci: 0.
  14. GSboxr3ci: 0.
  15. GSboxr4ci: 0.
  16. GSboxr5ci: 0.
  17. GSboxr6ci: 0.
  18. GSboxr7ci: 0.
  19. GSboxr8ci: 0.
  20. GSboxr9ci: 0.

GSboxr UTRs

Main article: UTR promoter gene transcriptions
  1. GSboxr6: TCCACGTGTC at 2907.

Acknowledgements

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

Initial content for this page in some instances came from Wikiversity.

See also

References

  1. ↑ Gary J. Loake, Ouriel Faktor, Christopher J. Lamb, and Richard A. Dixon (October 1992). "Combination of H-box [CCTACC(N)7CT] and G-box (CACGTG) cis elements is necessary for feed-forward stimulation of a chalcone synthase promoter by the phenylpropanoid-pathway intermediate p-coumaricacid" (PDF). Proceedings of the National Academy of Sciences USA. 89: 9230–4. Retrieved 5 May 2020.
  2. ↑ 2.0 2.1 2.2 K Oeda, J Salinas, and N H Chua (July 1991). "A tobacco bZip transcription activator (TAF-1) binds to a G-box-like motif conserved in plant genes". The EMBO Journal. 10 (7): 1793–1802. PMID 2050116. Retrieved 2017-02-13.
  3. ↑ Landschulz WH, Johnson PF, McKnight SL (June 1988). "The leucine zipper: a hypothetical structure common to a new class of DNA binding proteins". Science. 240 (4860): 1759–64. Bibcode:1988Sci...240.1759L. doi:10.1126/science.3289117. PMID 3289117.
  4. ↑ Z G E, Zhang YP, Zhou JH, Wang L (April 2014). "Mini review roles of the bZIP gene family in rice". Genetics and Molecular Research. 13 (2): 3025–36. doi:10.4238/2014.April.16.11. PMID 24782137.
  5. ↑ Nijhawan A, Jain M, Tyagi AK, Khurana JP (February 2008). "Genomic survey and gene expression analysis of the basic leucine zipper transcription factor family in rice". Plant Physiology. 146 (2): 333–50. doi:10.1104/pp.107.112821. PMID 18065552.
  6. ↑ Young Hun Song, Cheol Min Yoo, An Pio Hong, Seong Hee Kim, Hee Jeong Jeong, Su Young Shin, Hye Jin Kim, Dae-Jin Yun, Chae Oh Lim, Jeong Dong Bahk, Sang Yeol Lee, Ron T. Nagao, Joe L. Key, and Jong Chan Hong (April 2008). "DNA-Binding Study Identifies C-Box and Hybrid C/G-Box or C/A-Box Motifs as High-Affinity Binding Sites for STF1 and LONG HYPOCOTYL5 Proteins" (PDF). Plant Physiology. 146 (4): 1862–1877. doi:10.1104/pp.107.113217. PMID 18287490. Retrieved 26 March 2019.

External links


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