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 100: Line 100:
# GOboxr8: 0.
# GOboxr8: 0.
# GOboxr9: 0.
# GOboxr9: 0.
# GOboxr0ci: 0.
# GOboxr1ci: 0.
# GOboxr2ci: 0.
# GOboxr3ci: 0.
# GOboxr4ci: 0.
# GOboxr5ci: 0.
# GOboxr6ci: 0.
# GOboxr7ci: 0.
# GOboxr8ci: 0.
# GOboxr9ci: 0.
===GOboxr UTRs===
{{main|UTR promoter gene transcriptions}}
===GOboxr core promoters===
{{main|Core promoter gene transcriptions}}
===GOboxr proximal promoters===
{{main|Proximal promoter gene transcriptions}}
===GOboxr distal promoters===
{{main|Distal promoter gene transcriptions}}


==Song samplings==
==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.
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 AAAAAAAA (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:
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 AAAAAAAA, 0.
# negative strand, negative direction, looking for (G/T)CCACGTG(G/T)C, 0.
# positive strand, negative direction, looking for AAAAAAAA, 0.
# positive strand, negative direction, looking for (G/T)CCACGTG(G/T)C, 0.
# positive strand, positive direction, looking for AAAAAAAA, 0.
# positive strand, positive direction, looking for (G/T)CCACGTG(G/T)C, 0.
# negative strand, positive direction, looking for AAAAAAAA, 0.
# negative strand, positive direction, looking for (G/T)CCACGTG(G/T)C, 0.
# inverse complement, negative strand, negative direction, looking for TTTTTTTT, 0.
# inverse complement, negative strand, negative direction, looking for G(A/C)CACGTGG(A/C), 0.
# inverse complement, positive strand, negative direction, looking for TTTTTTTT, 0.
# inverse complement, positive strand, negative direction, looking for G(A/C)CACGTGG(A/C), 0.
# inverse complement, positive strand, positive direction, looking for TTTTTTTT, 0.
# inverse complement, positive strand, positive direction, looking for G(A/C)CACGTGG(A/C), 0.
# inverse complement, negative strand, positive direction, looking for TTTTTTTT, 0.
# inverse complement, negative strand, positive direction, looking for G(A/C)CACGTGG(A/C), 0.
 
===GSbox UTRs===
{{main|UTR promoter gene transcriptions}}
 
===GSbox core promoters===
{{main|Core promoter gene transcriptions}}
 
===GSbox proximal promoters===
{{main|Proximal promoter gene transcriptions}}
 
===GSbox distal promoters===
{{main|Distal promoter gene transcriptions}}


===GSbox random dataset samplings===
===GSbox random dataset samplings===
Line 156: Line 122:
# GSboxr4: 0.
# GSboxr4: 0.
# GSboxr5: 0.
# GSboxr5: 0.
# GSboxr6: 0.
# GSboxr6: 1, TCCACGTGTC at 2907.
# GSboxr7: 0.
# GSboxr7: 0.
# GSboxr8: 0.
# GSboxr8: 0.
Line 173: Line 139:
===GSboxr UTRs===
===GSboxr UTRs===
{{main|UTR promoter gene transcriptions}}
{{main|UTR promoter gene transcriptions}}
 
# GSboxr6: TCCACGTGTC at 2907.
===GSboxr core promoters===
{{main|Core promoter gene transcriptions}}
 
===GSboxr proximal promoters===
{{main|Proximal promoter gene transcriptions}}
 
===GSboxr distal promoters===
{{main|Distal promoter gene transcriptions}}


==Acknowledgements==
==Acknowledgements==
Line 206: Line 164:


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[[Category:Gene project/Lectures]]
[[Category:Resources last modified in September 2020]]

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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