A box gene transcriptions: Difference between revisions

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|accessdate=24 June 2021 }}</ref>
|accessdate=24 June 2021 }}</ref>


Most bZIP proteins show high binding affinity for the ACGT motifs, which include [...] TACGTA (A box) [...].<ref name=Landschulz>{{ cite journal
"Most bZIP proteins show high binding affinity for the ACGT motifs, which include CACGTG (G box), GACGTC (C box), TACGTA (A box), AACGTT (T box), and a GCN4 motif, namely TGA(G/C)TCA (Landschulz et al., 1988; Nijhawan et al., 2008)."<ref name=Zhang2014>{{ 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
| doi = 10.1126/science.3289117 | bibcode = 1988Sci...240.1759L
| url = https://semanticscholar.org/paper/3a61c172ddfa79ce9f4909ca6bea2f6f40f7893e }}</ref><ref name=Zhang2014>{{ cite journal
| vauthors = Z G E, Zhang YP, Zhou JH, Wang L
| vauthors = Z G E, Zhang YP, Zhou JH, Wang L
| title = Mini review roles of the bZIP gene family in rice
| title = Roles of the bZIP gene family in rice
| journal = Genetics and Molecular Research
| journal = Genetics and Molecular Research
| volume = 13
| volume = 13
Line 80: Line 77:
| 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>
 
Most bZIP proteins show high binding affinity for the ACGT motifs, which include [...] TACGTA (A 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
| doi = 10.1126/science.3289117 | bibcode = 1988Sci...240.1759L
| url = https://semanticscholar.org/paper/3a61c172ddfa79ce9f4909ca6bea2f6f40f7893e }}</ref><ref name=Zhang2014/><ref name=Nijhawan>{{ cite journal | vauthors = 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

Revision as of 15:17, 25 June 2021

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

The GC boxes are not apparently associated with the A box, B box, C box, and D box.[1]

"AS/T, serine/threonine-rich subdomain within the A box".[1] "AQ, glutamine-rich subdomain within the A box".[1]

Consensus sequences

Main article: Consensus sequence gene transcriptions

Box A

"The human [Transforming growth factor b1] TGFB1 promoter region contains two binding sequences for [Activator protein-1] AP-1, designated AP-1 box A (TGACTCT) and box B (TGTCTCA), which mediate the upregulation of promoter activity via a PKC-dependent pathway after exposure of cells to a high-glucose environment (Refs 37, 38)."[2]

"The human TGF-β1 promoter region contains two binding sequences for AP-1, designated AP-1 box A (TGACTCT) and box B (TGTCTCA), which mediate the up-regulation of promoter activity after [High glucose] HG stimulation."[3]

A-box

"Because of their sessile lifestyle, plants have developed advanced mechanisms to cope with many forms of environmental stress conditions. Under changing environmental conditions, the adaptive responses of plants largely depend on the proper integration of light signaling and stress response pathways. Plants are equipped with multiple photoreceptors, including red/far-red light-absorbing phytochromes, blue/UV (UV)-A light-absorbing cryptochromes and phototropins, and the UV-B light-absorbing UV RESISTANCE LOCUS 8 (1, 2). The downstream component ELONGATED HYPOCOTYL 5 (HY5), a basic leucine zipper (bZIP) transcription factor (TF), mediates photoreceptor responses to promote photomorphogenesis (3). Recently, genome-wide gene expression analyses and chromatin immunoprecipitation (ChIP) studies have shown that HY5 is a higher hierarchical regulator of transcriptional networks for photomorphogenesis (4, 5). In particular, HY5 binds to the promoter of light-responsive genes featuring "ACGT-containing elements" such as the G-box (CACGTG), C-box (GACGTC), Z-box (ATACGGT), and A-box (TACGTA) (4, 6)."[4]

"Most bZIP proteins show high binding affinity for the ACGT motifs, which include CACGTG (G box), GACGTC (C box), TACGTA (A box), AACGTT (T box), and a GCN4 motif, namely TGA(G/C)TCA (Landschulz et al., 1988; Nijhawan et al., 2008)."[5]

Most bZIP proteins show high binding affinity for the ACGT motifs, which include [...] TACGTA (A box) [...].[6][5][7]

TACGTA is the A-box.[8]

Hypotheses

  1. A1BG has no A boxes in either promoter.
  2. A1BG is not transcribed by an A box.
  3. An A box does not participate in the transcription of A1BG.

Box A samplings

Box A 3-TGACTCT-5' was not found using "⌘F" to locate any consensus sequences.

Hypothesis 1: A1BG is not transcribed by box A.

For the Basic programs testing consensus sequence 3'-TGACTCT-5' (starting with SuccessablesAbox.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 in the negative direction (from ZSCAN22 to A1BG) is SuccessablesAbox--.bas, looking for 3'-TGACTCT-5', 0.
  2. negative strand in the positive direction (from ZNF497 to A1BG) is SuccessablesAbox-+.bas, looking for 3'-TGACTCT-5', 0.
  3. positive strand in the negative direction (from ZSCAN22 to A1BG) is SuccessablesAbox+-.bas, looking for 3'-TGACTCT-5', 1, 3'-TGACTCT-5' at 2788.
  4. positive strand in the positive direction (from ZNF497 to A1BG) is SuccessablesAbox++.bas, looking for 3'-TGACTCT-5', 0.
  5. complement, negative strand, negative direction is SuccessablesAboxc--.bas, looking for 3'-ACTGAGA-5', 1, 3'-ACTGAGA-5' at 2788.
  6. complement, negative strand in the positive direction (from ZNF497 to A1BG) is SuccessablesAboxc-+.bas, looking for 3'-ACTGAGA-5', 0.
  7. complement, positive strand in the negative direction (from ZSCAN22 to A1BG) is SuccessablesAboxc+-.bas, looking for 3'-ACTGAGA-5', 0.
  8. complement, positive strand in the positive direction (from ZNF497 to A1BG) is SuccessablesAboxc++.bas, looking for 3'-ACTGAGA-5', 0.
  9. inverse complement, negative strand, negative direction is SuccessablesAboxci--.bas, looking for 3'-AGAGTCA-5', 0.
  10. inverse complement, negative strand in the positive direction (from ZNF497 to A1BG) is SuccessablesAboxci-+.bas, looking for 3'-AGAGTCA-5', 1, 3'-AGAGTCA-5' at 2613.
  11. inverse complement, positive strand in the negative direction (from ZSCAN22 to A1BG) is SuccessablesAboxci+-.bas, looking for 3'-AGAGTCA-5', 0.
  12. inverse complement, positive strand in the positive direction (from ZNF497 to A1BG) is SuccessablesAboxci++.bas, looking for 3'-AGAGTCA-5', 0.
  13. inverse negative strand in the negative direction (from ZSCAN22 to A1BG) is SuccessablesAboxi--.bas, looking for 3'-TCTCAGT-5', 0.
  14. inverse negative strand in the positive direction (from ZNF497 to A1BG) is SuccessablesAboxi-+.bas, looking for 3'-TCTCAGT-5', 0.
  15. inverse positive strand in the negative direction (from ZSCAN22 to A1BG) is SuccessablesAboxi+-.bas, looking for 3'-TCTCAGT-5', 0.
  16. inverse positive strand in the positive direction (from ZNF497 to A1BG) is SuccessablesAboxi++.bas, looking for 3'-TCTCAGT-5', 1, 3'-TCTCAGT-5' at 2613.

Box A distal promoters

Positive strand, negative direction: TGACTCT at 2788.

Positive strand, positive direction: TCTCAGT at 2613.

Box A random dataset samplings

  1. Aboxr0: 0.
  2. Aboxr1: 0.
  3. Aboxr2: 0.
  4. Aboxr3: 2, TGACTCT at 4481, TGACTCT at 2451.
  5. Aboxr4: 0.
  6. Aboxr5: 0.
  7. Aboxr6: 0.
  8. Aboxr7: 0.
  9. Aboxr8: 0.
  10. Aboxr9: 1, TGACTCT at 3523.
  11. Aboxr0ci: 0.
  12. Aboxr1ci: 0.
  13. Aboxr2ci: 0.
  14. Aboxr3ci: 0.
  15. Aboxr4ci: 0.
  16. Aboxr5ci: 0.
  17. Aboxr6ci: 3, AGAGTCA at 4503, AGAGTCA at 4449, AGAGTCA at 1109.
  18. Aboxr7ci: 0.
  19. Aboxr8ci: 0.
  20. Aboxr9ci: 0.

Aboxr UTRs

Main article: UTR promoter gene transcriptions
  1. Aboxr6ci: AGAGTCA at 4503, AGAGTCA at 4449.

Aboxr core promoters

Main article: Core promoter gene transcriptions
  1. Aboxr3: TGACTCT at 4481.

Aboxr distal promoters

Main article: Distal promoter gene transcriptions
  1. Aboxr6ci: AGAGTCA at 1109.


  1. Aboxr3: TGACTCT at 2451.
  2. Aboxr9: TGACTCT at 3523.

A box samplings

A box 5'-TACGTA-3' using "⌘F" has one location between ZSCAN22 and A1BG and none between ZNF497 and A1BG.

Hypothesis 1: A1BG is not transcribed by an A box.

For the Basic programs testing consensus sequence 3'-TACGTA-5' (starting with SuccessablesAbox1.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 in the negative direction (from ZSCAN22 to A1BG) is SuccessablesAbox1--.bas, looking for 3'-TACGTA-5', 1, 3'-TACGTA-5' at 4246.
  2. negative strand in the positive direction (from ZNF497 to A1BG) is SuccessablesAbox1-+.bas, looking for 3'-TACGTA-5', 0.
  3. positive strand in the negative direction (from ZSCAN22 to A1BG) is SuccessablesAbox1+-.bas, looking for 3'-TACGTA-5', 0.
  4. positive strand in the positive direction (from ZNF497 to A1BG) is SuccessablesAbox1++.bas, looking for 3'-TACGTA-5', 1, 3'-TACGTA-5', 3071.
  5. complement, negative strand, negative direction is SuccessablesAbox1c--.bas, looking for 3'-ATGCAT-5', 0.
  6. complement, negative strand in the positive direction (from ZNF497 to A1BG) is SuccessablesAbox1c-+.bas, looking for 3'-ATGCAT-5', 1, 3'-ATGCAT-5', 3071.
  7. complement, positive strand in the negative direction (from ZSCAN22 to A1BG) is SuccessablesAbox1c+-.bas, looking for 3'-ATGCAT-5', 1, 3'-ATGCAT-5', 4246.
  8. complement, positive strand in the positive direction (from ZNF497 to A1BG) is SuccessablesAbox1c++.bas, looking for 3'-ACTGAGA-5', 0.
  9. complement inverse is TACGTA.

A box proximal promoters

Main article: Proximal promoter gene transcriptions

Negative strand, negative direction: 5'-TACGTA-3' at 4246 and complement.

A box distal promoters

Main article: Distal promoter gene transcriptions

Positive strand, positive direction: 5'-TACGTA-3' at 3071 and complement.

Abox1 random dataset samplings

  1. Abox1r0: 1, TACGTA at 398.
  2. Abox1r1: 0.
  3. Abox1r2: 0.
  4. Abox1r3: 0.
  5. Abox1r4: 0.
  6. Abox1r5: 1, TACGTA at 3126.
  7. Abox1r6: 1, TACGTA at 2107.
  8. Abox1r7: 0.
  9. Abox1r8: 0.
  10. Abox1r9: 1, TACGTA at 3688.

Abox1r distal promoters

Main article: Distal promoter gene transcriptions
  1. Abox1r0: TACGTA at 398.
  2. Abox1r6: TACGTA at 2107.


  1. Abox1r5: TACGTA at 3126.
  2. Abox1r9: TACGTA at 3688.

Acknowledgements

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

See also

References

  1. ↑ 1.0 1.1 1.2 Huajun Jin, Arthi Kanthasamy, Dilshan S. Harischandra, Naveen Kondru, Anamitra Ghosh, Nikhil Panicker, Vellareddy Anantharam, Ajay Rana, and Anumantha G. Kanthasamy (December 12, 2014). "Histone Hyperacetylation Up-regulates Protein Kinase C􏰀 in Dopaminergic Neurons to Induce Cell Death RELEVANCE TO EPIGENETIC MECHANISMS OF NEURODEGENERATION IN PARKINSON DISEASE" (PDF). 289 (50): 34743–34767. doi:10.1074/jbc.M114.576702. Retrieved 10 April 2019.
  2. ↑ Amber Paratore Sanchez and Kumar Sharma (July 2009). "Transcription factors in the pathogenesis of diabetic nephropathy". Expert Reviews in Molecular Medicine. 11: e13. doi:10.1017/S1462399409001057. Retrieved 1 October 2018.
  3. ↑ Keiko Kokoroishi, Ayumu Nakashima, Shigehiro Doi, Toshinori Ueno, Toshiki Doi, Yukio Yokoyama, Kiyomasa Honda, Masami Kanawa, Yukio Kato, Nobuoki Kohno & Takao Masaki (28 May 2015). "High glucose promotes TGF-β1 production by inducing FOS expression in human peritoneal mesothelial cells". Clinical and Experimental Nephrology. 20 (1): 30–8. doi:10.1007/s10157-015-1128-9. PMID 26018137. Retrieved 14 August 2020.
  4. ↑ Ganesh M. Nawkar, Chang Ho Kanga, Punyakishore Maibam, Joung Hun Park, Young Jun Jung, Ho Byoung Chae, Yong Hun Chi, In Jung Jung, Woe Yeon Kim, Dae-Jin Yun, and Sang Yeol Lee (21 February 2017). "HY5, a positive regulator of light signaling, negatively controls the unfolded protein response in Arabidopsis" (PDF). Proceedings of the National Academy of Sciences USA. 114 (8): 2084–89. doi:10.1073/pnas.1609844114. Retrieved 24 June 2021.
  5. ↑ 5.0 5.1 Z G E, Zhang YP, Zhou JH, Wang L (April 2014). "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. Vancouver style error: name (help)
  6. ↑ 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.
  7. ↑ 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.
  8. ↑ 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. Retrieved 26 March 2019.

External links


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