A box gene transcriptions

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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]

"A majority of the plant bZIP proteins isolated to date recognize elements with an ACGT core (Foster et al., 1994)."[6]

"Most recombinant bZIP proteins can interact with ACGT elements derived from different plant genes, albeit with different affinity. Systematic protein/DNA binding studies have shown that sequences flanking the ACGT core affect bZIP protein binding specificity. These studies have provided the basis for a concise ACGT nomenclature and defined high-affinity A-box, C-box, and G-box elements."[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.

Box A analysis and results

Main article: Complex locus A1BG and ZNF497 § Box As

"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]

Reals or randoms Promoters direction Numbers Strands Occurrences Averages (± 0.1)
Reals UTR negative 0 2 0 0
Randoms UTR arbitrary negative 2 10 0.2 0.15 ± 0.05
Randoms UTR alternate negative 1 10 0.1 0.15 ± 0.05
Reals Core negative 0 2 0 0
Randoms Core arbitrary negative 0 10 0 0
Randoms Core alternate negative 0 10 0 0
Reals Core positive 0 2 0 0
Randoms Core arbitrary positive 0 10 0 0
Randoms Core alternate positive 0 10 0 0
Reals Proximal negative 0 2 0 0
Randoms Proximal arbitrary negative 0 10 0 0
Randoms Proximal alternate negative 0 10 0 0
Reals Proximal positive 0 2 0 0
Randoms Proximal arbitrary positive 0 10 0 0
Randoms Proximal alternate positive 0 10 0 0
Reals Distal negative 1 2 0.5 0.5 ± 0.5 (--0,+-1)
Randoms Distal arbitrary negative 1 10 0.1 0.1 ± 0
Randoms Distal alternate negative 1 10 0.1 0.1 ± 0
Reals Distal positive 1 2 0.5 0.5 ± 0.5 (-+0,++1)
Randoms Distal arbitrary positive 2 10 0.2 0.15 ± 0.05
Randoms Distal alternate positive 1 10 0.1 0.15 ± 0.05

Comparison:

The occurrences of box A consensus sequences are greater than the randoms. This suggests that the real box A consensus sequences are likely active or activable.

A-boxes 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, negative direction: 1, TACGTA at 4246.
  2. Negative strand, positive direction: 0.
  3. Positive strand, negative direction: 0.
  4. Positive strand, positive direction: 1, TACGTA at 3071.
  5. complement inverse is TACGTA.

A-box UTRs

Negative strand, negative direction: TACGTA at 4246.

A-box distal promoters

Positive strand, positive direction: TACGTA at 3071.

A-box random dataset samplings

  1. Aboxr0: 1, TACGTA at 398.
  2. Aboxr1: 0.
  3. Aboxr2: 0.
  4. Aboxr3: 0.
  5. Aboxr4: 0.
  6. Aboxr5: 1, TACGTA at 3126.
  7. Aboxr6: 1, TACGTA at 2107.
  8. Aboxr7: 0.
  9. Aboxr8: 0.
  10. Aboxr9: 1, TACGTA at 3688.

Aboxr distal promoters

  1. Aboxr0: TACGTA at 398.
  2. Aboxr6: TACGTA at 2107.


  1. Aboxr5: TACGTA at 3126.
  2. Aboxr9: TACGTA at 3688.

Discussion

For box A (TGACTCT) there is a consensus sequence on either side of A1BG whereas the random datasets have only 0.3 on either side.

In the A1BG promoters, the consensus sequence for A box: TACGTA occurs in the negative direction UTR at 4246 nucleotides from ZSCAN22 and the positive direction distal promoter at 3071 nucleotides from ZNF497.

For the random datasets, it occurs only in the distal promoters at 398 or 2107 (two out of ten datasets) of the assigned negative direction and at 3126 or 3688 (two out of ten datasets) of the assigned positive direction.

The real promoters have twice as many consensus sequences relative to any random dataset with a result and the real promoters have them located in the UTR or distal promoter instead of just the distal promoter, which suggests they are real rather than random.

A-boxes analysis and results

Main article: Complex locus A1BG and ZNF497 § A-boxes

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]

Reals or randoms Promoters direction Numbers Strands Occurrences Averages (± 0.1)
Reals UTR negative 1 2 0.5 0.5 ± 0.5 (--1,+-0)
Randoms UTR arbitrary negative 0 10 0 0.1 ± 0.1
Randoms UTR alternate negative 2 10 0.2 0.1 ± 0.1
Reals Core negative 0 2 0 0
Randoms Core arbitrary negative 0 10 0 0
Randoms Core alternate negative 0 10 0 0
Reals Core positive 0 2 0 0
Randoms Core arbitrary positive 0 10 0 0
Randoms Core alternate positive 0 10 0 0
Reals Proximal negative 0 2 0 0
Randoms Proximal arbitrary negative 0 10 0 0
Randoms Proximal alternate negative 0 10 0 0
Reals Proximal positive 0 2 0 0
Randoms Proximal arbitrary positive 0 10 0 0
Randoms Proximal alternate positive 0 10 0 0
Reals Distal negative 0 2 0 0
Randoms Distal arbitrary negative 2 10 0.2 0.1 ± 0.1
Randoms Distal alternate negative 0 10 0 0.1 ± 0.1
Reals Distal positive 1 2 0.5 0.5 ± 0.5 (-+0,++1)
Randoms Distal arbitrary positive 2 10 0.2 0.2 ± 0
Randoms Distal alternate positive 2 10 0.2 0.2 ± 0

Comparison:

The occurrences of real A-boxes are greater than the randoms. This suggests that the real A-boxes are likely active or activable.

Light signaling and stress response pathways

"Under changing environmental conditions, the adaptive responses of plants largely depend on the proper integration of light signaling and stress response pathways."[4]

"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]

PKC-dependent pathway

"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]

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. ↑ 2.0 2.1 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. ↑ 3.0 3.1 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. ↑ 4.0 4.1 4.2 4.3 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. ↑ 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. ↑ 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.
  7. ↑ Randy Foster, Takeshi Izawa and Nam-Hai Chua (1 February 1994). "Plant bZIP proteins gather at ACGT elements". FASEB. 8 (2): 192–200. doi:10.1096/fasebj.8.2.8119490. PMID 8119490. Retrieved 25 June 2021.
  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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