Z box gene transcriptions: Difference between revisions

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|pmid=
|pmid=
|accessdate=15 November 2018 }}</ref>
|accessdate=15 November 2018 }}</ref>
"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)."<ref name=Nawkar>{{ cite journal
|author=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
|title=HY5, a positive regulator of light signaling, negatively controls the unfolded protein response in ''Arabidopsis''
|journal=Proceedings of the National Academy of Sciences USA
|date=21 February 2017
|volume=114
|issue=8
|pages=2084-89
|url=https://www.pnas.org/content/pnas/114/8/2084.full.pdf
|arxiv=
|bibcode=
|doi=10.1073/pnas.1609844114
|pmid=
|accessdate=24 June 2021 }}</ref>


The more general Z-box consensus sequence accommodating these variations appears to be 3'-A(C/T)A(C/G)GT(A/G)T-5'.
The more general Z-box consensus sequence accommodating these variations appears to be 3'-A(C/T)A(C/G)GT(A/G)T-5'.

Revision as of 15:02, 25 June 2021

Editor-In-Chief: Henry A. Hoff

This female specimen is a zebrafish (Danio rerio) breed with fantails. Credit: Azul.{{free media}}

"Both miRNAs [miR‐141 and miR‐200c] map closely on human chromosome 12p13.31 and the stem–loop sequences are separated by only a 338‐base‐pair spacer sequence [...]. This spacer and the putative promoter 600 bp upstream from the hsa‐miR‐200c stem–loop contain six putative binding sequences for [zinc‐finger E‐box binding homeobox 1] ZEB1, two of which were restricted to ZEB factors (Z‐box 1 and 2, CAGGTA)."[1]

The "overall miRNA gene structure and the two Z‐boxes, as well as E‐box 2, are highly conserved in evolution from zebrafish to human [...]."[1]

"Mutation of the two highly conserved Z‐boxes showed that Z‐box 2 confers the strongest repressive function by ZEB1 [...] and also made the promoter activity insensitive to stable knockdown of ZEB1 [...]. A direct binding of ZEB1 to the two conserved ZEB1 sites (Z‐boxes) was shown by electromobility shift assay by using recombinant DNA‐binding domain of ZEB1 and nuclear extracts from SW480 colorectal cancer cells [...]. By applying chromatin immunoprecipitation (ChIP) with chromatin from SW480 or HCT116 colorectal cancer cells, we could show that endogenous ZEB1 binds to the native promoter region [...]. These data indicate that the transcriptional repressor ZEB1 can directly suppress expression of both miR‐141 and miR‐200c by binding to their putative common promoter."[1]

"The absolute transcriptional activity of the promoter was 55‐fold higher than the activity of the spacer sequence. [Mutations] (mut) of the Z‐boxes render the promoter less sensitive to suppression by ZEB1."[1]

"Mutation of the two conserved Z‐boxes (Z1, Z2) strongly reduced the specific binding complex [...]."[1]

Consensus sequences

"Snail-related and E2A factors bind to a consensus E-box promoter element (CANNTG), whereas ZEB factors bind to a related, but not necessarily identical sequence (CAGGTG/A), termed Z-Box. We detected 2 potential binding sites for Snail-related and E2A factors (E-box 1 and 2) and 3 for ZEB factors (E-box 2 and Z-box 1 and 2) in the human lama3a promoter [...]. Furthermore, sequence comparison of 1000 nucleotides upstream of the translation start site of the human and mouse lama3 gene showed that these sites are located in a highly conserved region of approximately 210 nucleotides, whereas further upstream sequences were not conserved [...]. Three of the 4 potential repressive elements were conserved between mouse and human, indicating their functional relevance."[2]

"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)."[3]

The more general Z-box consensus sequence accommodating these variations appears to be 3'-A(C/T)A(C/G)GT(A/G)T-5'.

HY5 proteins

"The HY5 protein interacts with both the G- (CACGTG) and Z- (ATACGTGT) boxes of the light-regulated promoter of RbcS1A (ribulose bisphosphate carboxylase small subunit) and the CHS (chalcone synthase) genes (Ang et al., 1998; Chattopadhyay et al., 1998; Yadav et al., 2002)."[4]

SIP1-mediated Epithelial Mesenchymal Transition (EMT)

In vivo SIP1, or Zinc finger E-box-binding homeobox 2 (ZEB2), binds "to potential SIP1-binding sites (Z-boxes) located in the vicinity of the cyclin D1 transcription start site."[5]

Three "Z-boxes with coordinates -1014 to -1010 (Z-box 1); -857 to -853 (Z-box 2); and -300 to -290 (Z-box 3) are occupied by SIP1 in [doxorubicin (DOX)] DOX-stimulated cells. In contrast, neither sequences upstream of Z-box 1 [...], nor sequences containing Z-boxes 4 and 5 located at the first exon/intron boundary (-390 to -409) [...] were detected in association with SIP1."[5]

Z-boxes 1-3 contain 5'-AGGTG-3'.[5]

The "mutation of Z-boxes 1–3 markedly activated reporter activity in SIP1-expressing cells [...]."[5]

"SIP1 represses cyclin D1 transcriptional activity via direct interaction with Z-boxes 1–3 in the cyclin D1 promoter."[5]

Hypotheses

  1. A1BG has no Z boxes in either promoter.

Samplings

Using the two versions of the consensus sequence and "⌘F" to locate these sequences in the nucleotides for A1BG listed in A1BG gene transcriptions revealed no occurrence of either.

For the Basic programs testing consensus sequence 3'-A(C/T)A(C/G)GT(A/G)T-5' (starting with SuccessablesZbox.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 SuccessablesZbox--.bas, looking for 3'-A(C/T)A(C/G)GT(A/G)T-5', 0.
  2. negative strand in the positive direction (from ZNF497 to A1BG) is SuccessablesZbox-+.bas, looking for 3'-A(C/T)A(C/G)GT(A/G)T-5', 1, 3'-ACAGGTGT-5' at 1969.
  3. positive strand in the negative direction (from ZSCAN22 to A1BG) is SuccessablesZbox+-.bas, looking for 3'-A(C/T)A(C/G)GT(A/G)T-5', 0.
  4. positive strand in the positive direction (from ZNF497 to A1BG) is SuccessablesZbox++.bas, looking for 3'-A(C/T)A(C/G)GT(A/G)T-5', 1, 3'-ACACGTGT-5', 2962.
  5. complement, negative strand, negative direction is SuccessablesZboxc--.bas, looking for 3'-T(A/G)T(C/G)CA(C/T)A-5', 0.
  6. complement, negative strand, positive direction is SuccessablesZboxc-+.bas, looking for 3'-T(A/G)T(C/G)CA(C/T)A-5', 1, 3'-TGTGCACA-5', 2962.
  7. complement, positive strand, negative direction is SuccessablesZboxc+-.bas, looking for 3'-T(A/G)T(C/G)CA(C/T)A-5', 0.
  8. complement, positive strand, positive direction is SuccessablesZboxc++.bas, looking for 3'-T(A/G)T(C/G)CA(C/T)A-5', 1, 3'-TGTCCACA-5', 1969.
  9. inverse complement, negative strand, negative direction is SuccessablesZboxci--.bas, looking for 3'-A(C/T)AC(C/G)T(A/G)T-5', 0.
  10. inverse complement, negative strand, positive direction is SuccessablesZboxci-+.bas, looking for 3'-A(C/T)AC(C/G)T(A/G)T-5', 0.
  11. inverse complement, positive strand, negative direction is SuccessablesZboxci+-.bas, looking for 3'-A(C/T)AC(C/G)T(A/G)T-5', 3, 3'-ACACCTGT-5', 1131, 3'-ATACCTAT-5', 2996, 3'-ACACCTGT-5', 3970.
  12. inverse complement, positive strand, positive direction is SuccessablesZboxci++.bas, looking for 3'-A(C/T)AC(C/G)T(A/G)T-5', 0.
  13. inverse negative strand, negative direction is SuccessablesZboxi--.bas, looking for 3'-T(A/G)TG(C/G)A(C/T)A-5', 3, 3'-TGTGGACA-5', 1131, 3'-TATGGATA-5', 2996, 3'-TGTGGACA-5', 3970.
  14. inverse negative strand, positive direction is Successableszboxi-+.bas, looking for 3'-T(A/G)TG(C/G)A(C/T)A-5', 1, 3'-TGTGCACA-5', 2962.
  15. inverse positive strand, negative direction is Successableszboxi+-.bas, looking for 3'-T(A/G)TG(C/G)A(C/T)A-5', 0.
  16. inverse positive strand, positive direction is SuccessablesAboxi++.bas, looking for 3'-T(A/G)TG(C/G)A(C/T)A-5', 0.

Zbox distal promoters

Main article: Distal promoter gene transcriptions

Negative strand, positive direction: ACAGGTGT at 1969.

Positive strand, positive direction: ACACGTGT at 2962.

Zbox random dataset samplings

  1. RDr0: 0.
  2. RDr1: 0.
  3. RDr2: 0.
  4. RDr3: 0.
  5. RDr4: 0.
  6. RDr5: 0.
  7. RDr6: 0.
  8. RDr7: 0.
  9. RDr8: 0.
  10. RDr9: 0.
  11. RDr0ci: 0.
  12. RDr1ci: 0.
  13. RDr2ci: 0.
  14. RDr3ci: 0.
  15. RDr4ci: 0.
  16. RDr5ci: 0.
  17. RDr6ci: 0.
  18. RDr7ci: 0.
  19. RDr8ci: 0.
  20. RDr9ci: 0.

RDr UTRs

Main article: UTR promoter gene transcriptions

RDr core promoters

Main article: Core promoter gene transcriptions

RDr proximal promoters

Main article: Proximal promoter gene transcriptions

RDr distal promoters

Main article: Distal promoter gene transcriptions

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. ↑ 1.0 1.1 1.2 1.3 1.4 Ulrike Burk, Jörg Schubert, Ulrich Wellner, Otto Schmalhofer, Elizabeth Vincan, Simone Spaderna, Thomas Brabletz (1 June 2008). "A reciprocal repression between ZEB1 and members of the miR‐200 family promotes EMT and invasion in cancer cells". EMBO Reports. 9 (6): 582–589. doi:10.1038/embor.2008.74. Retrieved 15 November 2018.
  2. ↑ Simone Spaderna, Otto Schmalhofer, Falk Hlubek, Geert Berx, Andreas Eger, Susanne Merkel, Andreas Jung, Thomas Kirchner, Thomas Brabletz (September 2006). "A Transient, EMT-Linked Loss of Basement Membranes Indicates Metastasis and Poor Survival in Colorectal Cancer". Gastroenterology. 131 (3): 830–840. doi:10.1053/j.gastro.2006.06.016. Retrieved 15 November 2018.
  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.
  4. ↑ 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.
  5. ↑ 5.0 5.1 5.2 5.3 5.4 Jakob Mejlvang, Marina Kriajevska, Cindy Vandewalle, Tatyana Chernova, A. Emre Sayan, Geert Berx, J. Kilian Mellon, and Eugene Tulchinsky (November 2007). "Direct Repression of Cyclin D1 by SIP1 Attenuates Cell Cycle Progression in Cells Undergoing an Epithelial Mesenchymal Transition". Molecular Biology of the Cell. 18 (11): 4615–4624. doi:10.1091/mbc.e07-05-0406. Retrieved 15 November 2018.

External links

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