P box gene transcriptions

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

"The proximal promoter region (bp -87 to -45) of the human PAI-1 gene contains several potent binding sites for transcription factors [two phorbol-ester-response-element (TRE)-like sequences; D-box (-82 to -76) and P-box (-61 to 54), and one Sp1 binding site-like sequence, Sp1-box 1 (-72 to -67)]."[1]

Pyrimidine boxes

Main article: Pyrimidine box gene transcriptions

"Functional analyses of a number of hydrolase gene promoters, induced by gibberellin (GA) in aleurone cells following germination, have identified a GA-responsive complex as a tripartite element containing a pyrimidine box motif 5′-CCTTTT-3′."[2]

"Although this GARC [GA responsive complex] may not always be tripartite, most often it includes three sequence motifs, the TAACAAA box or GA responsive element (GARE), the pyrimidine box CCTTTT, and the TATCCAC box (Skriver et al., 1991;Gubler and Jacobsen, 1992; Rogers et al., 1994)."[2]

"REV-ERBα and RORa are nuclear receptors rather than bZIP transcription factors like VRI and PDP1ϵ, and they regulate transcription by binding RORE elements rather than V/P-boxes (Bell-Pedersen et al., 2005)."[3]

P-boxes

The "complementary strand of the pyrimidine box element (5′-CTTTT-3′) in GA-induced hydrolase gene promoters was identical to the core sequence (5′-AAAAG-3′) recognized by PBF in prolamin gene promoters (P-box: 5′-T/AAAAG-3′; Vicente-Carbajosa et al., 1997; Mena et al., 1998; Yanagisawa and Schmidt, 1999)".[2]

Prolamin boxes

Main article: Prolamin box gene transcriptions

"The BPBF [barley prolamin-box (P-box) binding factor] expressed in bacteria as a GST-fusion binds a P-box 5′-TGTAAAG-3′ containing oligonucleotide derived from the promoter region of anHor2gene."[4]

"The primary structure of hordein [barley prolamins] polypeptides is closely related to that of prolamins from other grass species from the Pooideae subfamily, such as wheat and rye (Shewry & Tatham 1990;Shewry et al. 1995). The close evolutionary relationship is also manifested by the conservation of a putative regulatory element in their gene promoters, the endosperm box (Forde et al. 1985;Kreis et al. 1985). This conserved region consists of two motifs, a 7 bp element (5′TGTAAAG3′) termed the Prolamin Box (P-box) or endosperm motif (EM) followed at a distance of up to 8 nucleotides by the GCN4-like motif (GLM) which has the 5′(G/A)TGA(G/C)TCA(T/C)3′ consensus sequence (reviewed by Müller et al. 1995)."[4]

V and P-boxes

Main article: V and P box gene transcriptions

"As VRI [target gene: vrille (VRI)] accumulates in the nucleus during the mid to late day, it binds VRI/PDP1ϵ binding sites (V/P-boxes) [consensus A(/G)TTA(/T)T(/C):GTAAT(/C)], to repress Clk and cry transcription (Hardin, 2004)."[3]

Consensus sequences

Main article: Consensus sequence gene transcriptions

The P box is actually the prolamin box.[2]

Hypotheses

Main article: Hypotheses
  1. A1BG has no P-box in either promoter.
  2. A1BG is not transcribed by a P-box.
  3. No P-box participates in the transcription of A1BG.

P-box (Yu) samplings

Copying the apparent consensus sequence for the P box GTAA(T/C) and putting it in "⌘F" finds seven located between ZSCAN22 and one between ZNF497 and A1BG as can be found by the computer programs.

For the Basic programs (starting with SuccessablesPbox.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 SuccessablesPbox--.bas, looking for GTAA(C/T), 7, GTAAT at 3436, GTAAC at 3285, GTAAT at 2951, GTAAC at 1343, GTAAC at 886, GTAAT at 173, GTAAT at 153, and complements.
  2. negative strand in the positive direction (from ZNF497 to A1BG) is SuccessablesPbox-+.bas, looking for GTAA(C/T), 1, GTAAC at 3732, and complement.
  3. positive strand in the negative direction is SuccessablesPbox+-.bas, looking for GTAA(C/T), 15, GTAAT at 3973, GTAAT at 3064, GTAAT at 2675, GTAAT at 2088, GTAAT at 1914, GTAAT at 1779, GTAAT at 1707, GTAAT at 1261, GTAAT at 1134, GTAAT at 804, GTAAT at 670, GTAAC at 613, GTAAT at 534, GTAAT at 397, GTAAT at 248, and complements.
  4. positive strand in the positive direction is SuccessablesPbox++.bas, looking for GTAA(C/T), 4, GTAAC at 4310, GTAAC at 2903, GTAAC at 1703, GTAAC at 23, and complements.
  5. complement, negative strand, negative direction is SuccessablesPboxc--.bas, looking for CATT(A/G), 15, CATTA at 3973, CATTA at 3064, CATTA at 2675, CATTA at 2088, CATTA at 1914, CATTA at 1779, CATTA at 1707, CATTA at 1261, CATTA at 1134, CATTA at 804, CATTA at 670, CATTG at 613, CATTA at 534, CATTA at 397, CATTA at 248.
  6. complement, negative strand, positive direction is SuccessablesPboxc-+.bas, looking for CATT(A/G), 4, CATTG at 4310, CATTG at 2903, CATTG at 1703, CATTG at 23.
  7. complement, positive strand, negative direction is SuccessablesPboxc+-.bas, looking for CATT(A/G), 7, CATTA at 3436, CATTG at 3285, CATTA at 2951, CATTG at 1343, CATTG at 886, CATTA at 173, CATTA at 153.
  8. complement, positive strand, positive direction is SuccessablesPboxc++.bas, looking for CATT(A/G), 1, CATTG at 3732.
  9. inverse complement, negative strand, negative direction is SuccessablesPboxci--.bas, looking for (A/G)TTAC, 1, ATTAC at 3658, and complement.
  10. inverse complement, negative strand, positive direction is SuccessablesPboxci-+.bas, looking for (A/G)TTAC, 0.
  11. inverse complement, positive strand, negative direction is SuccessablesPboxci+-.bas, looking for (A/G)TTAC, 2, ATTAC at 3469, ATTAC at 1296, and complements.
  12. inverse complement, positive strand, positive direction is SuccessablesPboxci++.bas, looking for (A/G)TTAC, 2, GTTAC at 2909, GTTAC at 227, and complements.
  13. inverse, negative strand, negative direction, is SuccessablesPboxi--.bas, looking for (C/T)AATG, 2, TAATG at 3469, TAATG at 1296.
  14. inverse, negative strand, positive direction, is SuccessablesPboxi-+.bas, looking for (C/T)AATG, 2, CAATG at 2909, CAATG at 227.
  15. inverse, positive strand, negative direction, is SuccessablesPboxi+-.bas, looking for (C/T)AATG, 1, TAATG at 3658.
  16. inverse, positive strand, positive direction, is SuccessablesPboxi++.bas, looking for (C/T)AATG, 0.

P-box (Yu) core promoters

Main article: Core promoter gene transcriptions

Positive strand, positive direction: GTAAC at 4310.

P-box (Yu) distal promoters

Main article: Distal promoter gene transcriptions

Negative strand, negative direction: ATTAC at 3658, GTAAT at 3436, GTAAC at 3285, GTAAT at 2951, GTAAC at 1343, GTAAC at 886, GTAAT at 173, GTAAT at 153.

Positive strand, negative direction: GTAAT at 3973, ATTAC at 3469, GTAAT at 3064, GTAAT at 2675, GTAAT at 2088, GTAAT at 1914, GTAAT at 1779, GTAAT at 1707, ATTAC at 1296, GTAAT at 1261, GTAAT at 1134, GTAAT at 804, GTAAT at 670, GTAAC at 613, GTAAT at 534, GTAAT at 397, GTAAT at 248.

Negative strand, positive direction: GTAAC at 3732.

Positive strand, positive direction: GTTAC at 2909, GTAAC at 2903, GTAAC at 1703, GTTAC at 227, GTAAC at 23.

Consensus sequences

Main article: Consensus sequence gene transcriptions

P-box: 5′-(T/A)AAAG-3′.[2]

P-box (TGAGTTCA).[1]

P-box (Mena) samplings

Copying a responsive elements consensus sequence (T/A)AAAG 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 (T/A)AAAG (starting with SuccessablesAAA.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 (T/A)AAAG, 5, TAAAG at 3688, TAAAG at 2884, TAAAG at 1603, TAAAG at 1380, TAAAG at 22.
  2. negative strand, positive direction, looking for (T/A)AAAG, 3, AAAAG at 3928, AAAAG at 2708, AAAAG at 2004.
  3. positive strand, negative direction, looking for (T/A)AAAG, 24, AAAAG at 4391, AAAAG at 4386, AAAAG at 4379, AAAAG at 3440, AAAAG at 3344, TAAAG at 2857, AAAAG at 2835, AAAAG at 2823, AAAAG at 2818, AAAAG at 2806, AAAAG at 2797, AAAAG at 2477, AAAAG at 2471, TAAAG at 2174, AAAAG at 2052, AAAAG at 1627, TAAAG at 1548, AAAAG at 1399, AAAAG at 1106, AAAAG at 943, AAAAG at 223, AAAAG at 184, AAAAG at 104, AAAAG at 54.
  4. positive strand, positive direction, looking for (T/A)AAAG, 0.
  5. complement, negative strand, negative direction, looking for TTTTTTTT, 0.
  6. complement, negative strand, positive direction, looking for TTTTTTTT, 0.
  7. complement, positive strand, negative direction, looking for TTTTTTTT, 0.
  8. complement, positive strand, positive direction, looking for TTTTTTTT, 0.
  9. inverse complement, negative strand, negative direction, looking for TTTTTTTT, 0.
  10. inverse complement, negative strand, positive direction, looking for TTTTTTTT, 0.
  11. inverse complement, positive strand, negative direction, looking for TTTTTTTT, 0.
  12. inverse complement, positive strand, positive direction, looking for TTTTTTTT, 0.
  13. inverse negative strand, negative direction, looking for AAAAAAAA, 0.
  14. inverse negative strand, positive direction, looking for AAAAAAAA, 0.
  15. inverse positive strand, negative direction, looking for AAAAAAAA, 0.
  16. inverse positive strand, positive direction, looking for AAAAAAAA, 0.

P-box (Mena) core promoters

Main article: Core promoter gene transcriptions

P-box (Mena) proximal promoters

Main article: Proximal promoter gene transcriptions

P-box (Mena) distal promoters

Main article: Distal promoter gene transcriptions

P-box (Motojima) samplings

Copying a responsive elements consensus sequence TGAGTTCA 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 TGAGTTCA (starting with SuccessablesAAA.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 AAAAAAAA, 0.
  2. negative strand, positive direction, looking for AAAAAAAA, 0.
  3. positive strand, negative direction, looking for AAAAAAAA, 0.
  4. positive strand, positive direction, looking for AAAAAAAA, 0.
  5. complement, negative strand, negative direction, looking for TTTTTTTT, 0.
  6. complement, negative strand, positive direction, looking for TTTTTTTT, 0.
  7. complement, positive strand, negative direction, looking for TTTTTTTT, 0.
  8. complement, positive strand, positive direction, looking for TTTTTTTT, 0.
  9. inverse complement, negative strand, negative direction, looking for TTTTTTTT, 0.
  10. inverse complement, negative strand, positive direction, looking for TTTTTTTT, 0.
  11. inverse complement, positive strand, negative direction, looking for TTTTTTTT, 0.
  12. inverse complement, positive strand, positive direction, looking for TTTTTTTT, 0.
  13. inverse negative strand, negative direction, looking for AAAAAAAA, 0.
  14. inverse negative strand, positive direction, looking for AAAAAAAA, 0.
  15. inverse positive strand, negative direction, looking for AAAAAAAA, 0.
  16. inverse positive strand, positive direction, looking for AAAAAAAA, 0.

P-box (Motojima) core promoters

Main article: Core promoter gene transcriptions

P-box (Motojima) proximal promoters

Main article: Proximal promoter gene transcriptions

P-box (Motojima) distal promoters

Main article: Distal promoter gene transcriptions

Acknowledgements

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

See also

References

  1. ↑ 1.0 1.1 Masaru Motojima, Takao Ando and Toshimasa Yoshioka (10 July 2000). "Sp1-like activity mediates angiotensin-II-induced plasminogen-activator inhibitor type-1 (PAI-1) gene expression in mesangial cells" (PDF). Biomedical Journal. 349 (2): 435–441. doi:10.1042/0264-6021:3490435. PMID 10880342. Retrieved 13 August 2020.
  2. ↑ 2.0 2.1 2.2 2.3 2.4 Montaña Mena, Francisco Javier Cejudo, Ines Isabel-Lamoneda and Pilar Carbonero (1 September 2002). "A Role for the DOF Transcription Factor BPBF in the Regulation of Gibberellin-Responsive Genes in Barley Aleurone". Plant Physiology. 130 (1): 111–9. doi:10.1104/pp.0005561. Retrieved 2017-02-19.
  3. ↑ 3.0 3.1 Wangjie Yu and Paul E. Hardin (2006). "Circadian oscillators of Drosophila and mammals". Journal of Cell Science. 119: 4793–5. doi:10.1242/jcs.03174. Retrieved 2017-02-19.
  4. ↑ 4.0 4.1 Montaña Mena, Jesus Vicente-Carbajosa, Robert J. Schmidt and Pilar Carbonero (October 1998). "An endosperm-specific DOF protein from barley, highly conserved in wheat, binds to and activates transcription from the prolamin-box of a native B-hordein promoter in barley endosperm". The Plant Journal. 16 (1): 53–62. doi:10.1046/j.1365-313x.1998.00275.x. Retrieved 2017-02-19.

External links

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