H box gene transcriptions: Difference between revisions

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For the Basic programs testing consensus sequence CCTACC (starting with SuccessablesHL-box.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 CCTACC (starting with SuccessablesHL-box.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 CCTACC, 0.
# negative strand, negative direction, looking for CCTACC, 0.
# positive strand, negative direction, looking for AAAAAAAA, 0.
# positive strand, negative direction, looking for CCTACC, 0.
# positive strand, positive direction, looking for AAAAAAAA, 0.
# positive strand, positive direction, looking for CCTACC, 1, CCTACC at 1879.
# negative strand, positive direction, looking for AAAAAAAA, 0.
# negative strand, positive direction, looking for CCTACC, 1, CCTACC at 1196.
# complement, negative strand, negative direction, looking for TTTTTTTT, 0.
# complement, negative strand, negative direction, looking for GGATGG, 0.
# complement, positive strand, negative direction, looking for GGATGG, 0.
# complement, positive strand, negative direction, looking for GGATGG, 0.
# complement, positive strand, positive direction, looking for TTTTTTTT, 0.
# complement, positive strand, positive direction, looking for GGATGG, 1, GGATGG at 1196.
# complement, negative strand, positive direction, looking for TTTTTTTT, 0.
# complement, negative strand, positive direction, looking for GGATGG, 1, GGATGG at 1879.
# inverse complement, negative strand, negative direction, looking for GGTAGG, 0.
# inverse complement, negative strand, negative direction, looking for GGTAGG, 2, GGTAGG at 4456, GGTAGG at 1838.
# inverse complement, positive strand, negative direction, looking for TTTTTTTT, 0.
# inverse complement, positive strand, negative direction, looking for GGTAGG, 1, GGTAGG at 119.
# inverse complement, positive strand, positive direction, looking for TTTTTTTT, 0.
# inverse complement, positive strand, positive direction, looking for GGTAGG, 2, GGTAGG at 3629, GGTAGG at 3108.
# inverse complement, negative strand, positive direction, looking for TTTTTTTT, 0.
# inverse complement, negative strand, positive direction, looking for GGTAGG, 1, GGTAGG at 3753.
# inverse negative strand, negative direction, looking for CCATCC, 0.
# inverse negative strand, negative direction, looking for CCATCC, 1, CCATCC at 119.
# inverse positive strand, negative direction, looking for AAAAAAAA, 0.
# inverse positive strand, negative direction, looking for CCATCC, 2, CCATCC at 4456, CCATCC at 1838.
# inverse positive strand, positive direction, looking for AAAAAAAA, 0.
# inverse positive strand, positive direction, looking for CCATCC, 1, CCATCC at 3753.
# inverse negative strand, positive direction, looking for AAAAAAAA, 0.
# inverse negative strand, positive direction, looking for CCATCC, 2, CCATCC at 3629, CCATCC at 3108.


===AAA UTRs===
===H box (Lindsay) UTRs===
{{main|UTR promoter gene transcriptions}}
{{main|UTR promoter gene transcriptions}}
Negative strand: GGTAGG at 4456.


===AAA core promoters===
===H box (Lindsay) proximal promoters===
{{main|Core promoter gene transcriptions}}
{{main|Proximal promoter gene transcriptions}}
Negative strand: GGTAGG at 1838.


===AAA proximal promoters===
Positive strand: GGTAGG at 119.
{{main|Proximal promoter gene transcriptions}}


===AAA distal promoters===
===H box (Lindsay) distal promoters===
{{main|Distal promoter gene transcriptions}}
{{main|Distal promoter gene transcriptions}}
Negative strand: GGTAGG at 3753, CCTACC' at 1196.
Positive strand: GGTAGG at 3629, GGTAGG at 3108, CCTACC at 1879.


==Acknowledgements==
==Acknowledgements==

Revision as of 17:54, 17 March 2021

Editor-In-Chief: Henry A. Hoff

File:A green bean.jpg
Green beans grow from Phaseolus vulgaris. Credit: wanko from Japan.{{free media}}

The "H-box [is] from the bean chalcone synthase gene Chs15 [23,24]."[1]

The "Phaseolus vulgaris chalcone synthase (PvCHS15)" gene has three H boxes between the G box and the TATA box, where each binds to MYB, KAP 2, and KAP 1 downstream from the G box, respectively.[1]

"Functional studies with the H-box indicated that it cannot function to a high level alone. Gain of function experiments, however, show that it is active in combination with a G-Box element [...] in transgenic tobacco plants in establishing the characteristic tissue-specific pattern of expression and mutations in either the H-box or G-Box reduced the response to tobacco mosaic virus (TMV) infection [24,30]."[1]

"A bZIP protein from soybean binds to the G-Box in the bean Chs15 promoter [36•]. This protein, G/HBF-1, can also bind to the adjacent H-box."[1]

"Although the mRNA and protein levels of G/HBF-1 do not increase during the induction of its putative target genes, the protein itself is rapidly phosphorylated and in vitro phosphorylation enhances binding to one (H-box III) out of the three H-boxes present in the Chs15 promoter."[1]

H box in animals

"A testis/brain RNA-binding protein, TB-RBP, binds to the Y- and H-boxes in the Prm2 3′ UTR and represses translation of a reporter mRNA in rabbit reticulocyte lysates [9]. The Y- and H-boxes are found in many transcripts expressed in the testis and brain, including Prm1, Prm2, Tnp1, and Tau [10]."[2]

H-boxes

"Two distinct sequence elements, the H-box (consensus CCTACC(N)7CT) and the G-box (CACGTG), are required for stimulation of the chs15 promoter by 4-CA."[3]

H box consensus sequences

"The box H/ACA snoRNAs were most recently recognized as a small RNA family by virtue of an ACA trinucleotide located 3 nt upstream of the mature snoRNA 3' end (41). In addition to this ACA box, they have the consensus H box sequence (5'-ANANNA-3') but have no other primary sequence identity. Despite this lack of primary sequence conservation, the H and ACA boxes are embedded in an evolutionarily conserved hairpin-hinge-hairpin-tail core secondary structure with the H box in the single-stranded hinge region and the ACA box in the single-stranded tail (5, 16)."[4]

The "3' end of mature hTR (45) has an ACA trinucleotide 3 nt upstream of its 3' end. In addition, the 3' region of hTR contains a single H box consensus sequence (5'-AGAGGA-3')."[4]

"Comparison with the murine telomerase RNA (mTR) (7) suggests that the snoRNA-like features of hTR are evolutionarily conserved. The mTR 3' end (nt 169 to 397 as numbered in reference 25) has ~76% sequence identity with the corresponding region of hTR (nt 211 to 451) and includes consensus H (5'-ACAGGA-3') and ACA box sequences."[4]

An H box has a consensus sequence of 3'-ACACCA-5'.[5]

H-box consensus sequences

The earlier H-box consensus sequence is CCTACC(N)7CT.[3]

H box in Solanaceae has the following consensus sequence 3'-CC(A/T)ACCNNNNNNN(A/C)T-5'.[6]

H boxes in promoters of A1BG

For the Basic programs (starting with SuccessablesHACA.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 SuccessablesHACA--.bas, looking for 3'-ACACCA-5', 4, 3'-ACACCA-5', 788, 3'-ACACCA-5', 2659, 3'-ACACCA-5', 3187, 3'-ACACCA-5', 3811,
  2. negative strand in the positive direction (from ZNF497 to A1BG) is SuccessablesHACA-+.bas, looking for 3'-ACACCA-5', 1, 3'-ACACCA-5', 386,
  3. positive strand in the negative direction is SuccessablesHACA+-.bas, looking for 3'-ACACCA-5', 2, 3'-ACACCA-5', 883, 3'-ACACCA-5', 2419,
  4. positive strand in the positive direction is SuccessablesHACA++.bas, looking for 3'-ACACCA-5', 2, 3'-ACACCA-5', 204, 3'-ACACCA-5', 528,
  5. complement, negative strand, negative direction is SuccessablesHACAc--.bas, looking for 3'-TGTGGT-5', 2, 3'-TGTGGT-5', 883, 3'-TGTGGT-5', 2419,
  6. complement, negative strand, positive direction is SuccessablesHACAc-+.bas, looking for 3'-TGTGGT-5', 2, 3'-TGTGGT-5', 204, 3'-TGTGGT-5', 528,
  7. complement, positive strand, negative direction is SuccessablesHACAc+-.bas, looking for 3'-TGTGGT-5', 4, 3'-TGTGGT-5', 788, 3'-TGTGGT-5', 2659, 3'-TGTGGT-5', 3187, 3'-TGTGGT-5', 3811,
  8. complement, positive strand, positive direction is SuccessablesHACAc++.bas, looking for 3'-TGTGGT-5', 1, 3'-TGTGGT-5', 386,
  9. inverse complement, negative strand, negative direction is SuccessablesHACAci--.bas, looking for 3'-TGGTGT-5', 1, 3'-TGGTGT-5', 3764,
  10. inverse complement, negative strand, positive direction is SuccessablesHACAci-+.bas, looking for 3'-TGGTGT-5', 2, 3'-TGGTGT-5', 511, 3'-TGGTGT-5', 530,
  11. inverse complement, positive strand, negative direction is SuccessablesHACAci+-.bas, looking for 3'-TGGTGT-5', 3, 3'-TGGTGT-5', 608, 3'-TGGTGT-5', 793, 3'-TGGTGT-5', 1477,
  12. inverse complement, positive strand, positive direction is SuccessablesHACAci++.bas, looking for 3'-TGGTGT-5', 1, 3'-TGGTGT-5', 420,
  13. inverse, negative strand, negative direction, is SuccessablesHACAi--.bas, looking for 3'-ACCACA-5', 3, 3'-ACCACA-5', 608, 3'-ACCACA-5', 793, 3'-ACCACA-5', 1477,
  14. inverse, negative strand, positive direction, is SuccessablesHACAi-+.bas, looking for 3'-ACCACA-5', 1, 3'-ACCACA-5', 420,
  15. inverse, positive strand, negative direction, is SuccessablesHACAi+-.bas, looking for 3'-ACCACA-5', 1, 3'-ACCACA-5', 3764,
  16. inverse, positive strand, positive direction, is SuccessablesHACAi++.bas, looking for 3'-ACCACA-5', 2, 3'-ACCACA-5', 511, 3'-ACCACA-5', 530.

H-box (Loake) samplings

Main article: Model samplings

Copying a responsive elements consensus sequence CCTACCTGGCGGAT and putting the sequence in "⌘F" finds none between ZNF497 and A1BG or CCTACC finds none between ZSCAN22 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence CC(A/T)ACCNNNNNNN(A/C)T (starting with SuccessablesH-box.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 CC(A/T)ACCNNNNNNN(A/C)T, 0.
  2. positive strand, negative direction, looking for CC(A/T)ACCNNNNNNN(A/C)T, 0.
  3. positive strand, positive direction, looking for CC(A/T)ACCNNNNNNN(A/C)T, 0.
  4. negative strand, positive direction, looking for CC(A/T)ACCNNNNNNN(A/C)T, 0.
  5. complement, negative strand, negative direction, looking for GG(A/T)TGGNNNNNNN(G/T)A, 0.
  6. complement, positive strand, negative direction, looking for GG(A/T)TGGNNNNNNN(G/T)A, 0.
  7. complement, positive strand, positive direction, looking for GG(A/T)TGGNNNNNNN(G/T)A, 0.
  8. complement, negative strand, positive direction, looking for GG(A/T)TGGNNNNNNN(G/T)A, 0.
  9. inverse complement, negative strand, negative direction, looking for A(G/T)NNNNNNNGGT(A/T)GG, 0.
  10. inverse complement, positive strand, negative direction, looking for A(G/T)NNNNNNNGGT(A/T)GG, 1, AGAAGTGTTGGTTGG at 3946.
  11. inverse complement, positive strand, positive direction, looking for A(G/T)NNNNNNNGGT(A/T)GG, 0.
  12. inverse complement, negative strand, positive direction, looking for A(G/T)NNNNNNNGGT(A/T)GG, 0.
  13. inverse negative strand, negative direction, looking for T(A/C)NNNNNNNCCA(A/T)CC, 1, TCTTCACAACCAACC at 3946.
  14. inverse positive strand, negative direction, looking for T(A/C)NNNNNNNCCA(A/T)CC, 0.
  15. inverse positive strand, positive direction, looking for T(A/C)NNNNNNNCCA(A/T)CC, 0.
  16. inverse negative strand, positive direction, looking for T(A/C)NNNNNNNCCA(A/T)CC, 0.

H-box UTRs

Main article: UTR promoter gene transcriptions

Positive strand, negative direction: AGAAGTGTTGGTTGG at 3946.

H-box (Lindsay) samplings

Main article: Model samplings

Copying a responsive element consensus sequence CCTACC and putting the sequence in "⌘F" finds none between ZNF497 and A1BG or one between ZSCAN22 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence CCTACC (starting with SuccessablesHL-box.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 CCTACC, 0.
  2. positive strand, negative direction, looking for CCTACC, 0.
  3. positive strand, positive direction, looking for CCTACC, 1, CCTACC at 1879.
  4. negative strand, positive direction, looking for CCTACC, 1, CCTACC at 1196.
  5. complement, negative strand, negative direction, looking for GGATGG, 0.
  6. complement, positive strand, negative direction, looking for GGATGG, 0.
  7. complement, positive strand, positive direction, looking for GGATGG, 1, GGATGG at 1196.
  8. complement, negative strand, positive direction, looking for GGATGG, 1, GGATGG at 1879.
  9. inverse complement, negative strand, negative direction, looking for GGTAGG, 2, GGTAGG at 4456, GGTAGG at 1838.
  10. inverse complement, positive strand, negative direction, looking for GGTAGG, 1, GGTAGG at 119.
  11. inverse complement, positive strand, positive direction, looking for GGTAGG, 2, GGTAGG at 3629, GGTAGG at 3108.
  12. inverse complement, negative strand, positive direction, looking for GGTAGG, 1, GGTAGG at 3753.
  13. inverse negative strand, negative direction, looking for CCATCC, 1, CCATCC at 119.
  14. inverse positive strand, negative direction, looking for CCATCC, 2, CCATCC at 4456, CCATCC at 1838.
  15. inverse positive strand, positive direction, looking for CCATCC, 1, CCATCC at 3753.
  16. inverse negative strand, positive direction, looking for CCATCC, 2, CCATCC at 3629, CCATCC at 3108.

H box (Lindsay) UTRs

Main article: UTR promoter gene transcriptions

Negative strand: GGTAGG at 4456.

H box (Lindsay) proximal promoters

Main article: Proximal promoter gene transcriptions

Negative strand: GGTAGG at 1838.

Positive strand: GGTAGG at 119.

H box (Lindsay) distal promoters

Main article: Distal promoter gene transcriptions

Negative strand: GGTAGG at 3753, CCTACC' at 1196.

Positive strand: GGTAGG at 3629, GGTAGG at 3108, CCTACC at 1879.

Acknowledgements

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

See also

References

  1. ↑ 1.0 1.1 1.2 1.3 1.4 Paul J Rushton and Imre E Somssich (August 1998). "Transcriptional control of plant genes responsive to pathogens" (PDF). Current Opinion in Plant Biology. 1 (4): 311–5. doi:10.1016/1369-5266(88)80052-9. Retrieved 5 November 2018.
  2. ↑ Jun Zhong, Antoine H.F.M. Peters, Kathy Kafer, Robert E. Braun (1 June 2001). "A Highly Conserved Sequence Essential for Translational Repression of the Protamine 1 Messenger RNA in Murine Spermatids". Biology of Reproduction. 64 (6): 1784–1789. doi:10.1095/biolreprod64.6.1784. Retrieved 5 November 2018.
  3. ↑ 3.0 3.1 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 (19): 9230–9234. doi:10.1073/pnas.89.19.9230. Retrieved 16 March 2021.
  4. ↑ 4.0 4.1 4.2 James R. Mitchell, Jeffrey Cheng, ang Kathleen Collins (January 1999). "A Box H/ACA Small Nucleolar RNA-Like Domain at the Human Telomerase RNA 3' End" (PDF). Molecular and Cellular Biology. 19 (1): 567–576. Retrieved 5 November 2018.
  5. ↑ Timofey S. Rozhdestvensky, Thean Hock Tang, Inna V. Tchirkova, Jürgen Brosius, Jean‐Pierre Bachellerie and Alexander Hüttenhofer (2003). "Binding of L7Ae protein to the K‐turn of archaeal snoRNAs: a shared RNA binding motif for C/D and H/ACA box snoRNAs in Archaea". Nucleic Acids Research. 31 (3): 869–77. doi:10.1093/nar/gkg175. Retrieved 2014-06-08.
  6. ↑ M.-A. Grandbastien, C. Audeon, E. Bonnivard, J.M. Casacuberta, B. Chalhoub, A.-P.P. Costa, Q.H. Le, D. Melayah, M. Petit, C. Poncet, S.M. Tam, M.-A. Van Sluys, C. Mhiri (July 2005). "Stress activation and genomic impact of Tnt1 retrotransposons in Solanaceae" (PDF). Cytogenetic and Genomic Research. 110 (1–4): 229–41. doi:10.1159/000084957. Retrieved 5 November 2018.

External links

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