H box gene transcriptions: Difference between revisions

Revision as of 04:24, 13 October 2019

Editor-In-Chief: Henry A. Hoff

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]

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)."^[3]

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')."^[3]

"Comparison with the murine telomerase RNA (mTR) (7) suggests that the snoRNA-like features of hTR are evolution- arily 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."^[3]

An H box has a consensus sequence of 3'-ACACCA-5'.^[4]

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

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:

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,
negative strand in the positive direction (from ZNF497 to A1BG) is SuccessablesHACA-+.bas, looking for 3'-ACACCA-5', 1, 3'-ACACCA-5', 386,
positive strand in the negative direction is SuccessablesHACA+-.bas, looking for 3'-ACACCA-5', 2, 3'-ACACCA-5', 883, 3'-ACACCA-5', 2419,
positive strand in the positive direction is SuccessablesHACA++.bas, looking for 3'-ACACCA-5', 2, 3'-ACACCA-5', 204, 3'-ACACCA-5', 528,
complement, negative strand, negative direction is SuccessablesHACAc--.bas, looking for 3'-TGTGGT-5', 2, 3'-TGTGGT-5', 883, 3'-TGTGGT-5', 2419,
complement, negative strand, positive direction is SuccessablesHACAc-+.bas, looking for 3'-TGTGGT-5', 2, 3'-TGTGGT-5', 204, 3'-TGTGGT-5', 528,
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,
complement, positive strand, positive direction is SuccessablesHACAc++.bas, looking for 3'-TGTGGT-5', 1, 3'-TGTGGT-5', 386,
inverse complement, negative strand, negative direction is SuccessablesHACAci--.bas, looking for 3'-TGGTGT-5', 1, 3'-TGGTGT-5', 3764,
inverse complement, negative strand, positive direction is SuccessablesHACAci-+.bas, looking for 3'-TGGTGT-5', 2, 3'-TGGTGT-5', 511, 3'-TGGTGT-5', 530,
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,
inverse complement, positive strand, positive direction is SuccessablesHACAci++.bas, looking for 3'-TGGTGT-5', 1, 3'-TGGTGT-5', 420,
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,
inverse, negative strand, positive direction, is SuccessablesHACAi-+.bas, looking for 3'-ACCACA-5', 1, 3'-ACCACA-5', 420,
inverse, positive strand, negative direction, is SuccessablesHACAi+-.bas, looking for 3'-ACCACA-5', 1, 3'-ACCACA-5', 3764,
inverse, positive strand, positive direction, is SuccessablesHACAi++.bas, looking for 3'-ACCACA-5', 2, 3'-ACCACA-5', 511, 3'-ACCACA-5', 530.

References

↑ ^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.
↑ 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.
↑ ^3.0 ^3.1 ^3.2 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.
↑ 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.
↑ 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

Template:Sisterlinks

[Rushton-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.

[Thomsen-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.

[Mitchell-3] 3.0 ^3.1 ^3.2 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.

[Rozhdestvensky-4] 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.

[Grandbastien-5] 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.

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transcriptions MYB recognition element gene transcriptions Myelocytomatosis transcription factor gene transcriptions Myocyte enhancer factor gene transcriptions N-boxes Ndt80p gene transcriptions Nuclear factor 1 Nuclear factor 𝜿B Nuclear factor gene transcriptions Nuclear factor of activated T cell gene transcriptions (NFAT) Nuclear factor Y gene transcriptions Nutrient-sensing response element gene transcriptions Oaf1p gene transcriptions ORE1 binding site gene transcriptions p53 response element gene transcriptions P63 DNA-binding site gene transcriptions P box gene transcriptions Pdr1,3p gene transcriptions Peroxisome proliferator hormone response element gene transcriptions Phosphate starvation-response transcription factor gene transcriptions Pollen1 element gene transcriptions Polycomb response element gene transcriptions Preinitiation complex Preinitiation complex gene transcriptions Pribnow box gene transcriptions Prolamin box gene transcriptions Promoter gene transcriptions Proximal promoter gene transcriptions Promoter occurrence gene transcriptions Pyrimidine box gene transcriptions Q element gene transcriptions Rap1 regulatory factor gene transcriptions Reb1 general regulatory factor gene transcriptions Retinoblastoma control element gene transcriptions Retinoic acid response element gene transcriptions Rgt1p gene transcriptions Rlm1p gene transcriptions RNA polymerase II gene transcriptions RNA polymerase II holoenzyme complex Root specific element gene transcriptions ROR-response element gene transcriptions Rox1p gene transcriptions Rpn4p gene transcriptions R response element gene transcriptions SARE gene transcriptions Seed-specific element gene transcriptions Serum response element gene transcriptions Servenius sequence gene transcriptions Shoot specific element gene transcriptions Sip4p gene transcriptions Smp1p gene transcriptions Sp1 gene transcriptions Spaceflight gene expressions Specificity protein gene transcriptions STAT gene transcriptions Ste12p gene transcriptions Sterol response element gene transcriptions Sucrose box gene transcriptions Synaptic Activity-Responsive Elements TACTAAC box gene transcriptions TAGteam gene transcriptions Tapetum box gene transcriptions TATA binding protein associated factor gene transcriptions TATA binding protein gene transcriptions TATA box gene transcriptions TAT box gene transcriptions TATC box gene transcriptions Tbf1 regulatory factor gene transcriptions T box gene transcriptions TCCACCATA element gene transcriptions TC element gene transcriptions TCT gene transcriptions TEA consensus sequence gene transcriptions Tec1p gene transcriptions Telomeric repeat DNA-binding factor gene transcriptions Tetradecanoylphorbol-13-acetate response element gene transcriptions TGF-β control elements (TCEs) TGF-β inhibitory elements (TIEs) Thyroid hormone response element gene transcriptions Transcriptional regulation Transcription bubble gene transcriptions Transcription factor gene transcriptions Transcription factor 3 gene transcriptions Transcription factory gene transcriptions Transcription start site gene transcriptions Translational control sequence gene transcriptions U box gene transcriptions Unfolded protein response element gene transcriptions Upstream response element gene transcriptions Upstream stimulatory factor gene transcriptions UTR promoter gene transcriptions V and P box gene transcriptions V box gene transcriptions Vhr1p gene transcriptions Vitamin D response element gene transcriptions W box gene transcriptions X box gene transcriptions Xbp1p gene transcriptions X core promoter element gene transcriptions Xenobiotic response element gene transcriptions Xenobiotic responsive element gene transcriptions Yap1p,2p gene transcriptions Y box gene transcriptions YY1 gene transcriptions Zap1p gene transcriptions Z box gene transcriptions Zinc responsive element gene transcriptions