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Gene transcriptions/Boxes/Xs

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"The so-called X (or X1) box in the promoter of the human MHC class II DRA gene is the binding site for a ubiquitous mammalian sequence-specific DNA-binding protein called RFX, NF-X, NF-Xc, or RFX1 (4,19,23,24,27)."[1]

"RFX is MDBP [...] the MDBP (RFX) recognition site region in the DRA promoter can be considered to extend from positions -100 to -112 [...] a possible binding site for MDBP which begins 88 bp after the first residue of the presumably full-length RFX1 (MDBP) cDNA (26). This site (RFX+88) is as follows: 5'-GTTGGCATGGCAAC-3'."[1]

X-box motifs

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"Based on sequence variability in the X box region (position -188 to -152), three different sequence motifs can be distinguished (X-A, X-B and X-C). Identical bases are marked by a dash; the region of the X1 box is underlined; the region corresponding to the X2 box is given in italics."[2]

X2 box is 5'-AGGTCCA-3'.[2]

X-A box is 5'-AAAAAAAA//TCTGCCCAGAGACAGATGAGGTCCA-3', where TG is missing at //, which contains X1 = 5'-CCCAGAGACAGATGA-3' and disrupts the palindrome 5'- TGTCNNNNNNNNGACA-3' .[2]

X-B box is 5'-AAAAAAAATGTCTGCCTAGAGACAGATTAGGTCCA-3' which contains X1 = 5'-CCTAGAGACAGATTA-3' and the palindrome 5'-CCTANNNNNNNNNTAGG-3'.[2]

X-C box is 5'-AAAAAAAATGTCTGCCTAGAGACAGATGAGGTCCA-3' which contains X1 = 5'-TGCCTAGAGAC-3' and the palindrome 5'-CCTANNNNNNNNNTAGG-3'.[2]

Sampling of A1BG promoters

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For the Basic programs (starting with SuccessablesXbox.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 (+), including extending the number of nts from 958 to 4445, the programs are, are looking for, and found:

  1. negative strand in the negative direction (from ZSCAN22 to A1BG) is SuccessablesXbox--.bas, looking for 3'-GTTGGCATGGCAAC-5', 0,
  2. negative strand in the positive direction (from ZNF497 to A1BG) is SuccessablesXbox-+.bas, looking for 3'-GTTGGCATGGCAAC-5', 0,
  3. positive strand in the negative direction is SuccessablesXbox+-.bas, looking for 3'-GTTGGCATGGCAAC-5', 0,
  4. positive strand in the positive direction is SuccessablesXbox++.bas, looking for 3'-GTTGGCATGGCAAC-5', 0,
  5. complement, negative strand, negative direction is SuccessablesXboxc--.bas, looking for 3'-CAACCGTACCGTTG-5', 0,
  6. complement, negative strand, positive direction is SuccessablesXboxc-+.bas, looking for 3'-CAACCGTACCGTTG-5', 0,
  7. complement, positive strand, negative direction is SuccessablesXboxc+-.bas, looking for 3'-CAACCGTACCGTTG-5', 0,
  8. complement, positive strand, positive direction is SuccessablesXboxc++.bas, looking for 3'-CAACCGTACCGTTG-5', 0,
  9. inverse complement, negative strand, negative direction is SuccessablesXboxci--.bas, looking for 3'-GTTGCCATGCCAAC-5', 0,
  10. inverse complement, negative strand, positive direction is SuccessablesXboxci-+.bas, looking for 3'-GTTGCCATGCCAAC-5', 0,
  11. inverse complement, positive strand, negative direction is SuccessablesXboxci+-.bas, looking for 3'-GTTGCCATGCCAAC-5', 0,
  12. inverse complement, positive strand, positive direction is SuccessablesXboxci++.bas, looking for 3'-GTTGCCATGCCAAC-5', 0,
  13. inverse, negative strand, negative direction, is SuccessablesXboxi--.bas, looking for 3'-CAACGGTACGGTTG-5', 0,
  14. inverse, negative strand, positive direction, is SuccessablesXboxi-+.bas, looking for 3'-CAACGGTACGGTTG-5', 0,
  15. inverse, positive strand, negative direction, is SuccessablesXboxi+-.bas, looking for 3'-CAACGGTACGGTTG-5', 0,
  16. inverse, positive strand, positive direction, is SuccessablesXboxi++.bas, looking for 3'-CAACGGTACGGTTG-5', 0.

See also

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References

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  1. ↑ 1.0 1.1 XIAN-YANG ZHANG, NABILA JABRANE-FERRAT, CLEMENT K. ASIEDU, SANJA SAMAC, B. MATIJA PETERLIN, AND MELANIE EHRLICH (November 1993). "The Major Histocompatibility Complex Class II Promoter-Binding Protein RFX (NF-X) Is a Methylated DNA-Binding Protein". MOLECULAR AND CELLULAR BIOLOGY 13 (11): 6810-8. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC364743/pdf/molcellb00023-0210.pdf. Retrieved 2017-04-05. 
  2. ↑ 2.0 2.1 2.2 2.3 2.4 B. Ferstl, T. Zacher, B. Lauer, N. Blagitko-Dorfs, A. Carl and R. Wassmuth (2004). "Allele-specific quantification of HLA-DQB1 gene expression by real-time reverse transcriptase-polymerase chain reaction". Genes and Immunity 5: 405–416. doi:10.1038/sj.gene.6364108. https://www.researchgate.net/profile/Nadja_Blagitko-Dorfs/publication/8530481_Allele-specific_quantification_of_HLA-DQB1_gene_expression_by_real-time_reverse_transcriptase-polymerase_chain_reaction/links/0c9605320213f30bfd000000.pdf. Retrieved 23 November 2018. 
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