DNA damage response element gene transcriptions: Difference between revisions

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For the Basic programs testing consensus sequence CCGCC (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:
For the Basic programs testing consensus sequence CCGCC (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:
# negative strand, negative direction, looking for CCGCC, 13, ACTCCGCCC at 4000, ACTCCGCCC at 3091, CCGCCGCCT at 2728, GACCCGCCG at 2725, CGTCCGCCT at 2393, ACTCCGCCA at 2232, CACCCGCCT at 1810, CCTCCGCCG at 1753, CCACCGCCC at 1251, GTACCGCCG at 957, CCTCCGCCT at 857, CGTCCGCCT at 701, TGTCCGCCT at 428.
# negative strand, negative direction, looking for CCGCC, 13, CCGCC at 3999, CCGCC at 3090, CCGCC at 2727, CCGCC at 2724, CCGCC at 2392, CCGCC at 2231, CCGCC at 1809, CCGCC at 1752, CCGCC at 1250, CCGCC at 956, CCGCC at 856, CCGCC at 700, CCGCC at 427.
# negative strand, positive direction, looking for CCGCC, 4, CCACCGCCC at 4292, CCCCCGCCT at 4239, GGGCCGCCG at 1758, CTGCCGCCT at 905.
# negative strand, positive direction, looking for CCGCC, 4, CCGCC at 4291, CCGCC at 4238, CCGCC at 1757, CCGCC at 904.
# positive strand, negative direction, looking for CCGCC, 1, GCTCCGCCT at 1504.
# positive strand, negative direction, looking for CCGCC, 1, CCGCC at 1503.
# positive strand, positive direction, looking for CCGCC, 11, CCCCCGCCC at 4440, ACCCCGCCC at 4430, GATCCGCCA at 3488, GATCCGCCC at 2486, CTCCCGCCG at 1902, TCCCCGCCG at 1794, GGACCGCCT at 1203, ACACCGCCC at 1026, CACCCGCCC at 407, CCGCCGCCT at 357, CCCCCGCCG at 354.
# positive strand, positive direction, looking for CCGCC, 11, CCGCC at 4439, CCGCC at 4429, CCGCC at 3487, CCGCC at 2485, CCGCC at 1901, CCGCC at 1793, CCGCC at 1202, CCGCC at 1025, CCGCC at 406, CCGCC at 356, CCGCC at 353.
# complement, negative strand, negative direction, looking for nnnGGCGGn, 1, CGAGGCGGA at 1504.
# complement, negative strand, negative direction, looking for GGCGG, 1, GGCGG at 1503.
# complement, negative strand, positive direction, looking for nnnGGCGGn, 11, GGGGGCGGG at 4440, TGGGGCGGG at 4430, CTAGGCGGT at 3488, CTAGGCGGG at 2486, GAGGGCGGC at 1902, AGGGGCGGC at 1794, CCTGGCGGA at 1203, TGTGGCGGG at 1026, GTGGGCGGG at 407, GGCGGCGGA at 357, GGGGGCGGC at 354.
# complement, negative strand, positive direction, looking for GGCGG, 11, GGCGG at 4439, GGCGG at 4429, GGCGG at 3487, GGCGG at 2485, GGCGG at 1901, GGCGG at 1793, GGCGG at 1202, GGCGG at 1025, GGCGG at 406, GGCGG at 356, GGCGG at 353.
# complement, positive strand, negative direction, looking for nnnGGCGGn, 13, TGAGGCGGG at 4000, TGAGGCGGG at 3091, GGCGGCGGA at 2728, CTGGGCGGC at 2725, GCAGGCGGA at 2393, TGAGGCGGT at 2232, GTGGGCGGA at 1810, GGAGGCGGC at 1753, GGTGGCGGG at 1251, CATGGCGGC at 957, GGAGGCGGA at 857, GCAGGCGGA at 701, ACAGGCGGA at 428.
# complement, positive strand, negative direction, looking for GGCGG, 13, GGCGG at 3999, GGCGG at 3090, GGCGG at 2727, GGCGG at 2724, GGCGG at 2392, GGCGG at 2231, GGCGG at 1809, GGCGG at 1752, GGCGG at 1251, GGCGG at 956, GGCGG at 856, GGCGG at 700, GGCGG at 427.
# complement, positive strand, positive direction, looking for nnnGGCGGn, 4, GGTGGCGGG at 4292, GGGGGCGGA at 4239, CCCGGCGGC at 1758, GACGGCGGA at 905.
# complement, positive strand, positive direction, looking for GGCGG, 4, GGCGG at 4291, GGCGG at 4238, GGCGG at 1757, GGCGG at 904.
# inverse complement, negative strand, negative direction, looking for nGGCGGnnn, 1, AGGCGGAGG at 1506.
# inverse complement, negative strand, positive direction, looking for nGGCGGnnn, 11, GGGCGGGAA at 4442, GGGCGGGAG at 4432, AGGCGGTTG at 3490, AGGCGGGTC at 2488, GGGCGGCAG at 1904, GGGCGGCCT at 1796, TGGCGGAGC at 1205, TGGCGGGGC at 1028, GGGCGGGAC at 409, CGGCGGACG at 359, GGGCGGCGG at 356.
# inverse complement, positive strand, negative direction, looking for nGGCGGnnn, 13, AGGCGGGAG at 4002, AGGCGGGTG at 3093, CGGCGGAAG at 2730, GGGCGGCGG at 2727, AGGCGGAGG at 2395, AGGCGGTTG at 2234, GGGCGGATC at 1812, AGGCGGCTG at 1755, TGGCGGGTG at 1253, TGGCGGCAC at 959, AGGCGGAGG at 859, AGGCGGATC at 703, AGGCGGATC at 430.
# inverse complement, positive strand, positive direction, looking for nGGCGGnnn, 4, TGGCGGGAG at 4294, GGGCGGAAG at 4241, CGGCGGCCA at 1760, CGGCGGACG at 907.
# inverse negative strand, negative direction, looking for CCGCC, 13, TCCGCCCTC at 4002, TCCGCCCAC at 3093, GCCGCCTTC at 2730, CCCGCCGCC at 2727, TCCGCCTCC at 2395, TCCGCCAAC at 2234, CCCGCCTAG at 1812, TCCGCCGAC at 1755, ACCGCCCAC at 1253, ACCGCCGTG at 959, TCCGCCTCC at 859, TCCGCCTAG at 703, TCCGCCTAG at 430.
# inverse negative strand, positive direction, looking for CCGCC, 4, ACCGCCCTC at 4294, CCCGCCTTC at 4241, GCCGCCGGT at 1760, GCCGCCTGC at 907.
# inverse positive strand, negative direction, looking for CCGCC, 1, TCCGCCTCC at 1506.
# inverse positive strand, positive direction, looking for CCGCC, 11, CCCGCCCTT at 4442, CCCGCCCTC at 4432, TCCGCCAAC at 3490, TCCGCCCAG at 2488, CCCGCCGTC at 1904, CCCGCCGGA at 1796, ACCGCCTCG at 1205, ACCGCCCCG at 1028, CCCGCCCTG at 409, GCCGCCTGC at 359, CCCGCCGCC at 356.


==DRE (Smith) samplings==
==DRE (Smith) samplings==

Revision as of 23:27, 28 January 2021

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

"The corepressor complex is recruited to the RNR genes by the sequence-specific DNA-binding protein Crt1, which recognizes the DNA damage response elements (DREs) in the upstream repression sequence (URS) (19, 35)."[1]

Human genes

Consensus sequences

"A consensus sequence, 5'-TAGCCGCCGRRRR-3' (where R = an unspecified purine nucleoside [A/G],was generated from these data."[2]

"The extent of homology for the entire 13 bp ranged from 56 to 100%. However, for the symmetrical core sequence CCGCC 75 to 100% homology was observed with only conservative substitutions occurring in the nonhomologous positions."[2]

DNA damage response element (DRE) has the consensus sequence TTTCAAT.[3]

Hypotheses

Main article: Hypotheses
  1. A1BG has no DNA damage response elements in either promoter.
  2. A1BG is not transcribed by a DNA damage response element.
  3. A DNA damage response element does not participate in the transcription of A1BG.

DRE (Sumrada) samplings

Copying the consensus URS: TAGCCGCCG and putting the sequence in "⌘F" finds no locations between ZNF497 and A1BG or between ZSCAN22 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence nnnCCGCCn (starting with SuccessablesDRES.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 nnnCCGCCn, 13, ACTCCGCCC at 4000, ACTCCGCCC at 3091, CCGCCGCCT at 2728, GACCCGCCG at 2725, CGTCCGCCT at 2393, ACTCCGCCA at 2232, CACCCGCCT at 1810, CCTCCGCCG at 1753, CCACCGCCC at 1251, GTACCGCCG at 957, CCTCCGCCT at 857, CGTCCGCCT at 701, TGTCCGCCT at 428.
  2. negative strand, positive direction, looking for nnnCCGCCn, 4, CCACCGCCC at 4292, CCCCCGCCT at 4239, GGGCCGCCG at 1758, CTGCCGCCT at 905.
  3. positive strand, negative direction, looking for nnnCCGCCn, 1, GCTCCGCCT at 1504.
  4. positive strand, positive direction, looking for nnnCCGCCn, 11, CCCCCGCCC at 4440, ACCCCGCCC at 4430, GATCCGCCA at 3488, GATCCGCCC at 2486, CTCCCGCCG at 1902, TCCCCGCCG at 1794, GGACCGCCT at 1203, ACACCGCCC at 1026, CACCCGCCC at 407, CCGCCGCCT at 357, CCCCCGCCG at 354.
  5. complement, negative strand, negative direction, looking for nnnGGCGGn, 1, CGAGGCGGA at 1504.
  6. complement, negative strand, positive direction, looking for nnnGGCGGn, 11, GGGGGCGGG at 4440, TGGGGCGGG at 4430, CTAGGCGGT at 3488, CTAGGCGGG at 2486, GAGGGCGGC at 1902, AGGGGCGGC at 1794, CCTGGCGGA at 1203, TGTGGCGGG at 1026, GTGGGCGGG at 407, GGCGGCGGA at 357, GGGGGCGGC at 354.
  7. complement, positive strand, negative direction, looking for nnnGGCGGn, 13, TGAGGCGGG at 4000, TGAGGCGGG at 3091, GGCGGCGGA at 2728, CTGGGCGGC at 2725, GCAGGCGGA at 2393, TGAGGCGGT at 2232, GTGGGCGGA at 1810, GGAGGCGGC at 1753, GGTGGCGGG at 1251, CATGGCGGC at 957, GGAGGCGGA at 857, GCAGGCGGA at 701, ACAGGCGGA at 428.
  8. complement, positive strand, positive direction, looking for nnnGGCGGn, 4, GGTGGCGGG at 4292, GGGGGCGGA at 4239, CCCGGCGGC at 1758, GACGGCGGA at 905.
  9. inverse complement, negative strand, negative direction, looking for nGGCGGnnn, 1, AGGCGGAGG at 1506.
  10. inverse complement, negative strand, positive direction, looking for nGGCGGnnn, 11, GGGCGGGAA at 4442, GGGCGGGAG at 4432, AGGCGGTTG at 3490, AGGCGGGTC at 2488, GGGCGGCAG at 1904, GGGCGGCCT at 1796, TGGCGGAGC at 1205, TGGCGGGGC at 1028, GGGCGGGAC at 409, CGGCGGACG at 359, GGGCGGCGG at 356.
  11. inverse complement, positive strand, negative direction, looking for nGGCGGnnn, 13, AGGCGGGAG at 4002, AGGCGGGTG at 3093, CGGCGGAAG at 2730, GGGCGGCGG at 2727, AGGCGGAGG at 2395, AGGCGGTTG at 2234, GGGCGGATC at 1812, AGGCGGCTG at 1755, TGGCGGGTG at 1253, TGGCGGCAC at 959, AGGCGGAGG at 859, AGGCGGATC at 703, AGGCGGATC at 430.
  12. inverse complement, positive strand, positive direction, looking for nGGCGGnnn, 4, TGGCGGGAG at 4294, GGGCGGAAG at 4241, CGGCGGCCA at 1760, CGGCGGACG at 907.
  13. inverse negative strand, negative direction, looking for nCCGCCnnn, 13, TCCGCCCTC at 4002, TCCGCCCAC at 3093, GCCGCCTTC at 2730, CCCGCCGCC at 2727, TCCGCCTCC at 2395, TCCGCCAAC at 2234, CCCGCCTAG at 1812, TCCGCCGAC at 1755, ACCGCCCAC at 1253, ACCGCCGTG at 959, TCCGCCTCC at 859, TCCGCCTAG at 703, TCCGCCTAG at 430.
  14. inverse negative strand, positive direction, looking for nCCGCCnnn, 4, ACCGCCCTC at 4294, CCCGCCTTC at 4241, GCCGCCGGT at 1760, GCCGCCTGC at 907.
  15. inverse positive strand, negative direction, looking for AAAAAAAA, 1, TCCGCCTCC at 1506.
  16. inverse positive strand, positive direction, looking for AAAAAAAA, 11, CCCGCCCTT at 4442, CCCGCCCTC at 4432, TCCGCCAAC at 3490, TCCGCCCAG at 2488, CCCGCCGTC at 1904, CCCGCCGGA at 1796, ACCGCCTCG at 1205, ACCGCCCCG at 1028, CCCGCCCTG at 409, GCCGCCTGC at 359, CCCGCCGCC at 356.

DRE (Sumrada, core) samplings

Copying the consensus URS: CCGCC and putting the sequence in "⌘F" finds no locations between ZNF497 and A1BG or between ZSCAN22 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence CCGCC (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 CCGCC, 13, CCGCC at 3999, CCGCC at 3090, CCGCC at 2727, CCGCC at 2724, CCGCC at 2392, CCGCC at 2231, CCGCC at 1809, CCGCC at 1752, CCGCC at 1250, CCGCC at 956, CCGCC at 856, CCGCC at 700, CCGCC at 427.
  2. negative strand, positive direction, looking for CCGCC, 4, CCGCC at 4291, CCGCC at 4238, CCGCC at 1757, CCGCC at 904.
  3. positive strand, negative direction, looking for CCGCC, 1, CCGCC at 1503.
  4. positive strand, positive direction, looking for CCGCC, 11, CCGCC at 4439, CCGCC at 4429, CCGCC at 3487, CCGCC at 2485, CCGCC at 1901, CCGCC at 1793, CCGCC at 1202, CCGCC at 1025, CCGCC at 406, CCGCC at 356, CCGCC at 353.
  5. complement, negative strand, negative direction, looking for GGCGG, 1, GGCGG at 1503.
  6. complement, negative strand, positive direction, looking for GGCGG, 11, GGCGG at 4439, GGCGG at 4429, GGCGG at 3487, GGCGG at 2485, GGCGG at 1901, GGCGG at 1793, GGCGG at 1202, GGCGG at 1025, GGCGG at 406, GGCGG at 356, GGCGG at 353.
  7. complement, positive strand, negative direction, looking for GGCGG, 13, GGCGG at 3999, GGCGG at 3090, GGCGG at 2727, GGCGG at 2724, GGCGG at 2392, GGCGG at 2231, GGCGG at 1809, GGCGG at 1752, GGCGG at 1251, GGCGG at 956, GGCGG at 856, GGCGG at 700, GGCGG at 427.
  8. complement, positive strand, positive direction, looking for GGCGG, 4, GGCGG at 4291, GGCGG at 4238, GGCGG at 1757, GGCGG at 904.

DRE (Smith) samplings

Copying the consensus of the DDRE: 5'-TTTCAAT-3' and putting the sequence in "⌘F" finds no locations for this sequence in any A1BG direction as can be found by the computer programs.

For the Basic programs testing consensus sequence 5'-TTTCAAT-3' (starting with SuccessablesDDRE.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 5'-TTTCAAT-3', 0.
  2. negative strand, positive direction, looking for 5'-TTTCAAT-3', 0.
  3. positive strand, negative direction, looking for 5'-TTTCAAT-3', 0.
  4. positive strand, positive direction, looking for 5'-TTTCAAT-3', 0.
  5. complement, negative strand, negative direction, looking for 5'-AAAGTTA-3', 0.
  6. complement, negative strand, positive direction, looking for 5'-AAAGTTA-3', 0.
  7. complement, positive strand, negative direction, looking for 5'-AAAGTTA-3', 0.
  8. complement, positive strand, positive direction, looking for 5'-AAAGTTA-3', 0.
  9. inverse complement, negative strand, negative direction, looking for 5'-ATTGAAA-3', 0.
  10. inverse complement, negative strand, positive direction, looking for 5'-ATTGAAA-3', 0.
  11. inverse complement, positive strand, negative direction, looking for 5'-ATTGAAA-3', 0.
  12. inverse complement, positive strand, positive direction, looking for 5'-ATTGAAA-3', 0.
  13. inverse negative strand, negative direction, looking for 5'-TAACTTT-3', 0.
  14. inverse negative strand, positive direction, looking for 5'-TAACTTT-3', 0.
  15. inverse positive strand, negative direction, looking for 5'-TAACTTT-3', 0.
  16. inverse positive strand, positive direction, looking for 5'-TAACTTT-3', 0.

Acknowledgements

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

See also

References

  1. ↑ Zhengjian Zhang and Joseph C. Reese (17 September 2004). "Redundant Mechanisms Are Used by Ssn6-Tup1 in Repressing Chromosomal Gene Transcription in Saccharomyces cerevisiae". The Journal of Biological Chemistry. 279 (38): 39240–39250. doi:10.1074/jbc.M407159200. PMID 15254041. Retrieved 4 September 2020.
  2. ↑ 2.0 2.1 Roberta A. Sumrada and Terrance G. Cooper (June 1987). "Ubiquitous upstream repression sequences control activation of the inducible arginase gene in yeast" (PDF). Proceedings of the National Academy of Sciences USA. 84: 3997–4001. doi:10.1073/pnas.84.12.3997. PMID 3295874. Retrieved 6 September 2020.
  3. ↑ Joshua J. Smith, Eric S. Cole, Daniel P. Romero (15 July 2004). "Transcriptional control of RAD51 expression in the ciliate Tetrahymena thermophila". Nucleic Acids Research. 32 (14): 4313–4321. doi:10.1093/nar/gkh771. PMID 15304567. Retrieved 4 September 2020.

External links

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