CadC binding domain gene transcriptions

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

"Dimerization of [cadaverine C-terminal] CadC enables the binding of two DBDs to the two Cad1 consensus target sites."[1]

Consensus sequences

Main article: Consensus sequence gene transcriptions

"Altogether, the specific contacts observed suggest a consensus binding motif of 5′-T-T-A-x-x-x-x-T-3′."[1]

"The DNA consensus sequence 5′-T-T-A-x-x-x-x-T-3′ is present once in the quasi-palindromic Cad1 17-mer DNA, consistent with the formation of a 1:1 complex. However, a second consensus facilitates the formation of the 2:1 complex of CadC with Cad1 41-mer DNA as evidenced by the CadC model with the minimal Cad1 26-mer DNA that spans the two AT-rich regions, i.e. consensus sites."[1]

Hypotheses

Main article: Hypotheses
  1. A1BG has no CadC binding domain in either promoter.
  2. A1BG is not transcribed by a CadC binding domain.
  3. CadC binding domain does not participate in the transcription of A1BG.

Samplings

Main article: Model samplings

Copying the cadaverine C-terminal binding domain consensus sequence 5'-T-T-A-x-x-x-x-T-3' and putting the sequence in "⌘F" finds one location between ZNF497 and A1BG or four locations between ZSCAN22 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence 5'-TTANNNNT-3' (starting with SuccessablesCadC.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'-TTANNNNT-3', 24, 5'-TTATTAAT-3' at 4227, 5'-TTATTATT-3' at 4224, '-TTATCTTT-3' at 4081, 5'-TTATTTAT-3' at 4074, 5'-TTAGGGTT-3' at 3978, 5'-TTACCCTT-3' at 3662, 5'-TTATGACT-3' at 3542, 5'-TTAACTAT-3' at 3360, 5'-TTATTTGT-3' at 3337, 5'-TTACCGAT-3' at 3007, 5'-TTACGAAT-3' at 2935, 5'-TTATATAT-3' at 2872, 5'-TTATATGT-3' at 2641, 5'-TTATCATT-3' at 2501, 5'-TTATGTTT-3' at 2306, 5'-TTATGTTT-3' at 1879, 5'-TTATCTCT-3' at 1712, 5'-TTACGGTT-3' at 1636, 5'-TTATGTCT-3' at 1567, 5'-TTAGTCCT-3' at 985, 5'-TTATGTTT-3' at 770, 5'-TTATGTTT-3' at 636, 5'-TTATGCTT-3' at 493, 5'-TTAAGATT-3' at 9, and complements.
  2. negative strand, positive direction, looking for 5'-TTANNNNT-3', 9, 5'-TTATAATT-3' at 4169, 5'-TTATTGAT-3' at 4162, 5'-TTAATCAT-3' at 4148, 5'-TTATTAAT-3' at 4145, 5'-TTATCACT-3' at 4126, 5'-TTATGACT-3' at 3029, 5'-TTAGGGCT-3' at 2768, 5'-TTAAAATT-3' at 2447, 5'-TTAAACAT-3' at 2139.
  3. positive strand, negative direction, looking for 5'-TTANNNNT-3', 6, 5'-TTATTAAT-3' at 4540, 5'-TTAAAAAT-3' at 3355, 5'-TTAGATAT-3' at 2982, 5'-TTATCTTT-3' at 1733, 5'-TTAAGTGT-3' at 322, 5'-TTAAGAAT-3' at 196.
  4. positive strand, positive direction, looking for 5'-TTANNNNT-3', 5, 5'-TTACTCCT-3' at 4097, 5'-TTATACCT-3' at 3163, 5'-TTATCTTT-3' at 2629, 5'-TTAAAATT-3' at 2443, 5'-TTACACTT-3' at 231.
  5. complement, negative strand, negative direction, looking for 5'-AATNNNNA-3', 6, 5'-AATAATTA-3' at 4540, 5'-AATTTTTA-3' at 3355, 5'-AATCTATA-3' at 2982, 5'-AATAGAAA-3' at 1733, 5'-AATTCACA-3' at 322, 5'-AATTCTTA-3' at 196.
  6. complement, negative strand, positive direction, looking for 5'-AATNNNNA-3', 5, 5'-AATGAGGA-3' at 4097, 5'-AATATGGA-3' at 3163, 5'-AATAGAAA-3' at 2629, 5'-AATTTTAA-3' at 2443, 5'-AATGTGAA-3' at 231.
  7. complement, positive strand, negative direction, looking for 5'-AATNNNNA-3', 24, 5'-AATAATTA-3' at 4227, 5'-AATAATAA-3' at 4224, 5'-AATAGAAA-3' at 4081, 5'-AATAAATA-3' at 4074, 5'-AATCCCAA-3' at 3978, 5'-AATGGGAA-3' at 3662, 5'-AATACTGA-3' at 3542, 5'-AATTGATA-3' at 3360, 5'-AATAAACA-3' at 3337, 5'-AATGGCTA-3' at 3007, 5'-AATGCTTA-3' at 2935, 5'-AATATATA-3' at 2872, 5'-AATATACA-3' at 2641, 5'-AATAGTAA-3' at 2501, 5'-AATACAAA-3' at 2306, 5'-AATACAAA-3' at 1879, 5'-AATAGAGA-3' at 1712, 5'-AATGCCAA-3' at 1636, 5'-AATACAGA-3' at 1567, 5'-AATCAGGA-3' at 985, 5'-AATACAAA-3' at 770, 5'-AATACAAA-3' at 636, 5'-AATACGAA-3' at 493, 5'-AATTCTAA-3' at 9.
  8. complement, positive strand, positive direction, looking for 5'-AATNNNNA-3', 9, 5'-AATATTAA-3' at 4169, 5'-AATAACTA-3' at 4162, 5'-AATTAGTA-3' at 4148, 5'-AATAATTA-3' at 4145, 5'-AATAGTGA-3' at 4126, 5'-AATACTGA-3' at 3029, 5'-AATCCCGA-3' at 2768, 5'-AATTTTAA-3' at 2447, 5'-AATTTGTA-3' at 2139.
  9. inverse complement, negative strand, negative direction, looking for 5'-ANNNNTAA-3', 10, 5'-ATAATTAA-3' at 4541, 5'-AAGTGTAA-3' at 4533, 5'-ATTATTAA-3' at 4226, 5'-ATCTATAA-3' at 3467, 5'-ATTTTTAA-3' at 3356, 5'-ATTTTTAA-3' at 3174, 5'-ATGGATAA-3' at 2997, 5'-ATCTCTAA-3' at 1714, 5'-ACCCTTAA-3' at 1694, 5'-ATATATAA-3' at 1601.
  10. inverse complement, negative strand, positive direction, looking for 5'-ANNNNTAA-3', 2, 5'-AATTTTAA-3' at 2443, 5'-ACAGTTAA-3' at 2135.
  11. inverse complement, positive strand, negative direction, looking for 5'-ANNNNTAA-3', 28, 5'-AATAATAA-3' at 4224, 5'-AAAAATAA-3' at 4221, 5'-ATAAATAA-3' at 4075, 5'-AAAAATAA-3' at 4071, 5'-ACCTGTAA-3' at 3972, 5'-AGGGATAA-3' at 3656, 5'-ATTACTAA-3' at 3472, 5'-ATTGATAA-3' at 3361, 5'-ACAAATAA-3' at 3334, 5'-AAACATAA-3' at 3169, 5'-AAAACTAA-3' at 3030, 5'-ATGGCTAA-3' at 3008, 5'-ATGCTTAA-3' at 2936, 5'-ATATATAA-3' at 2873, 5'-AATAGTAA-3' at 2501, 5'-ATCTTTAA-3' at 1735, 5'-AAACCTAA-3' at 1591, 5'-ACACTTAA-3' at 1546, 5'-ACCTGTAA-3' at 1133, 5'-ACCTGTAA-3' at 803, 5'-ACACGTAA-3' at 533, 5'-ACCTGTAA-3' at 396, 5'-AGTGCTAA-3' at 337, 5'-AACCTTAA-3' at 318, 5'-AGATGTAA-3' at 247, 5'-AGGTATAA-3' at 181, 5'-ACACCTAA-3' at 64, 5'-AATTCTAA-3' at 9.
  12. inverse complement, positive strand, positive direction, looking for 5'-ANNNNTAA-3', 10, 5'-AATATTAA-3' at 4169, 5'-ATAACTAA-3' at 4163, 5'-ACTAATAA-3' at 4159, 5'-AGAACTAA-3' at 4133, 5'-ATCCATAA-3' at 2643, 5'-AACCCTAA-3' at 2545, 5'-AATTTTAA-3' at 2447, 5'-ACAAATAA-3' at 2347, 5'-ACCGATAA-3' at 1976, 5'-AAACATAA-3' at 115.
  13. inverse negative strand, negative direction, looking for 5'-TNNNNATT-3', 28, 5'-TTATTATT-3' at 4224, 5'-TTTTTATT-3' at 4221, 5'-TATTTATT-3' at 4075, 5'-TTTTTATT-3' at 4071, 5'-TGGACATT-3' at 3972, 5'-TCCCTATT-3' at 3656, 5'-TAATGATT-3' at 3472, 5'-TAACTATT-3' at 3361, 5'-TGTTTATT-3' at 3334, 5'-TTTGTATT-3' at 3169, 5'-TTTTGATT-3' at 3030, 5'-TACCGATT-3' at 3008, 5'-TACGAATT-3' at 2936, 5'-TATATATT-3' at 2873, 5'-TTATCATT-3' at 2501, 5'-TAGAAATT-3' at 1735, 5'-TTTGGATT-3' at 1591, 5'-TGTGAATT-3' at 1546, 5'-TGGACATT-3' at 1133, 5'-TGGACATT-3' at 803, 5'-TGTGCATT-3' at 533, 5'-TGGACATT-3' at 396, 5'-TCACGATT-3' at 337, 5'-TTGGAATT-3' at 318, 5'-TCTACATT-3' at 247, 5'-TCCATATT-3' at 181, 5'-TGTGGATT-3' at 64, 5'-TTAAGATT-3' at 9.
  14. inverse negative strand, positive direction, looking for 5'-TNNNNATT-3', 10, 5'-TTATAATT-3' at 4169, 5'-TATTGATT-3' at 4163, 5'-TGATTATT-3' at 4159, 5'-TCTTGATT-3' at 4133, 5'-TAGGTATT-3' at 2643, 5'-TTGGGATT-3' at 2545, 5'-TTAAAATT-3' at 2447, 5'-TGTTTATT-3' at 2347, 5'-TGGCTATT-3' at 1976, 5'-TTTGTATT-3' at 115.
  15. inverse positive strand, negative direction, looking for 5'-TNNNNATT-3', 10, 5'-TATTAATT-3' at 4541, 5'-TTCACATT-3' at 4533, 5'-TAATAATT-3' at 4226, 5'-TAGATATT-3' at 3467, 5'-TAAAAATT-3' at 3356, 5'-TAAAAATT-3' at 3174, 5'-TACCTATT-3' at 2997, 5'-TAGAGATT-3' at 1714, 5'-TGGGAATT-3' at 1694, 5'-TATATATT-3' at 1601.
  16. inverse positive strand, positive direction, looking for 5'-TNNNNATT-3', 2, 5'-TTAAAATT-3' at 2443, 5'-TGTCAATT-3' at 2135.

CadC UTRs

Negative strand, negative direction: ATAATTAA at 4541, AAGTGTAA at 4533, TTATTAAT at 4227, ATTATTAA at 4226, TTATTATT at 4224, TTTTTATT at 4221, TTATCTTT-3' at 4081, TATTTATT at 4075, TTATTTAT at 4074, TTTTTATT at 4071, TTAGGGTT at 3978, TGGACATT at 3972, TTACCCTT at 3662, TCCCTATT at 3656, TTATGACT at 3542, TAATGATT at 3472, ATCTATAA at 3467, TAACTATT at 3361, TTAACTAT at 3360, ATTTTTAA at 3356, TTATTTGT at 3337, TGTTTATT at 3334, ATTTTTAA at 3174, TTTGTATT at 3169, TTTTGATT at 3030, TACCGATT at 3008, TTACCGAT at 3007, ATGGATAA at 2997, TACGAATT at 2936, TTACGAAT at 2935, TATATATT at 2873, TTATATAT at 2872.

Positive strand, negative direction: TTATTAAT at 4540, TTAAAAAT at 3355, TTAGATAT at 2982.

CadC proximal promoters

Main article: Proximal promoter gene transcriptions

Negative strand, negative direction: TTATATGT-3' at 2641.

Negative strand, positive direction: 5'-TTATAATT-3' at 4169, 5'-TATTGATT-3' at 4163, 5'-TTATTGAT-3' at 4162, 5'-TGATTATT-3' at 4159, 5'-TTAATCAT-3' at 4148, 5'-TTATTAAT-3' at 4145, 5'-TCTTGATT-3' at 4133, 5'-TTATCACT-3' at 4126, and complements.

Positive strand, positive direction: 5'-TTACTCCT-3' at 4097, and complement.

CadC distal promoters

Main article: Distal promoter gene transcriptions

Negative strand, negative direction: TTATCATT at 2501, TTATGTTT at 2306, TTATGTTT at 1879, TAGAAATT at 1735, ATCTCTAA at 1714, TTATCTCT at 1712, ACCCTTAA at 1694, TTACGGTT at 1636, ATATATAA at 1601, TTTGGATT at 1591, TTATGTCT at 1567, TGTGAATT at 1546, TGGACATT at 1133, TTAGTCCT at 985, TGGACATT at 803, TTATGTTT at 770, TTATGTTT at 636, TGTGCATT at 533, TTATGCTT at 493, TGGACATT at 396, TCACGATT at 337, TTGGAATT at 318, TCTACATT at 247, TCCATATT at 181, TGTGGATT at 64, TTAAGATT at 9.

Positive strand, negative direction: TTATCTTT at 1733, TTAAGTGT at 322, TTAAGAAT at 196.

Negative strand, positive direction: TTATGACT at 3029, TTAGGGCT at 2768, TAGGTATT at 2643, TTGGGATT at 2545, TTAAAATT at 2447, AATTTTAA at 2443, TGTTTATT at 2347, TTAAACAT at 2139, ACAGTTAA at 2135, TGGCTATT at 1976, TTTGTATT at 115.

Positive strand, positive direction: TTATACCT at 3163, TTATCTTT at 2629, TTACACTT at 231.

Acknowledgements

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

See also

References

  1. ↑ 1.0 1.1 1.2 Andreas Schlundt, Sophie Buchner, Robert Janowski, Thomas Heydenreich, Ralf Heermann, Jürgen Lassak, Arie Geerlof, Ralf Stehle, Dierk Niessing, Kirsten Jung & Michael Sattler (21 April 2017). "Structure-function analysis of the DNA-binding domain of a transmembrane transcriptional activator". Scientific Reports. 7: 1051. doi:10.1038/s41598-017-01031-9. PMID 28432336. Retrieved 28 August 2020.

External links

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