CCCTC-binding factor gene transcriptions: Difference between revisions

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# inverse, positive strand, negative direction, looking for 5'-(C/T)(C/G)(A/G)-CGG-N(A/G)G-ANN-ACN-3', 0.
# inverse, positive strand, negative direction, looking for 5'-(C/T)(C/G)(A/G)-CGG-N(A/G)G-ANN-ACN-3', 0.
# inverse, positive strand, positive direction, looking for 5'-(C/T)(C/G)(A/G)-CGG-N(A/G)G-ANN-ACN-3', 0.
# inverse, positive strand, positive direction, looking for 5'-(C/T)(C/G)(A/G)-CGG-N(A/G)G-ANN-ACN-3', 0.
==CCCTC samplings==
CCCTC-Binding factor or CTCF was initially discovered as a negative regulator of the chicken [[c-myc]] gene. This protein was found to be binding to three regularly spaced repeats of the core sequence CCCTC and thus was named CCCTC binding factor.<ref name=Lobanenkov>{{cite journal | authors = Lobanenkov VV, Nicolas RH, Adler VV, Paterson H, Klenova EM, Polotskaja AV, Goodwin GH | title = A novel sequence-specific DNA binding protein which interacts with three regularly spaced direct repeats of the CCCTC-motif in the 5'-flanking sequence of the chicken c-myc gene | journal = Oncogene | volume = 5 | issue = 12 | pages = 1743–53 |date=December 1990 | pmid = 2284094 }}</ref>
For the Basic programs testing consensus sequence CCCTC (starting with SuccessablesCTCF.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 AAAAAAAA, 0.
# positive strand, negative direction, looking for AAAAAAAA, 0.
# negative strand, positive direction, looking for AAAAAAAA, 0.
# positive strand, positive direction, looking for AAAAAAAA, 0.
# inverse complement, negative strand, negative direction, looking for TTTTTTTT, 0.
# inverse complement, positive strand, negative direction, looking for TTTTTTTT, 0.
# inverse complement, negative strand, positive direction, looking for TTTTTTTT, 0.
# inverse complement, positive strand, positive direction, looking for TTTTTTTT, 0.
===AAA (4560-2846) UTRs===
===AAA negative direction (2846-2811) core promoters===
===AAA positive direction (4445-4265) core promoters===
===AAA negative direction (2811-2596) proximal promoters===
===AAA positive direction (4265-4050) proximal promoters===
===AAA negative direction (2596-1) distal promoters===
===AAA positive direction (4050-1) distal promoters===


==Acknowledgements==
==Acknowledgements==

Revision as of 18:08, 8 May 2023

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

Consensus sequences

"Experiments using chromatin immunoprecipitation exonuclease (ChIP-exo) uncovered a broad CTCF-binding motif that contains a 12–15 bp consensus sequence, 5′-NCA-NNA-G(G/A)N-GGC-(G/A)(C/G)(T/C)-3′ (Nakahashi et al., 2013, Rhee and Pugh, 2011) [...]."[1]

Hashimoto samplings

Copying the consensus of the CTCF: 5'-CACCAGG-3' and putting the sequence in "⌘F" finds no locations between ZSCAN22 and A1BG and CTCF: 5'-CACCAGGAGG-3' finds no locations between ZNF497 and A1BG as can be found by the computer programs.

For the Basic programs SuccessablesCFbox.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'-NCA-NNA-G(A/G)N-GGC-(A/G)(C/G)(C/T)-3'[1], 0.
  2. negative strand, positive direction, looking for 5'-NCA-NNA-G(A/G)N-GGC-(A/G)(C/G)(C/T)-3', 0.
  3. positive strand, negative direction, looking for 5'-NCA-NNA-G(A/G)N-GGC-(A/G)(C/G)(C/T)-3', 0.
  4. positive strand, positive direction, looking for 5'-NCA-NNA-G(A/G)N-GGC-(A/G)(C/G)(C/T)-3', 0.
  5. complement, negative strand, negative direction, looking for 5'-NGT-NNT-C(C/T)N-CCG-(C/T)(C/G)(A/G)-3', 0.
  6. complement, negative strand, positive direction, looking for 5'-NGT-NNT-C(C/T)N-CCG-(C/T)(C/G)(A/G)-3', 0.
  7. complement, positive strand, negative direction, looking for 5'-NGT-NNT-C(C/T)N-CCG-(C/T)(C/G)(A/G)-3', 0.
  8. complement, positive strand, positive direction, looking for 5'-NGT-NNT-C(C/T)N-CCG-(C/T)(C/G)(A/G)-3', 0.
  9. inverse complement, negative strand, negative direction, looking for 5'-(A/G)(C/G)(C/T)-GCC-N(C/T)C-TNN-TGN-3', 0.
  10. inverse complement, negative strand, positive direction, looking for 5'-(A/G)(C/G)(C/T)-GCC-N(C/T)C-TNN-TGN-3', 0.
  11. inverse complement, positive strand, negative direction, looking for 5'-(A/G)(C/G)(C/T)-GCC-N(C/T)C-TNN-TGN-3', 0.
  12. inverse complement, positive strand, positive direction, looking for 5'-(A/G)(C/G)(C/T)-GCC-N(C/T)C-TNN-TGN-3', 0.
  13. inverse, negative strand, negative direction, looking for 5'-(C/T)(C/G)(A/G)-CGG-N(A/G)G-ANN-ACN-3', 0.
  14. inverse, negative strand, positive direction, looking for 5'-(C/T)(C/G)(A/G)-CGG-N(A/G)G-ANN-ACN-3', 0.
  15. inverse, positive strand, negative direction, looking for 5'-(C/T)(C/G)(A/G)-CGG-N(A/G)G-ANN-ACN-3', 0.
  16. inverse, positive strand, positive direction, looking for 5'-(C/T)(C/G)(A/G)-CGG-N(A/G)G-ANN-ACN-3', 0.

CCCTC samplings

CCCTC-Binding factor or CTCF was initially discovered as a negative regulator of the chicken c-myc gene. This protein was found to be binding to three regularly spaced repeats of the core sequence CCCTC and thus was named CCCTC binding factor.[2]

For the Basic programs testing consensus sequence CCCTC (starting with SuccessablesCTCF.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 AAAAAAAA, 0.
  2. positive strand, negative direction, looking for AAAAAAAA, 0.
  3. negative strand, positive direction, looking for AAAAAAAA, 0.
  4. positive strand, positive direction, looking for AAAAAAAA, 0.
  5. inverse complement, negative strand, negative direction, looking for TTTTTTTT, 0.
  6. inverse complement, positive strand, negative direction, looking for TTTTTTTT, 0.
  7. inverse complement, negative strand, positive direction, looking for TTTTTTTT, 0.
  8. inverse complement, positive strand, positive direction, looking for TTTTTTTT, 0.

AAA (4560-2846) UTRs

AAA negative direction (2846-2811) core promoters

AAA positive direction (4445-4265) core promoters

AAA negative direction (2811-2596) proximal promoters

AAA positive direction (4265-4050) proximal promoters

AAA negative direction (2596-1) distal promoters

AAA positive direction (4050-1) distal promoters

Acknowledgements

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

See also

References

  1. ↑ 1.0 1.1 Hideharu Hashimoto, Dongxue Wang, John R. Horton, Xing Zhang, Victor G. Corces and Xiaodong Cheng (1 June 2017). "Structural Basis for the Versatile and Methylation-Dependent Binding of CTCF to DNA". Molecular Cell. 66 (5): 711–720.e3. doi:10.1016/j.molcel.2017.05.004. PMID 28529057. Retrieved 28 August 2020.
  2. ↑ Lobanenkov VV, Nicolas RH, Adler VV, Paterson H, Klenova EM, Polotskaja AV, Goodwin GH (December 1990). "A novel sequence-specific DNA binding protein which interacts with three regularly spaced direct repeats of the CCCTC-motif in the 5'-flanking sequence of the chicken c-myc gene". Oncogene. 5 (12): 1743–53. PMID 2284094.

External links

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