Cbf1 regulatory factor gene transcriptions

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

"Cbf1 is a GRF that binds the palindromic E-box motif (CACGTG) and utilizes DNA shape to discriminate between potential binding sites (Gordan et al. 2013). [...] Like the other GRFs, almost all (88% of 113) in vivo Cbf1-bound promoter sites were also detected in vitro [...]. There were also a substantial number of low occupancy “in vitro-only sites,” typically in ORFs [...]."^[1]

Human genes

Consensus sequences

"Previous studies have shown that Cbf1 prefers to bind E-boxes with a “T” at the 5′ end of the E-box (Zhou and O'Shea 2011) [TCACGTG]. This manifests as a specific DNA shape flanking both sides of the palindromic core motif (Gordan et al. 2013). Our PB-exo experiments confirmed these preferences for Cbf1 in DNA sequence [...] and DNA shape readout [...]. [...] While the discriminatory DNA shape (and DNA sequence) information at one end of the motif is sufficient to support binding, at the strongly bound Cbf1 motifs it is enriched at both ends ([...] with a “T” on the 5′ and “A” on the 3′ end)."^[1]

Likely consensus sequences: (TCACGTGA).^[1]

Rossi samplings

Copying the consensus Cbf1: 3'-TCACGTGA-5' and putting the sequence in "⌘F" finds no locations or zero for these sequences respectively between ZSCAN22 or ZNF497 and A1BG as can be found by the computer programs.

For the Basic programs (starting with SuccessablesCbf.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 looking for, and found:

negative strand, negative direction, is SuccessablesCbf--.bas, looking for 5'-TCACGTGA-3', 0.
negative strand, positive direction is SuccessablesCbf-+.bas, looking for 5'-TCACGTGA-3', 0.
positive strand, negative direction is SuccessablesCbf+-.bas, looking for 5'-TCACGTGA-3', 0.
positive strand, positive direction is SuccessablesCbf++.bas, looking for 5'-TCACGTGA-3', 0.
complement inverse, negative strand, negative direction is SuccessablesCbfci--.bas, looking for TCACGTGA, 0.
complement inverse, negative strand, positive direction is SuccessablesCbfci-+.bas, looking for TCACGTGA, 0.
complement inverse, positive strand, negative direction is SuccessablesCbfci+-.bas, looking for TCACGTGA, 0.
complement inverse, positive strand, positive direction is SuccessablesCbfci++.bas, looking for TCACGTGA, 0.

Rossi random dataset samplings

Cbf1Rr0: 0.
Cbf1Rr1: 0.
Cbf1Rr2: 0.
Cbf1Rr3: 0.
Cbf1Rr4: 0.
Cbf1Rr5: 0.
Cbf1Rr6: 0.
Cbf1Rr7: 0.
Cbf1Rr8: 0.
Cbf1Rr9: 0.

References

↑ ^1.0 ^1.1 ^1.2 Matthew J. Rossi, William K.M. Lai and B. Franklin Pugh (21 March 2018). "Genome-wide determinants of sequence-specific DNA binding of general regulatory factors". Genome Research. 28: 497–508. doi:10.1101/gr.229518.117. PMID 29563167. Retrieved 31 August 2020.

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