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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gene transcriptions Hsf1p gene transcriptions HY box gene transcriptions Hybrid C, A boxes Hybrid C, G boxes Hybrid C, T boxes Hypoxia-inducible factor gene transcriptions Hypoxia response elements I box gene transcriptions Immunoglobulin like domain containing family Initiator element gene transcriptions Initiator-like element gene transcriptions Inositol/choline-responsive elements Interaction gene transcriptions Interferon regulatory factors Inverse copy gene transcriptions Jasmonic acid-responsive element gene transcriptions K-boxes Kozak sequence gene transcriptions Kruppel-associated box gene transcriptions Krüppel-like factor gene transcriptions L box gene transcriptions Leu3 gene transcriptions M35 box gene transcriptions MADS box gene transcriptions Maf recognition element gene transcriptions M box gene transcriptions Mcm1 regulatory factor gene transcriptions Met3 gene transcriptions Met31p box gene transcriptions Metal responsive element gene transcriptions Middle 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transcriptions Shoot specific element gene transcriptions Sip4p gene transcriptions Smp1p gene transcriptions Sp1 gene transcriptions Spaceflight gene expressions Specificity protein gene transcriptions STAT gene transcriptions Ste12p gene transcriptions Sterol response element gene transcriptions Sucrose box gene transcriptions Synaptic Activity-Responsive Elements TACTAAC box gene transcriptions TAGteam gene transcriptions Tapetum box gene transcriptions TATA binding protein associated factor gene transcriptions TATA binding protein gene transcriptions TATA box actin/cytoskeleton/contractile family TATA box albumin family TATA box aldolase family TATA box alkaline phosphatase family TATA box annexin family TATA box cytochrome superfamily TATA box gene transcriptions TATA box heat shock family TATA box histone family TATA box human genes TATA box keratin family TATA box lipase family TATA box peptidase family TATA box platelet-derived growth factor family TATA box selenium-binding family TATA box serine protease family TATA box serpin superfamily TATA box transforming growth factor superfamily TATA box trefoil family TATA box tumor necrosis factor superfamily TATA box zinc metalloenzyme family TAT box gene transcriptions TATC box gene transcriptions Tbf1 regulatory factor gene transcriptions T box gene transcriptions TCCACCATA element gene transcriptions TC element gene transcriptions TCT gene transcriptions TEA consensus sequence gene transcriptions Tec1p gene transcriptions Telomeric repeat DNA-binding factor gene transcriptions Tetradecanoylphorbol-13-acetate response element gene transcriptions TGF-β control elements (TCEs) TGF-β inhibitory elements (TIEs) Thyroid hormone response element gene transcriptions Transcriptional regulation Transcription bubble gene transcriptions Transcription factor gene transcriptions Transcription factor 3 gene transcriptions Transcription factory gene transcriptions Transcription start site gene transcriptions Translational 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