Tbf1 regulatory factor gene transcriptions

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

"Ribosome biogenesis in Saccharomyces cerevisiae involves a regulon of >200 genes (Ribi genes) coordinately regulated in response to nutrient availability and cellular growth rate. [...] Abf1/Reb1/Tbf1 promoter association was required for full Ribi gene expression in rich medium and for its modulation in response to glucose starvation, characterized by a rapid drop followed by slow recovery. [...] Extensive mutational analysis of the DBP7 promoter revealed a complex interplay of Tbf1 sites, PAC and RRPE [motifs] in the transcriptional regulation of this Ribi gene. [...] GRFs [are] multifaceted players in Ribi gene regulation both during exponential growth and under repressive conditions."^[1]

The "promoter regions of some genes involved in ribosome biogenesis are associated with transcription factors (TF) like Tbf1 and Abf1, known to bind large sets of promoters (1,18–21)."^[1]

The "vast majority of Ribi gene promoters contain, at positions typical of upstream activating sequences (UASs), binding sites for Abf1, Reb1 and, less frequently, Rap1 and Tbf1 proteins, collectively referred to as General Regulatory Factors (GRFs) because of their widespread presence as multipurpose DNA binding proteins in yeast (23,24). These TFs were found to associate with and to be required for full expression of target Ribi gene promoters under rich medium growth conditions. The transcriptional response to glucose starvation was also profoundly altered at Ribi genes unable to bind the cognate GRFs, and in the case of the DBP7 gene it was found to rely on the simultaneous presence of GRF, PAC and RRPE recognition elements."^[1]

Human genes

Gene expressions

The "majority of Ribi gene promoter region alignments clearly displayed well-conserved sequence blocks upstream of the RRPE that corresponded to motifs recognized by the GRFs Abf1 (98 Ribi promoters), Reb1 (78 Ribi promoters), Rap1 and Tbf1 (19 and 15 Ribi gene promoters, respectively) [...]."^[1]

"Tbf1-marked promoters tend to display multiple binding sites for this GRF, a previously noted general trend for Tbf1-bound non-snoRNA promoters (18). Notably, 31 Ribi gene promoters had binding sites for more than one GRF protein. In a few promoters, binding sites for three different GRFs were also observed (e.g. YPL126W, which displays two Tbf1 binding sites together with an Abf1 and a Reb1 site within a ∼60 bp region [...]. Noteworthy, of the 134 promoters with both RRPE and PAC, 107 (80%) also had a GRF binding motif. These observations suggest that Ribi gene transcription might be regulated through a complex interplay of positively and negatively acting cis elements."^[1]

Interactions

Consensus sequences

"The consensus sequences considered for the different elements reported are: PAC, GCGATGAGMT; RRPE, TGAAAAWTTTY; Abf1, RTCAYNNNN(N)ACGR; Reb1, RTTACCCK; Tbf1, ARCCCTAA; Rap1, WACAYCCRTACATY (M, A or C; W, A or T; R, A or G; Y, C or T; K, G or T; N, any nucleotide). These consensus sequences are based on the following references: PAC and RRPE (1); Abf1 (10,12,55); Reb1 (10,55); Tbf1 (10,12,18); Rap1 (56)."^[1]

Binding site for

"Rap1 and Tbf1 recognition motifs are found at more variable distances from the TSS, with a tendency towards more upstream placements with respect to Abf1 and Reb1. There is no significant orientation preference of the evolutionarily conserved Abf1-binding nor of the Reb1 binding motifs found in Ribi promoter regions. Rap1 and Tbf1 binding sites are also equally represented in the two possible orientations, in agreement with the notion that UAS function is generally orientation-independent (17)."^[1]

Complement copies

Inverse copies

Complement-inverse copies

Enhancer activity

Promoter occurrences

Considering "previously published genome-wide location data for Tbf1 (18), we could confirm that 9 of the 15 Ribi genes computationally identified as Tbf1 targets are indeed Tbf1-associated according to ChIP-seq analysis."^[1]

"The promoter of DBP7 contains three Tbf1 binding motifs within a region from ∼250 to ∼175 bp upstream of the ATG, followed by contiguous RRPE and PAC elements; the ARX1 promoter region has a similar organization, with two Tbf1-binding sites only. [Mutation] of both Tbf1 binding motifs in ARX1 promoter region resulted in loss of Tbf1 binding and a marked decrease in ARX1 expression. In the case of DBP7 [...], additive effects of Tbf1 site mutations were observed on both Tbf1 enrichment at the promoter region and gene expression, with the triple Tbf1 site mutant displaying DBP7 mRNA levels corresponding to ∼25% of the wt. It must be noted that considerable levels of residual transcription were observed for all Ribi gene promoter mutants, ranging from ∼20% to ∼60% of wt indicating that Abf1, Reb1 and Tbf1 are not absolutely required, yet contribute to full expression of Ribi genes, at least in rich medium, as we previously observed for Tbf1-dependent expression of yeast snoRNA genes (18) and Abf1-dependent expression of RP gene promoters (46)."^[1]

Hypotheses

A1BG has no regulatory elements in either promoter.
A1BG is not transcribed by a regulatory element.
No regulatory element participates in the transcription of A1BG.

Tbf1 samplings

Copying a responsive elements consensus sequence A(A/G)CCCTAA and putting the sequence in "⌘F" finds none between ZNF497 and A1BG or none between ZSCAN22 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence A(A/G)CCCTAA (starting with SuccessablesTbf1.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 A(A/G)CCCTAA, 0.
positive strand, negative direction, looking for A(A/G)CCCTAA, 0.
positive strand, positive direction, looking for A(A/G)CCCTAA, 1, AACCCTAA at 2545.
negative strand, positive direction, looking for A(A/G)CCCTAA, 0.
inverse complement, negative strand, negative direction, looking for TTAGGG(C/T)T, 1, TTAGGGTT at 3978.
inverse complement, positive strand, negative direction, looking for TTAGGG(C/T)T, 0.
inverse complement, positive strand, positive direction, looking for TTAGGG(C/T)T, 0.
inverse complement, negative strand, positive direction, looking for TTAGGG(C/T)T, 1, TTAGGGCT at 2768.

Tbf1 (4560-2846) UTRs

Negative strand, negative direction: TTAGGGTT at 3978.

Tbf1 positive direction (4050-1) distal promoters

Negative strand, positive direction: TTAGGGCT at 2768.
Positive strand, positive direction: AACCCTAA at 2545.

Random dataset samplings

Tbf1r0: 0.
Tbf1r1: 0.
Tbf1r2: 0.
Tbf1r3: 0.
Tbf1r4: 0.
Tbf1r5: 0.
Tbf1r6: 0.
Tbf1r7: 0.
Tbf1r8: 0.
Tbf1r9: 0.
Tbf1r0ci: 0.
Tbf1r1ci: 2, TTAGGGCT at 3616, TTAGGGTT at 198.
Tbf1r2ci: 0.
Tbf1r3ci: 0.
Tbf1r4ci: 0.
Tbf1r5ci: 0.
Tbf1r6ci: 0.
Tbf1r7ci: 0.
Tbf1r8ci: 0.
Tbf1r9ci: 0.

Tbf1r alternate (odds) (4560-2846) UTRs

Tbf1r1ci: TTAGGGCT at 3616.

Tbf1r alternate negative direction (odds) (2596-1) distal promoters

Tbf1r1ci: TTAGGGTT at 198.

Tbf1r arbitrary positive direction (odds) (4050-1) distal promoters

Tbf1r1ci: TTAGGGCT at 3616, TTAGGGTT at 198.

Response element analysis and results

"The consensus sequences considered for the different elements reported are: [...] Tbf1, ARCCCTAA [...] ([...] R, A or G; [...]). These consensus sequences are based on the following references: PAC and RRPE (1); Abf1 (10,12,55); Reb1 (10,55); Tbf1 (10,12,18); Rap1 (56)."^[1]

Reals or randoms	Promoters	direction	Numbers	Strands	Occurrences	Averages (± 0.1)
Reals	UTR	negative	1	2	0.5	0.5 ± 0.5 (--1,+-0)
Randoms	UTR	arbitrary negative	0	10	0	0.05
Randoms	UTR	alternate negative	1	10	0.1	0.05
Reals	Core	negative	0	2	0	0
Randoms	Core	arbitrary negative	0	10	0	0
Randoms	Core	alternate negative	0	10	0	0
Reals	Core	positive	0	2	0	0
Randoms	Core	arbitrary positive	0	10	0	0
Randoms	Core	alternate positive	0	10	0	0
Reals	Proximal	negative	0	2	0	0
Randoms	Proximal	arbitrary negative	0	10	0	0
Randoms	Proximal	alternate negative	0	10	0	0
Reals	Proximal	positive	0	2	0	0
Randoms	Proximal	arbitrary positive	0	10	0	0
Randoms	Proximal	alternate positive	0	10	0	0
Reals	Distal	negative	0	2	0	0
Randoms	Distal	arbitrary negative	0	10	0	0.05
Randoms	Distal	alternate negative	1	10	0.1	0.05
Reals	Distal	positive	2	2	1	1 ± 0 (-+1,++1)
Randoms	Distal	arbitrary positive	2	10	0.2	0.1
Randoms	Distal	alternate positive	0	10	0	0.1

Comparison:

The occurrences of real Tbf1s are greater than the randoms. This suggests that the real Tbf1s are likely active or activable.

Discussion

The usual consensus sequence for Tbf1 ARCCCTAA^[1] occurs three times around A1BG: once in the negative direction within the UTR: the inverse complement TTAGGGTT at 3978 and twice in the positive direction: negative strand TTAGGGCT at 2768 and positive strand AACCCTAA at 2545. Both are closer to A1BG than either zinc finger.

In the random datasets, only the inverse complements occur in one data set: TTAGGGCT at 3616, TTAGGGTT at 198 representing the positive direction, distal promoter. The second is less than halfway from ZNF497.

Acknowledgements

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

References

↑ ^1.00 ^1.01 ^1.02 ^1.03 ^1.04 ^1.05 ^1.06 ^1.07 ^1.08 ^1.09 ^1.10 Maria Cristina Bosio, Beatrice Fermi, Gloria Spagnoli, Elisabetta Levati, Ludmilla Rubbi, Roberto Ferrari, Matteo Pellegrini, Giorgio Dieci (5 May 2017). "Abf1 and other general regulatory factors control ribosome biogenesis gene expression in budding yeast". Nucleic Acids Research. 45 (8): 4493–4506. doi:10.1093/nar/gkx058. Retrieved 8 June 2021.

External links

[Bosio-1] 1.00 ^1.01 ^1.02 ^1.03 ^1.04 ^1.05 ^1.06 ^1.07 ^1.08 ^1.09 ^1.10 Maria Cristina Bosio, Beatrice Fermi, Gloria Spagnoli, Elisabetta Levati, Ludmilla Rubbi, Roberto Ferrari, Matteo Pellegrini, Giorgio Dieci (5 May 2017). "Abf1 and other general regulatory factors control ribosome biogenesis gene expression in budding yeast". Nucleic Acids Research. 45 (8): 4493–4506. doi:10.1093/nar/gkx058. Retrieved 8 June 2021.

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