General regulatory factors

"General regulatory factors (GRFs), such as Reb1, Abf1, Rap1, Mcm1, and Cbf1, positionally organize yeast chromatin through interactions with a core consensus DNA sequence."^[1]

"Ribosome biogenesis in Saccharomyces cerevisiae involves a regulon of >200 genes (Ribi genes) coordinately regulated in response to nutrient availability and cellular growth rate. Two cis-acting elements called PAC and RRPE are known to mediate Ribi gene repression in response to nutritional downshift. [Most] Ribi gene promoters also contain binding sites for one or more General Regulatory Factors (GRFs), most frequently Abf1 and Reb1, and that these factors are enriched in vivo at Ribi promoters. 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. Such a response did not entail changes in Abf1 occupancy, but it was paralleled by a quick increase, followed by slow decrease, in Rpd3L histone deacetylase occupancy. [...] Abf1 site disruption also abolished Rpd3L complex recruitment in response to starvation. Extensive mutational analysis of the DBP7 promoter revealed a complex interplay of Tbf1 sites, PAC and RRPE in the transcriptional regulation of this Ribi gene. [...] GRFs [are] multifaceted players in Ribi gene regulation both during exponential growth and under repressive conditions."^[2]

Abfm regulatory factors

The general consensus sequence for Abf1 CGTNNNNN(A/G)(C/T)GA(C/T) occurs on both sides of A1BG but only in the distal promoters. Random datasets, even numbered assigned to the negative direction and odd numbered assigned to the positive direction yielded a sequence in the UTR, core promoter and distal promoter for the negative direction and a sequence in the distal promoter for the positive direction. The real consensus sequence yielded only three results: one in the negative direction and two in the positive, all in the distal promoters. The random sequences (four total) occurred in the UTR, proximal promoter and distal promoter for the negative direction and one in the distal promoter for the positive direction. While the differences between real and random are small (three vs. four), (all distal vs. UTR, proximal and two distal), they are likely significant as the random datasets (10) should have encompassed the real (2, each side of A1BG) but this did not occur.

Cbf1 regulatory factors

Consensus sequence TCACGTGA^[1] did not have any real or random results.

Mcm1 regulatory factors

Neither TT(A/T)CCNN(A/T)TNGG(A/T)AA nor TTNCCNNNTNNGGNAA produced any real or random results.

Rap1 regulatory factors

When the Rap1 motif was held constant to ACCCRNRCA^[1], no real results occurred. However, using the ten random datasets for testing ACCCRNRCA and its inverse complement yielded five consensus sequence results and four inverse complements. Two were in the UTR of A1BG from the negative direction. One was in the proximal promoter from the positive direction, and the remaining five were in the distal promoters.

The reduced consensus (A/G)(A/C)ACCC(A/G)N(A/G)C(A/C)(C/T)(A/C)^[1] had one result GAACCCACACCTC in the positive direction at 1807, less than half way from ZNF497. Of ten random datasets only one had a result: GCACCCGGGCATC at 1454. Also, for the inverse complement, there was only one TATGCCTGGGTTT at 1380. In both the real sequences and random sequences, each was in the distal promoter closer to the zinc finger than A1BG. The occurrence of one random result per ten datasets suggests that such a result is rarely random. While the real occurrence is likely active as a regulatory response.

The full consensus sequence C(A/C/G)(A/C/G)(A/G)(C/G/T)C(A/C/T)(A/G/T)(C/G/T)(A/G/T)(A/C/G)(A/C)(A/C/T)(A/C/T)^[1] gave four to six results in the UTR negative direction, one in the core promoter in the positive direction, two in the proximal promoter in the negative direction and one in the positive direction. In the distal promoter each direction had eight to nine results.

For the random data sets: UTR ranged from zero to four in the UTR, core promoter produced only zero to one, proximal promoter produced zero to one, and the distal promoter contained one to seven for either direction.

Comparing the two, the real UTR, proximal promoter, and distal promoter usually exceeded the random results. This suggests that some of the real results could just be due to random associations of nucleotides, but the rest are likely real.

Reb1 regulatory factors

Reb1 consensus sequences TTACCC(G/T) have three occurrences in A1BG: UTR at 3661 and two distal promoters at 3170 and 2912 in the positive direction all more than half way from either Zn finger.

Using the random datasets: there are three sequences in two datasets within the UTR: TTACCCG at 4135 and CGGGTAA at 3979, with AGGGTAA at 3112; the core promoters contained only TTACCCG at 4416 in the positive direction; the proximal promoters contained only TTACCCT at 4250 in the positive direction; and the distal promoters contained four to five sequences: five in the negative direction all more than half way to ZSCAN22 and four in the positive direction: one TTACCCG at 2965 more than halfway toward A1BG and the remaining three less than halfway.

The extended Reb1 consensus sequence ATTACCCGAA had no locations in either direction or in random datasets for either the extended consensus sequence or its inverse complement.

Tbf1 regulatory factors

The usual consensus sequence for Tbf1 ARCCCTAA^[2] 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.

References

↑ ^1.0 ^1.1 ^1.2 ^1.3 ^1.4 Matthew J. Rossi; William K.M. Lai; 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.
↑ ^2.0 ^2.1 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

{{Phosphate biochemistry}}

[Rossi-1] 1.0 ^1.1 ^1.2 ^1.3 ^1.4 Matthew J. Rossi; William K.M. Lai; 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.

[Bosio-2] 2.0 ^2.1 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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