The ABF1 factor is the transcriptional activator of the L2 ribosomal protein genes in Saccharomyces cerevisiae.

Seta, Flavio Della; Ciafrè, Silvia Anna; Marck, Christian; Santoro, Bina; Presutti, Carlo; Sentenac, André; Bozzoni, Irene

doi:10.1128/mcb.10.5.2437

Cited by 100 publications

(11 citation statements)

References 26 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Abf1 was assigned to the first split and was determined to control genes that were downregulated early on. This agrees with previous studies that implicated Abf1 in being involved in regulating the ribosome (Della Seta et al , 1990; Planta 1997). Two G1 cell‐cycle activators, Swi4 and Mbp1, now appear on a split starting at the 2‐h point on the recovery path.…”

Section: Resultssupporting

confidence: 94%

Reconstructing dynamic regulatory maps

Ernst

Vainas

Harbison

et al. 2007

Molecular Systems Biology

186

184

View full text Add to dashboard Cite

Even simple organisms have the ability to respond to internal and external stimuli. This response is carried out by a dynamic network of protein-DNA interactions that allows the specific regulation of genes needed for the response. We have developed a novel computational method that uses an input-output hidden Markov model to model these regulatory networks while taking into account their dynamic nature. Our method works by identifying bifurcation points, places in the time series where the expression of a subset of genes diverges from the rest of the genes. These points are annotated with the transcription factors regulating these transitions resulting in a unified temporal map. Applying our method to study yeast response to stress, we derive dynamic models that are able to recover many of the known aspects of these responses. Predictions made by our method have been experimentally validated leading to new roles for Ino4 and Gcn4 in controlling yeast response to stress. The temporal cascade of factors reveals common pathways and highlights differences between master and secondary factors in the utilization of network motifs and in condition-specific regulation.

show abstract

Section: Resultssupporting

confidence: 94%

Reconstructing dynamic regulatory maps

Ernst

Vainas

Harbison

et al. 2007

Molecular Systems Biology

186

184

View full text Add to dashboard Cite

show abstract

“…Northern analysis showed that PRO3 mRNA levels decreased considerably after 1 h at 37°C in the ts mutants both in the background of full-length and the C-terminal deletion of Abf1, but not in the corresponding wild-type strains (Figure 5B). In contrast, neither QCR8 nor TCM1/RPL3 , both of which depend on Abf1 binding sites for transcription (39,40), showed significantly decreased transcript levels at 37°C in either abf1-1 mutant, consistent with previous work (10), nor in the abf1(1–592) ts mutant (Figure 5B). Similar results were also seen with SPT15 and RPS28A (data not shown), both of which rely on Abf1 binding sites for their expression [(10) and Figure 3B].…”

Section: Resultssupporting

confidence: 91%

“…Fewer promoters that are likely to bind Rap1 but that are not affected by loss of Rap1 binding were identified than for Abf1, and none have thus far been verified by mutagenesis of Rap1 binding sites, as has been done for Abf1 (37–40). Promoters known to depend on Rap1 binding sites, such as HIS4 and many RP gene promoters (3,28) show decreased transcription in our microarray experiments, suggesting that at least most promoters that depend on Rap1 binding sites for full expression also require continued Rap1 binding.…”

Section: Discussionmentioning

confidence: 99%

“…We have also identified 80 promoters that are likely to bind Abf1 but are unaffected by loss of binding, and 31 such promoters for Rap1. At least some, and perhaps many, of the promoters that bind Abf1 but whose transcription is unaffected by loss of binding nonetheless depend on an Abf1 binding site (37–40). The mechanism by which Abf1 ‘marks’ such promoters remains enigmatic, but the phenomenon is reminiscent of regulation of many of the genes responsible for pattern formation in Drosophila , for which repressed or active states are maintained by PcG or Trx complexes even after the initial transcriptional repressors or activators have dissipated (44).…”

Section: Discussionmentioning

confidence: 99%

See 1 more Smart Citation

Genome-wide analysis of transcriptional dependence and probable target sites for Abf1 and Rap1 in Saccharomyces cerevisiae

Yarragudi

Parfrey

Morse

2006

Nucleic Acids Research

111

107

View full text Add to dashboard Cite

Abf1 and Rap1 are general regulatory factors (GRFs) that contribute to transcriptional activation of a large number of genes, as well as to replication, silencing and telomere structure in yeast. In spite of their widespread roles in transcription, the scope of their functional targets genome-wide has not been previously determined. Here, we use microarrays to examine the contribution of these essential GRFs to transcription genome-wide, by using ts mutants that dissociate from their binding sites at 37°C. We then combine this data with published ChIP-chip studies and motif analysis to identify probable direct targets for Abf1 and Rap1. We also identify a substantial number of genes likely to bind Rap1 or Abf1, but not affected by loss of GRF binding. Interestingly, the results strongly suggest that Rap1 can contribute to gene activation from farther upstream than can Abf1. Also, consistent with previous work, more genes that bind Abf1 are unaffected by loss of binding than those that bind Rap1. Finally, we show for several such genes that the Abf1 C-terminal region, which contains the putative activation domain, is not needed to confer this peculiar ‘memory effect’ that allows continued transcription after loss of Abf1 binding.

show abstract

“…Nuclear import not only plays a pivotal role in ensuring the function of nuclear proteins at their desired subcellular location, but also provides an important mechanism by which the activities of these proteins are regulated in response to changes in physiological conditions. Given the constitutive presence of Abf1p at ARS1 throughout the cell cycle (35), as well as its relatively high abundance (10,36), CS1 may simply function to sustain a constitutive presence of the protein in the nucleus. However, it remains possible that under certain conditions the nuclear function of Abf1p may be modulated through masking the NLS activity of CS1.…”

Section: Discussionmentioning

confidence: 99%

Functional and Physical Interactions between Autonomously Replicating Sequence‐Binding Factor 1 and the Nuclear Transport Machinery

Loc’h¹,

Mosammaparast²,

Miyake³

et al. 2004

Traffic

View full text Add to dashboard Cite

Autonomously replicating sequence-binding factor 1 (Abf1p) is a site-specific DNA binding protein in Saccharomyces cerevisiae that functions to regulate multiple nuclear events including DNA replication, transcriptional activation, and gene silencing. Previous work indicates that the multiple functions of Abf1p are conferred by the carboxy-terminus of the protein, which can be further dissected into two important clusters of amino acid residues (CS1 and CS2). Here we present genetic and cell biological evidence for a critical role of CS1 in proper nuclear localization of Abf1p. Mutations in CS1 cause severe defects in cell growth, nuclear translocation, and Abf1p-mediated gene regulation, which can be rescued by a heterologous nuclear localization sequence (NLS). In addition, the CS1-domain can mediate the import of a CS1-GFP fusion protein. Importantly, the CS1-mediated nuclear import depends on the Ran guanine nucleotide exchange factor Prp20p. Interestingly, a single amino acid change in CS1 (K625I) also causes the protein to be exported out of the nucleus via the Crm1p-dependent pathway. The temperature-sensitive growth phenotype of this particular mutant can be overcome by overexpression of Kap121p/Pse1p, a well-established nuclear transport receptor. Biochemical studies indicate that Pse1p binds to a region of Abf1p upstream of CS1 in a RanGTP-sensitive manner, suggesting that Abf1p has a second distinct NLS and can be imported into the nucleus by several overlapping pathways. We propose that the link between Abf1p and the nuclear transport machinery may also be important for partitioning multiple Abf1p-mediated nuclear processes.

show abstract

The ABF1 factor is the transcriptional activator of the L2 ribosomal protein genes in Saccharomyces cerevisiae.

Cited by 100 publications

References 26 publications

Reconstructing dynamic regulatory maps

Reconstructing dynamic regulatory maps

Genome-wide analysis of transcriptional dependence and probable target sites for Abf1 and Rap1 in Saccharomyces cerevisiae

Functional and Physical Interactions between Autonomously Replicating Sequence‐Binding Factor 1 and the Nuclear Transport Machinery

Contact Info

Product

Resources

About