ABF1 DNA-binding protein ABF1 [Saccharomyces cerevisiae S288C] - Gene

Summary

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Gene symbol: ABF1
Gene description: DNA-binding protein ABF1
Primary source: SGD:S000001595
Locus tag: YKL112W
See related: AllianceGenome:SGD:S000001595
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Saccharomyces cerevisiae S288C (strain: S288C)
Lineage: Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces
Also known as: BAF1; EBF2; OBF1; REB2; SBF1
Summary: Enables DNA-binding transcription activator activity, RNA polymerase II-specific and sequence-specific double-stranded DNA binding activity. Involved in several processes, including chromatin organization; global genome nucleotide-excision repair; and regulation of transcription by RNA polymerase II. Located in nucleus. Part of nucleotide-excision repair factor 4 complex. [provided by Alliance of Genome Resources, Apr 2022]
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Genomic context

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Location:: chromosome: XI

Exon count:: 1

Sequence:: Chromosome: XI; NC_001143.9 (226570..228765)

Chromosome XI - NC_001143.9 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:: NC_001143.9

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Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Genome-wide off-rates reveal how DNA binding dynamics shape transcription factor function.
Title: Genome-wide off-rates reveal how DNA binding dynamics shape transcription factor function.
Abf1, Reb1, and Tbf1 control ribosome biogenesis gene expression in budding yeast.
Title: Abf1 and other general regulatory factors control ribosome biogenesis gene expression in budding yeast.
We present evidence that Abf1 recruitment upon nutritional stress, also observed for representative ribosome biogenesis genes, favours RPG transcriptional rescue upon nutrient replenishment, thus pointing to nutrient-regulated Abf1 dynamics at promoters as a novel mechanism in ribosome biogenesis control.
Title: Promoter architecture and transcriptional regulation of Abf1-dependent ribosomal protein genes in Saccharomyces cerevisiae.
It was found that ABF1, FKH2, and REB1 overexpression decreased the growth of strains in a prion-dependent manner and, thus, might influence [PSI;(+)] prion toxicity.
Title: [Identification of new genes that affect [PSI^(+)] prion toxicity in Saccharomyces cerevisiae yeast].
Results show that Abf1 contributes to local regions of chromatin structure by acting at both strong and weak binding sites, at proximal promoter regions and at sites farther upstream, over a very large fraction of the yeast genome.
Title: Extensive role of the general regulatory factors, Abf1 and Rap1, in determining genome-wide chromatin structure in budding yeast.
Data suggest an involvement of Abf1p transcription factor in intergenomic signaling.
Title: Multiple pathways of mitochondrial-nuclear communication in yeast: intergenomic signaling involves ABF1 and affects a different set of genes than retrograde regulation.
Mutation of the I silencer ABF1-binding site at the HMLalpha locus caused loss of ABF1 binding, which resulted in a domain of reduced global genome nucleotide excision repair efficiency on one side of the ABF1-binding site
Title: ABF1-binding sites promote efficient global genome nucleotide excision repair.
The present study revealed numerous loci previously unknown to be under Abf1 control, and it yielded evidence for the protein's variable DNA binding pattern during mitotic growth and meiotic development.
Title: Genome-wide expression profiling, in vivo DNA binding analysis, and probabilistic motif prediction reveal novel Abf1 target genes during fermentation, respiration, and sporulation in yeast.
DNA sequences were found that are bound by ABF1 with nearly two-magnitude higher affinity as compared to the hitherto accepted ABF1 consensus sequence.
Title: In vitro selection of DNA binding sites for ABF1 protein from Saccharomyces cerevisiae.
Results compare the ability of RAP1 and ABF1 to create a region of open chromatin near and to contribute to activated transcription at promoters.
Title: Comparison of ABF1 and RAP1 in chromatin opening and transactivator potentiation in the budding yeast Saccharomyces cerevisiae.

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Homology

Orthologs from OrthoDB

Gene Ontology Provided by SGD

Function	Evidence Code	Pubs
enables DNA binding	IEA Inferred from Electronic Annotation more info
enables DNA replication origin binding	IDA Inferred from Direct Assay more info	PubMed
enables DNA-binding transcription activator activity, RNA polymerase II-specific	IDA Inferred from Direct Assay more info	PubMed
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables sequence-specific DNA binding	HDA more info	PubMed
enables sequence-specific DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables sequence-specific DNA binding, bending	IDA Inferred from Direct Assay more info	PubMed
enables zinc ion binding	RCA inferred from Reviewed Computational Analysis more info	PubMed

Process	Evidence Code	Pubs
involved_in DNA repair	IEA Inferred from Electronic Annotation more info
involved_in DNA replication	IEA Inferred from Electronic Annotation more info
involved_in DNA-templated DNA replication	IDA Inferred from Direct Assay more info	PubMed
involved_in chromatin remodeling	IDA Inferred from Direct Assay more info	PubMed
involved_in chromatin remodeling	IEA Inferred from Electronic Annotation more info
involved_in chromatin remodeling	IGI Inferred from Genetic Interaction more info	PubMed
involved_in global genome nucleotide-excision repair	IDA Inferred from Direct Assay more info	PubMed
involved_in global genome nucleotide-excision repair	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of transcription by RNA polymerase II	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of transcription by RNA polymerase II	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in silent mating-type cassette heterochromatin formation	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
part_of nucleotide-excision repair factor 4 complex	IDA Inferred from Direct Assay more info	PubMed
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in nucleus	IEA Inferred from Electronic Annotation more info
located_in nucleus	IMP Inferred from Mutant Phenotype more info	PubMed

General protein information

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Preferred Names: DNA-binding protein ABF1

NP_012810.1

DNA binding protein with possible chromatin-reorganizing activity; involved in transcriptional activation, gene silencing, and DNA replication and repair

NCBI Reference Sequences (RefSeq)

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Genome Annotation

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference assembly

Genomic

NC_001143.9 Reference assembly

Range

226570..228765

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001179678.1 → NP_012810.1 TPA: DNA-binding protein ABF1 [Saccharomyces cerevisiae S288C]

See identical proteins and their annotated locations for NP_012810.1

Status: REVIEWED

UniProtKB/Swiss-Prot

D6VXH6, P14164

UniProtKB/TrEMBL

A0A8H4C0A0, A6ZZK5, G2WHS2, N1P0S4

Conserved Domains (1) summary

pfam04684
Location:7 → 731

BAF1_ABF1; BAF1 / ABF1 chromatin reorganising factor