ArticleMolecular biology of the cell2008
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.
Article in Molecular biology of the cell, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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20 citing papers in PubMed, 36 citations in OpenAlex.
- Nucleosome remodeling at origins of global genome-nucleotide excision repair occurs at the boundaries of higher-order chromatin structure.Genome research · 2019Article
- A global function for transcription factors in assisting RNA polymerase II termination.Transcription · 2018Review
- Abf1 and other general regulatory factors control ribosome biogenesis gene expression in budding yeast.Nucleic acids research · 2017Article
- Multiple roles of the general regulatory factor Abf1 in yeast ribosome biogenesis.Current genetics · 2017Review
- Global genome nucleotide excision repair is organized into domains that promote efficient DNA repair in chromatin.Genome research · 2016Article
- Decoupling of divergent gene regulation by sequence-specific DNA binding factors.Nucleic acids research · 2015Article
- Sandcastle: software for revealing latent information in multiple experimental ChIP-chip datasets via a novel normalisation procedure.Scientific reports · 2015Article
- Research resource: the dynamic transcriptional profile of sertoli cells during the progression of spermatogenesis.Molecular endocrinology (Baltimore, Md.) · 2015Article
- Chromatin mediation of a transcriptional memory effect in yeast.G3 (Bethesda, Md.) · 2015Article
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- Promoter architectures in the yeast ribosomal expression program.Transcription · 2011Article
- Extensive role of the general regulatory factors, Abf1 and Rap1, in determining genome-wide chromatin structure in budding yeast.Nucleic acids research · 2011Article
- Mitotic expression of Spo13 alters M-phase progression and nucleolar localization of Cdc14 in budding yeast.Genetics · 2010Article
- GermOnline 4.0 is a genomics gateway for germline development, meiosis and the mitotic cell cycle.Database : the journal of biological databases and curation · 2010Article
- Correlating gene expression variation with cis-regulatory polymorphism in Saccharomyces cerevisiae.Genome biology and evolution · 2010Article
- Uncovering transcriptional interactions via an adaptive fuzzy logic approach.BMC bioinformatics · 2009Article
- Impact of DNA-binding position variants on yeast gene expression.Nucleic acids research · 2009Article
- Identification of yeast transcriptional regulation networks using multivariate random forests.PLoS computational biology · 2009Article
- MIMAS 3.0 is a Multiomics Information Management and Annotation System.BMC bioinformatics · 2009Article
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Authors and funding
8 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The autonomously replicating sequence binding factor 1 (Abf1) was initially identified as an essential DNA replication factor and later shown to be a component of the regulatory network controlling mitotic and meiotic cell cycle progression in budding yeast. The protein is thought to exert its functions via specific interaction with its target site as part of distinct protein complexes, but its roles during mitotic growth and meiotic development are only partially understood. Here, we report a comprehensive approach aiming at the identification of direct Abf1-target genes expressed during fermentation, respiration, and sporulation. Computational prediction of the protein's target sites was integrated with a genome-wide DNA binding assay in growing and sporulating cells. The resulting data were combined with the output of expression profiling studies using wild-type versus temperature-sensitive alleles. This work identified 434 protein-coding loci as being transcriptionally dependent on Abf1. More than 60% of their putative promoter regions contained a computationally predicted Abf1 binding site and/or were bound by Abf1 in vivo, identifying them as direct targets. 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.
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