ArticleNucleic acids research2000
Different roles for abf1p and a T-rich promoter element in nucleosome organization of the yeast RPS28A gene.
Article in Nucleic acids research, 2000. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
32 citing papers in PubMed, 57 citations in OpenAlex.
- Transcriptional control of ribosome biogenesis in yeast: links to growth and stress signals.Biochemical Society transactions · 2021Review
- Genome-wide off-rates reveal how DNA binding dynamics shape transcription factor function.Molecular systems biology · 2020Article
- Promoter Architecture and Promoter Engineering inMetabolites · 2020Review
- Evolutionary conservation of MLO gene promoter signatures.BMC plant biology · 2019Article
- Genome-wide determinants of sequence-specific DNA binding of general regulatory factors.Genome research · 2018Article
- Promoter architecture and transcriptional regulation of Abf1-dependent ribosomal protein genes in Saccharomyces cerevisiae.Nucleic acids research · 2016Article
- Chromatin mediation of a transcriptional memory effect in yeast.G3 (Bethesda, Md.) · 2015Article
- Archaeal nucleosome positioning in vivo and in vitro is directed by primary sequence motifs.BMC genomics · 2013Article
- Evolutionary divergence of intrinsic and trans-regulated nucleosome positioning sequences reveals plastic rules for chromatin organization.Genome research · 2011Article
- Multiple sequence-specific factors generate the nucleosome-depleted region on CLN2 promoter.Molecular cell · 2011Article
- Hmo1 directs pre-initiation complex assembly to an appropriate site on its target gene promoters by masking a nucleosome-free region.Nucleic acids research · 2011Article
- Extensive role of the general regulatory factors, Abf1 and Rap1, in determining genome-wide chromatin structure in budding yeast.Nucleic acids research · 2011Article
- A dynamic Bayesian network for identifying protein-binding footprints from single molecule-based sequencing data.Bioinformatics (Oxford, England) · 2010Article
- Many sequence-specific chromatin modifying protein-binding motifs show strong positional preferences for potential regulatory regions in the Saccharomyces cerevisiae genome.Nucleic acids research · 2010Article
- Nucleosome positioning: how is it established, and why does it matter?Developmental biology · 2010Review
- BayesPI - a new model to study protein-DNA interactions: a case study of condition-specific protein binding parameters for Yeast transcription factors.BMC bioinformatics · 2009Article
- Article
- Global transcriptional response of Saccharomyces cerevisiae to the deletion of SDH3.BMC systems biology · 2009Article
- Poly(dA:dT) tracts: major determinants of nucleosome organization.Current opinion in structural biology · 2009Review
- ABF1-binding sites promote efficient global genome nucleotide excision repair.The Journal of biological chemistry · 2009Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
In vivo mutational analysis of the yeast RPS28A ribosomal protein (rp-)gene promoter demonstrated that both the Abf1p binding site and the adjacent T-rich element are essential for efficient transcription. In vivo Mnase and DNaseI digestion showed that the RPS28A promoter contains a 50-60 bp long nucleosome-free region directly downstream from the Abf1p binding site, followed by an ordered array of nucleosomes. Mutating either the Abf1p binding site or the T-rich element has dramatic, but different, effects on the local chromatin structure. Failure to bind Abf1p appears to cause nucleosome positioning to become disorganized as concluded from the complete disappearance of Mnase hypersensitive sites. On the other hand, mutation of the T-rich element causes the downstream nucleosomal array to shift by approximately 50 bp towards the Abf1p site, resulting in loss of the nucleosome-free region downstream of Abf1p. We conclude that Abf1p is a strong organizer of local chromatin structure that appears to act as a nucleosomal boundary factor requiring the downstream T-rich element to create a nucleosome-free region.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.