A library of yeast transcription factor motifs
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ABSTRACT:
ORGANISM(S): synthetic construct Saccharomyces cerevisiae
PROVIDER: GSE12349 | GEO | 2008/12/26
SECONDARY ACCESSION(S): PRJNA113175
REPOSITORIES: GEO
Similar Datasets
Project description:The sequence specificity of DNA-binding proteins is the primary mechanism by which the cell recognizes genomic features. Here, we describe systematic determination of yeast transcription factor DNA-binding specificities. We obtained binding specificities for 112 DNA-binding proteins representing 19 distinct structural classes. One-third of the binding specificities have not been previously reported. Several binding sequences have striking genomic distributions relative to transcription start sites, supporting their biological relevance and suggesting a role in promoter architecture. Among these are Rsc3 binding sequences, containing the core CGCG, which are found preferentially ~100 bp upstream of transcription start sites. Mutation of RSC3 results in a dramatic increase in nucleosome occupancy in hundreds of proximal promoters containing a Rsc3 binding element, but has little impact on promoters lacking Rsc3 binding sequences, indicating that Rsc3 plays a broad role in targeting nucleosome exclusion at yeast promoters. Keywords: Protein binding microarrays, DNA, proteins Protein binding microarray (PBM), ChIP-chip and DIP-chip experiments of yeast transcription factor DNA-binding domains were performed. Briefly, the PBMs involved binding GST-tagged DNA-binding proteins to custom-designed, double-stranded 44K Agilent microarrays in order to determine their sequence preferences. The method is described in Berger et al., Nature Biotechnology 2006. A key feature is that the microarrays are composed of de Bruijn sequences that contain each 10-base sequence once and only once, providing an evenly balanced sequence distribution. Individual de Bruijn sequences have different properties, including representation of gapped patterns. Here we provide the data transformed into median intensities for all 32,896 8-base sequences, Z-scores for these intensities, and E-scores. E-scores are a modified version of AUC, and describe how well each 8-mer ranks the intensities of the spots. In general the E-scores are slightly more reproducible than Z-scores, but contain less information about relative binding affinity. Additional experimental details are found in Berger et al., Nature Biotechnology 2006, Berger et al., Cell 2008, and the accompanying Supplementary information. Raw 35-mer array data is available on the web link provided. For the DIP-chip experiments [GSM345371, GSM345403, GSM345414-GSM345421, GSM345429-GSM345432], genomic DNA isolated from S288C yeast was incubated with 40nM of the MBP-tagged DNA binding domain (DBD) of either Cbf1, Pho2, Pho4, Leu3, Rap1, or Swi5 and incubated for 30 minutes prior to purification of protein-DNA complexes. The bound DNA was then isolated, amplified via Invitrogen's WGA protocol, and hybridized against input DNA on NimbleGen 385k 32bp-tiling whole genome arrays. ChIPOTle was used to identify peaks of binding from the data and motifs were identified by BioProspector and MDScan and then scored for their ability to predict the identified peaks by GOMER. Motifs with the best ROC AUC are reported in the paper. For the ChIP-chip experiments [GSM346493 and GSM346494], isogenic wildtype and rsc3-1 strains carrying Rsc8-TAP were grown in parallel under rsc3-1 restrictive growth conditions (37°C). Following formaldehyde crosslinking, cells were homogenized and extracts were sonicated to shear the chromatin to an average size of ~500 bp. A single pulldown was then performed with IgG sepharose beads and after decrosslinking and LM-PCR amplification of purified IP DNA, samples were labeled and hybridized on Nimblegen 32bp whole genome tiling arrays, comparing the pulled-down DNA to input genomic DNA.
2008-12-26 | E-GEOD-12349 | biostudies-arrayexpress
Project description:The preinitiation complex (PIC) assembles on promoters of protein-coding genes to position RNA polymerase II (Pol II) for transcription initiation. Previous structural studies revealed the PIC on different promoters, but did not address how the PIC assembles in chromatin. In the yeast Saccharomyces cerevisiae, PIC assembly occurs adjacent to the +1 nucleosome that is positioned downstream of the core promoter. Here we present the cryo-EM structure of the yeast PIC bound to promoter DNA and the +1 nucleosome at a resolution of 3.4–3.9 Å. The general transcription factor TFIIH forms four contacts with the nucleosome, indicating how PIC assembly can be assisted by the +1 nucleosome. The TFIIH subunit Ssl2 (XPB in human TFIIH) forms a wedge between promoter DNA and the nucleosome, stabilizing two turns of DNA that are detached from the nucleosome. During subsequent scanning for the transcription start site (TSS), three additional turns of DNA can be detached before the partially unraveled nucleosome may counteract further scanning, explaining why TSSs are located at a distance of ~60 bp from the dyad of the +1 nucleosome in yeast.
2023-03-11 | PXD029840 | Pride
Project description:The Nuclear Factor I (NFI) family of DNA binding proteins (also called CAAT box transcription factors or CTF) is involved both in replication of adenoviral DNA and in regulation of gene expression. Using chromatin immuno-precipitation and high throughput sequencing (method termed ChIP-Seq) we performed genome-wide mapping of Nuclear Factor I DNA binding sites in mouse embryonic fibroblasts. We found that in vivo and in vitro NFI binding specificities are identical, since previously established position weight matrix was found to accurately predict binding sites for NFI group of proteins. Positional correlation between + and - strand ChIP-Seq tags revealed that NFI is a nucleosome-binding protein, unlike some other transcription factors. We further found that NFI binding correlates with the specific histone modification H3K4me3, the marker of transcribed promoters. Combining ChIP-Seq with the microarray expression data, we found that NFI associates with promoters with higher transcription level. We estimate that transcribed promoters may be more accessible to transcription factor binding than their nearby regions since NFI preferentially bind their DNA target sites located around transcription start sites. Knocking-out one of the NFI proteins (NFI-C), reduced the occupancy of predicted sites, however at the same time indicating that cells could compensate the missing protein with the other members of the family. Keywords: ChIP-Seq (chromatin immunoprecipitation and high throughput sequencing) ChIP-Seq (chromatin immunoprecipitation and high throughput sequencing) using antibody against NFI family of transcription factors in two cell types (wild type and NFI-C knock-out mouse embryonic fibroblasts MEFs)
2010-04-24 | E-GEOD-15844 | biostudies-arrayexpress
Project description:The Nuclear Factor I (NFI) family of DNA binding proteins (also called CAAT box transcription factors or CTF) is involved both in replication of adenoviral DNA and in regulation of gene expression. Using chromatin immuno-precipitation and high throughput sequencing (method termed ChIP-Seq) we performed genome-wide mapping of Nuclear Factor I DNA binding sites in mouse embryonic fibroblasts. We found that in vivo and in vitro NFI binding specificities are identical, since previously established position weight matrix was found to accurately predict binding sites for NFI group of proteins. Positional correlation between + and - strand ChIP-Seq tags revealed that NFI is a nucleosome-binding protein, unlike some other transcription factors. We further found that NFI binding correlates with the specific histone modification H3K4me3, the marker of transcribed promoters. Combining ChIP-Seq with the microarray expression data, we found that NFI associates with promoters with higher transcription level. We estimate that transcribed promoters may be more accessible to transcription factor binding than their nearby regions since NFI preferentially bind their DNA target sites located around transcription start sites. Knocking-out one of the NFI proteins (NFI-C), reduced the occupancy of predicted sites, however at the same time indicating that cells could compensate the missing protein with the other members of the family. Keywords: ChIP-Seq (chromatin immunoprecipitation and high throughput sequencing)
2010-04-24 | GSE15844 | GEO
Project description:Despite extensive research, our understanding of the rules according to which cis-regulatory sequences are converted into gene expression is limited We devised a method for obtaining parallel, highly accurate gene expression measurements from thousands of designed promoters and applied it to measure the effect of systematic changes in the location, number, orientation, affinity and organization of transcription-factor binding sites and nucleosome-disfavoring sequences. Our analyses reveal a clear relationship between expression and binding-site multiplicity, as well as dependencies of expression on the distance between transcription-factor binding sites and gene starts which are transcription-factor specific, including a striking ~10-bp periodic relationship between gene expression and binding-site location. We show how this approach can measure transcription-factor sequence specificities and the sensitivity of transcription-factor sites to the surrounding sequence context, and we compare the activity of 75 yeast transcription factors. Our method can be used to study both cis and trans effects of genotype on transcriptional, post-transcriptional and translational control. Expression profiling of 6500 synthetic promoters in yeast (Saccharomyces cerevisiae). The results were achieved using a method for obtaining pooled and highly accurate expression measurements (closely related to MPRA). In short, the synthetic promoters, which contain unique barcodes, are inserted upstream to a yellow florescence reporter gene, the cells are sorted by their florescence level (using FACS) to expression bins, the promoters in each expression bin are amplified and are send to parallel sequencing (SOLiD) to determine the percent of cells of each promoter in each expression bin; finally an mean expression value is extracted from the raw results. The measurements contain two replicates of exponentially growing yeast cells in SC-Gal-URA (synthetic complete media with 2% galactose and without uracil).
2012-05-20 | E-GEOD-37851 | biostudies-arrayexpress
Project description:Despite extensive research, our understanding of the rules according to which cis-regulatory sequences are converted into gene expression is limited We devised a method for obtaining parallel, highly accurate gene expression measurements from thousands of designed promoters and applied it to measure the effect of systematic changes in the location, number, orientation, affinity and organization of transcription-factor binding sites and nucleosome-disfavoring sequences. Our analyses reveal a clear relationship between expression and binding-site multiplicity, as well as dependencies of expression on the distance between transcription-factor binding sites and gene starts which are transcription-factor specific, including a striking ~10-bp periodic relationship between gene expression and binding-site location. We show how this approach can measure transcription-factor sequence specificities and the sensitivity of transcription-factor sites to the surrounding sequence context, and we compare the activity of 75 yeast transcription factors. Our method can be used to study both cis and trans effects of genotype on transcriptional, post-transcriptional and translational control.
2012-05-20 | GSE37851 | GEO
Project description:The nucleosome is a fundamental unit of chromatin in eukaryotes, and generally prevents the binding of transcription factors to genomic DNA. Pioneer transcription factors overcome the nucleosome barrier, and bind their target DNA sequences in chromatin. OCT4 is a representative pioneer transcription factor that plays a role in stem cell pluripotency. In the present study, we biochemically analyzed the nucleosome binding by OCT4. Crosslinking mass spectrometry showed that OCT4 binds the nucleosome.
2020-05-13 | PXD019160 | JPOST Repository
Project description:Binding specificities of human RNA binding proteins towards structured and linear RNA sequences
| PRJEB25907 | ENA
Project description:Open chromatin provides access to a wide spectrum of DNA binding proteins for DNA metabolism processes such as transcription, repair, recombination, and replication. In this regard, open chromatin profiling has been widely used to identify the location of regulatory regions, including promoters, enhancers, insulators, silencers, replication origins, and recombination hotspots. Regulatory DNA elements are made accessible by nucleosome-depeleted states. Thus, nucleosome remodelling and modification should be intimately coupled with open chromatin formation and regulation. However, our knowledge of nucleosome regulation is largely limited to promoter regions, which comprise only a subset of all regulatory loci in the genome. In order to examine nucleosome patterns in open chromatin regions, we performed micrococcal nuclease (MNase) sequencing for a laboratory strain of yeast. Nucleosome occupancy profiled by Micrococcal nuclease (MNase) digestion
2013-01-06 | E-GEOD-34923 | biostudies-arrayexpress
Project description:Positioned nucleosomes limit the access of proteins to DNA and implement regulatory features encoded in eukaryotic genomes. Here we generated the first genome-wide nucleosome positioning map for Schizosaccharomyces pombe and annotated transcription start and termination sites genome-wide. Using this resource we found surprising differences compared to the nucleosome organization in the distantly related yeast Saccharomyces cerevisiae [the cerevisiae data has been published by others (PMID: 17873876) and the raw data is deposited at ArrayExpress(E-MEXP-1172)]. DNA sequence guides nucleosome positioning differently, e.g., poly(dA:dT) elements are not enriched in S. pombe nucleosome-depleted regions (NDRs). Regular nucleosomal arrays emanate more asymmetrically, i.e., mainly co-directionally with transcription, from promoter NDRs, but promoters harbouring the histone variant H2A.Z show regular arrays also upstream. Regular nucleosome phasing in S. pombe has a very short repeat length of 154 base pairs, and requires a remodeler, Mit1, conserved in humans but not found in S. cerevisiae. Nucleosome positioning mechanisms are evidently not universal but evolutionarily plastic.
2010-02-01 | GSE16040 | GEO