Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

A Novel mode of half site binding in budding yeast II

ABSTRACT: Despite decades of research, predicting where a transcription factor (TF) binds using its sequences alone continues to be an outstanding problem. Here, our thermodynamic model of Gal4p-DNA binding revealed a new mechanism of binding site selection in which Gal4p can bind to promoters that lacks it consensus site. Further investigation revealed that these sequences that Gal4p unexpectedly binds to have a high density of its half site, CGG. Analyses showed the ability of CGG half sites to predict zinc cluster TF in vivo binding and exposed a clear relationship between CGG half sites and zinc cluster binding in multiple binding datasets. To dissect the molecular logic of this half site mode of binding we designed a Sort-seq library containing 6,798 yeast promoter sequences and measured their expression. We learned that there is a linear relationship between CGG half site density and zinc cluster driven expression in vivo. Additionally, we found that promoters encoding 10 half sites have the same transcriptional output as a single consensus site and found no clear effects of half site orientation and spacing on strength of activation. Our experiments demonstrate that this novel mode of half site binding is widespread across the yeast genome and expands our knowledge about TF binding specificity that can be applied to higher eukaryotes.

ORGANISM(S): Saccharomyces cerevisiae

PROVIDER: GSE216839 | GEO | 2022/11/04

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

A Novel mode of half site binding in budding yeast I

Project description:Despite decades of research, predicting where a transcription factor (TF) binds using its sequences alone continues to be an outstanding problem. Here, our thermodynamic model of Gal4p-DNA binding revealed a new mechanism of binding site selection in which Gal4p can bind to promoters that lacks it consensus site. Further investigation revealed that these sequences that Gal4p unexpectedly binds to have a high density of its half site, CGG. Analyses showed the ability of CGG half sites to predict zinc cluster TF in vivo binding and exposed a clear relationship between CGG half sites and zinc cluster binding in multiple binding datasets. To dissect the molecular logic of this half site mode of binding we designed a Sort-seq library containing 6,798 yeast promoter sequences and measured their expression. We learned that there is a linear relationship between CGG half site density and zinc cluster driven expression in vivo. Additionally, we found that promoters encoding 10 half sites have the same transcriptional output as a single consensus site and found no clear effects of half site orientation and spacing on strength of activation. Our experiments demonstrate that this novel mode of half site binding is widespread across the yeast genome and expands our knowledge about TF binding specificity that can be applied to higher eukaryotes.

2022-11-04 | GSE216838 | GEO

Unraveling determinants of transcription factor binding outside the core binding site

Project description:Binding of transcription factors (TFs) to regulatory sequences is a pivotal step in the control of gene expression. Despite many advances in the characterization of sequence motifs recognized by TFs, our ability to quantitatively predict TF binding to different regulatory sequences is still limited. Here, we present a novel experimental assay termed BunDLE-seq that provides quantitative measurements of TF binding to thousands of fully designed sequences of 200 bp in length within a single experiment. Applying this binding assay to two yeast TFs we demonstrate that sequences outside the core TF binding site profoundly affect TF binding. We show that TF-specific models based on the sequence or DNA shape of the regions flanking the core binding site are highly predictive of the measured differential TF binding. We further characterize the dependence of TF binding, accounting for measurements of single and co-occurring binding events, on the number and location of binding sites and on the TF concentration. Finally, by coupling our in vitro TF binding measurements, and another application of our method probing nucleosome formation, to in vivo expression measurements carried out with the same template sequences now serving and promoters, we offer insights into mechanisms that may determine the different expression outcomes observed. Our assay thus paves the way to a more comprehensive understanding of TF binding to regulatory sequences, and allows the characterization of TF binding determinants within and outside of core binding sites.

2015-03-04 | GSE66143 | GEO

5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) increase CREB1 binding to the C/EBP half-site GCAA

Project description:In human and mouse stem cells and brain, 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) can occur outside of CG dinucleotides. Using protein binding microarrays (PBMs) containing 60-mer DNA probes, we evaluated the effect of 5mC and 5hmC on one DNA strand on the double-stranded DNA binding of the mouse B-ZIP transcription factors (TFs) CREB1, ATF1, and JUND. 5mC inhibited CREB1 binding to the canonical CRE half-site |GTCA, but increased binding to the C/EBP half-site |GCAA. 5hmC inhibited CREB1 binding to all 8-mers except TGAT|GCAA, where binding is enhanced. We observed similar DNA binding patterns with the closely related TF: ATF1. In contrast, both 5mC and 5hmC inhibited binding of JUND. These results identify new DNA sequences that are well-bound by CREB1 and ATF1 only when they contain 5mC or 5hmC. Analysis of two x-ray structures examines the consequences of 5mC and 5hmC on DNA binding by CREB and FOS|JUN.

2016-10-19 | GSE88897 | GEO

ChIP-Seq of ES-E14 mouse embryonic stem cells investigating changes in Sall4

Project description:Sall4 is a stem cell factor which is important for embryogenesis. We have genetically modified Sall4 in mouse embryonic stem cells to access the preference of Sall4 binding site. There are three different genetic modifications for the ES cells in the form of Sall4 Knockout (KO), Sall4 Zinc Finger Cluster 4 Mutation (ZFC4mut) and Sall4 Zinc Finger Cluster 1-2 Deletion (ZFC1-2Δ) respectively that we have considered for our study.

2021-01-05 | E-MTAB-9197 | biostudies-arrayexpress

Comprehensive, high-resolution binding energy landscapes reveal context dependencies of transcription factor binding

Project description:Transcription factors (TFs) are primary regulators of gene expression in cells, where they bind specific genomic target sites to control transcription. Quantitative measurements of TF-DNA binding energies can improve the accuracy of predictions of TF occupancy and downstream gene expression in vivo and shed light on how transcriptional networks are rewired throughout evolution. Here, we present a novel sequencing-based TF binding assay and analysis pipeline (BET-seq, for Binding Energy Topography by sequencing) capable of providing quantitative estimates of binding energies for more than one million DNA sequences in parallel at high energetic resolution. Using this platform, we measured the binding energies associated with all possible combinations of 10 nucleotides flanking the known consensus DNA target for two model yeast TFs, Pho4 and Cbf1. A large fraction of these flanking mutations change overall binding energies by an amount equal to or greater than consensus site mutations, suggesting that current definitions of TF binding sites may be too restrictive. By systematically comparing estimates of binding energies output by deep neural networks (NN) and biophysical models trained on these data, we establish that dinucleotide specificities are sufficient to explain essentially all variance in observed binding behavior, with Cbf1 binding exhibiting significantly more non-additivity than Pho4. NN-derived binding energies agree with orthogonal biochemical measurements and reveal that dynamically occupied sites in vivo are both energetically and mutationally distant from the highest-affinity sites.

2018-03-17 | GSE111936 | GEO

Coop-Seq Analysis Demonstrates that Sox2 Evokes Latent Specificities in the DNA Recognition by Pax6

Project description:Sox2 and Pax6 co-regulate genes in neural lineages and the eye by forming a ternary complex likely facilitated allosterically through DNA. We used the quantitative and scalable Cooperativity-by-sequencing (Coop-seq) approach to interrogate Sox2/Pax6 dimerization on a DNA library where five positions of the Pax6 half site are randomized yielding 1024 cooperativity factors. Consensus positions normally required for the high-affinity DNA binding by Pax6 need to be mutated for effective dimerization with Sox2. Out of the five randomized bases, a 5’ thymidin is present in most of the top ranking elements. However, according to structural models, this thymidin maps to a spacer region separating Sox and Pax half –sites and is not expected to directly interact with the binding proteins. Cooperative binding to the Coop-seq defined sequence signature was validated by classical EMSAs. Re-analysis of ChiPseq data identified several candidate elements in genomic regions co-bound by Sox2 and Pax6. A highly conserved Sox2/Pax6 bound site near the Sprouty2 locus consists of a prototype cooperativity signature. This element was verified to promote cooperative dimerization designating Sprouty2 as candidate target of Sox2/Pax6 in several mouse and human tissues including the brain and the eye. Collectively, the functional interplay of Sox2 and Pax6 demands the relaxation of high affinity binding sites and is enabled by alternative DNA sequences. We conclude that this binding mode evolved to warrant that a subset of target genes is only regulated in the presence of suitable partner factors.

2017-11-15 | GSE101529 | GEO

The specific DNA sequence recognized by the yeast transcription factor Gcn4 is sufficient to predict high-affinity binding on a genome-wide scale

Project description:Sequence-specific DNA-binding transcription factors are central to gene regulation. They are often associated with consensus binding sites that predict far more genomic sites than are bound in vivo. One explanation is that most sites are blocked by nucleosomes, such that only sites in nucleosome-depleted regulatory regions are bound. Alternatively, the consensus site may be poorly defined. We compared the binding of the yeast transcription factor Gcn4 in vivo using published ChIP-seq data (546 sites) and in vitro, using a modified SELEX method ("G-SELEX"), which utilizes short genomic DNA fragments to quantify binding at all sites. We confirm that Gcn4 binds strongly to an AP1-like sequence (TGACTCA) and weakly to half-sites. However, Gcn4 binds only some of the 1078 exact matches to this sequence, even in vitro. We show that the high-affinity site is RTGACTCAY (exact match), of which there are only 166 copies in the yeast genome, all occupied in vivo. Generally, RTGACTCAR/YTGACTCAY sites are bound much more weakly and YTGACTCAR sites are unbound, with biological implications for determining induction levels. We conclude that Gcn4 binding can be predicted using the genome sequence. Our study suggests that transcription factor consensus sequences should be defined more precisely using quantitative data.

2021-12-06 | GSE180114 | GEO

Deep sequencing of HetR-bound DNA reveals novel HetR targets in Anabaena sp. strain PCC 7120

Project description:We employed chromatin pull-down and deep sequencing to globally identify HetR DNA targets in vivo at 6 hours after fixed-nitrogen deprivation. We identified novel DNA binding targets of tagged HetR-6xHis and defined a consensus HetR binding site from these HetR target sequences.

2013-10-31 | GSE51886 | GEO

Co-regulation of transcription factor binding and nucleosome occupancy through DNA features of mammalian enhancers

Project description:In mammalian cells transcription factors (TFs) preferentially bind sites contained in regions of high nucleosomal occupancy, as determined by nucleotide-dependent computational analysis. This observation suggests that nucleosomes may act as gatekeepers of TF binding sites. We hypothesized that in mammalian genomes the information controlling nucleosome assembly may partially coincide with the information that enables TFs to recognize cognate sites in cis-regulatory elements while ignoring the myriad of non-functional, randomly occurring consensus binding sites. This way, nucleosome-mediated masking would be coupled to TF binding site functionality. The hematopoietic master regulator Pu.1 maintained nucleosome depletion at macrophage-specific enhancers that were otherwise occupied by nucleosomes in other cell types and in reconstituted chromatin. We identified a minimal set of DNA sequence and shape features that predicted Pu.1 binding with 78% accuracy. The same features predicted nucleosome occupancy in cells where Pu.1 was not expressed with higher accuracy than specifically designed models. Control of nucleosome deposition by DNA sequence and shape features that also specify TF consensus site functionality may allow maintaining the gatekeeper function of nucleosomes during evolution of cis-regulatory elements.

2014-05-08 | GSE50762 | GEO

DNase I hypersensitivity and algorithmic prediction of TF binding in early pancreatic mES directed differentiation

Project description:This dataset uses DNase-seq to profile the genome-wide DNase I hypersensitivity of mES and mES-derived cells along an early pancreatic lineage and provides the locations of putative Transcription Factor (TF) binding sites using the PIQ algorithm. DNase-seq takes advantage of the preferential cutting of DNase I in open chromatin and steric blockage of of DNase I by tightly bound TFs that protect associated genomic DNA sequences. After deep sequencing of DNase IM-bM-^@M-^Sdigested genomic DNA from intact nuclei, genome-wide data on chromatin accessibility as well as TF-specific DNase I protection profiles that reveal the genomic binding locations of a majority of TFs are obtained. Such TF signature M-bM-^@M-^XDNase profilesM-bM-^@M-^Y reflect the effect of the TF on DNA shape and local chromatin architecture, extending hundreds of base pairs from a TF binding site, and these profiles are centered on M-bM-^@M-^XDNase footprintsM-bM-^@M-^Y at the binding motif itself, which reflects the biophysics of protein-DNA binding. An algorithm, PIQ, is then applied that models the specific profile of each factor, and in combination with sequence information predicts the likely binding locations of over 700 TFs genome wide. This dataset includes DNase-seq hypersensitivity data from 6 mES-derived cell types: mESC, Mesendoderm, Mesoderm, Endoderm, Intestinal Endoderm, and Prepancreatic Endoderm. For each cell type, TF binding site predictions are made based on the identification TF-specific DNase-seq profiles over any of 1331 possible binding motifs. After significance thesholding, genome-wide binding site predictions for <700 TFs are included.

2014-01-19 | E-GEOD-53776 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data