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| Dataset | Description | Keywords | Number of Conditions | Reference |
|---|---|---|---|---|
| 5P-Seq analysis of wt and new1-knockout yeast strain as well as New1:80S pull-down samples | We present two sets of 5P-Seq experiments: i) comparison of wt and new1-KO S. cerevisiae ii) analysis of New1:80S pulldown samples. Collectively our results unravel codon-dependent nature of ribosomal stalling in S. cerevisiae lacking New1. | transcriptional regulation | 20 | |
| 5PSeq supporting study Probing 3’UTRs as modular regulators of gene expression | The goal of the study is to analyse the function of 3'-UTR motifs in the non-native context. Several 3'-UTR motifs predicted to have stabilizing or destabilizing effects on mRNA were inserted into terminators controlling the expression of reporter mCherry gene in following contexts: pRps3-mCherry-tRps3, pPgk1-mCherry-tRps3, pTsa1-mCherry-tTsa. 5'P sequencing was used to determine whether or not modifications in the 3'-UTR region affect ribosomal dynamics and co-translational degradation of mRNA in the 3' end region of reporter coding sequence. | transcriptional regulation | 16 | |
| A conserved transcriptional regulator governs fungal morphology in widely diverged species [expression data] | In this paper, we examine orthologs of a transcriptional regulator in three fungal species, Saccharomyces cerevisiae, Candida albicans, and Histoplasma capsulatum | cell morphogenesis, transcriptional regulation | 8 | Cain CW, et al. (2012) PMID:22095082 |
| A Dynamic Model for the Function of Mediator Modules In Vivo | Mediator is a highly conserved transcriptional coactivator organized into four modules, namely Tail, Middle, Head and Kinase (CKM) | transcriptional regulation | 12 | Jeronimo C, et al. (2016) PMID:27773677 |
| A library of native and synthetic yeast core promoters driving YFP expression | The core promoter is the regulatory sequence to which RNA polymerase is recruited and where it acts to initiate transcription | transcriptional regulation | 1 | Lubliner S, et al. (2015) PMID:25969468 |
| A Novel mode of half site binding in budding yeast | This SuperSeries is composed of the SubSeries listed below. | transcriptional regulation | 26 | Recio PS, et al. (2023) PMID:37125648 |
| A Novel mode of half site binding in budding yeast I | 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. | transcriptional regulation | 16 | |
| A Novel mode of half site binding in budding yeast II | 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. | transcriptional regulation | 10 | |
| A role for condensin in mediating transcriptional adaptation to environmental stimuli. | This SuperSeries is composed of the SubSeries listed below. | transcriptional regulation, transcription, chromatin organization | 42 | |
| A role for condensin in mediating transcriptional adaptation to environmental stimuli. [RNA-Seq] | The relationship between chromatin and transcription was investigated through condensin, a key regulator of higher order chromatin structure. We use rapid conditional condensin depletion in cell cycle-staged budding yeast S. cerevisiae cells to study condensin’s role in transcriptional regulation. We observe a large number of small gene expression changes close to condensin binding sites | transcriptional regulation | 24 |