Similar Datasets
Project description:Chromosomes and plasmids are two forms of genetic carriers. Exogenous yeast artificial chromosomes are also considered as yeast centromeric plasmids in many cases. Here, we used state-of-the-art sequencing technologies to comprehensively profile the genetic, epigenetic, transcriptional and proteomic characteristics of an exogenous data-carrying chromosome. We found that the data-carrying DNA formed active chromatin with high chromatin accessibility and H3K4 tri-methylation levels. We also confirmed that the data-carrying chromosome had a circular shape in the nucleus and was arranged in the Rabl configuration, which may contribute to the self-replication and haploidy of the chromosome in vivo. The data-carrying chromosome displayed highly pervasive transcriptional ability and transcribed hundreds of non-coding RNAs. In summary, this work explores the chromatin epigenetic state, chromatin structure and transcriptional landscape of an exogenous artificial chromosome. The results demonstrated that the exogenous artificial chromosome did form a chromatin structure and was not a naked and incompact plasmid, which strengthen our understanding of artificial chromosomes.
2022-09-30 | GSE183491 | GEO
Project description:Chromosomes and plasmids are two forms of genetic carriers. Exogenous yeast artificial chromosomes are also considered as yeast centromeric plasmids in many cases. Here, we used state-of-the-art sequencing technologies to comprehensively profile the genetic, epigenetic, transcriptional and proteomic characteristics of an exogenous data-carrying chromosome. We found that the data-carrying DNA formed active chromatin with high chromatin accessibility and H3K4 tri-methylation levels. We also confirmed that the data-carrying chromosome had a circular shape in the nucleus and was arranged in the Rabl configuration, which may contribute to the self-replication and haploidy of the chromosome in vivo. The data-carrying chromosome displayed highly pervasive transcriptional ability and transcribed hundreds of non-coding RNAs. In summary, this work explores the chromatin epigenetic state, chromatin structure and transcriptional landscape of an exogenous artificial chromosome. The results demonstrated that the exogenous artificial chromosome did form a chromatin structure and was not a naked and incompact plasmid, which strengthen our understanding of artificial chromosomes.
2022-09-30 | GSE183490 | GEO
Project description:Exogenous artificial DNA forms chromatin structure with active transcription in yeast
| PRJNA761028 | ENA
Project description:Exogenous artificial DNA forms chromatin structure with active transcription in yeast [RNA-seq]
| PRJNA761032 | ENA
Project description:Exogenous artificial DNA forms chromatin structure with active transcription in yeast [ChIP-seq]
| PRJNA761033 | ENA
Project description:Transcription factor (TF) binding is determined by the presence of specific sequence motifs (SM) and chromatin accessibility, where the latter is influenced by both chromatin state (CS) and DNA structure (DS) properties. Although SM, CS, and DS have been used to predict TF binding sites, a predictive model that jointly considers CS and DS has not been developed to predict either TF-specific binding or general binding properties of TFs. Using budding yeast as model, we found that machine learning classifiers trained with either CS or DS features alone perform better in predicting TF-specific binding compared to SM-based classifiers. In addition, simultaneously considering CS and DS further improves the accuracy of the TF binding predictions, indicating the highly complementary nature of these two properties. The contributions of SM, CS, and DS features to binding site predictions differ greatly between TFs, allowing TF-specific predictions and potentially reflecting different TF binding mechanisms. In addition, a "TF-agnostic" predictive model based on three DNA "intrinsic properties" (in silico predicted nucleosome occupancy, major groove geometry, and dinucleotide free energy) that can be calculated from genomic sequences alone has performance that rivals the model incorporating experiment-derived data. This intrinsic property model allows prediction of binding regions not only across TFs, but also across DNA-binding domain families with distinct structural folds. Furthermore, these predicted binding regions can help identify TF binding sites that have a significant impact on target gene expression. Because the intrinsic property model allows prediction of binding regions across DNA-binding domain families, it is TF agnostic and likely describes general binding potential of TFs. Thus, our findings suggest that it is feasible to establish a TF agnostic model for identifying functional regulatory regions in potentially any sequenced genome.
| S-EPMC4546298 | biostudies-literature
Project description:BackgroundStructural maintenance of chromosomes (SMC) complexes are central organizers of chromatin architecture throughout the cell cycle. The SMC family member condensin is best known for establishing long-range chromatin interactions in mitosis. These compact chromatin and create mechanically stable chromosomes. How condensin contributes to chromatin organization in interphase is less well understood.ResultsHere, we use efficient conditional depletion of fission yeast condensin to determine its contribution to interphase chromatin organization. We deplete condensin in G2-arrested cells to preempt confounding effects from cell cycle progression without condensin. Genome-wide chromatin interaction mapping, using Hi-C, reveals condensin-mediated chromatin interactions in interphase that are qualitatively similar to those observed in mitosis, but quantitatively far less prevalent. Despite their low abundance, chromatin mobility tracking shows that condensin markedly confines interphase chromatin movements. Without condensin, chromatin behaves as an unconstrained Rouse polymer with excluded volume, while condensin constrains its mobility. Unexpectedly, we find that condensin is required during interphase to prevent ongoing transcription from eliciting a DNA damage response.ConclusionsIn addition to establishing mitotic chromosome architecture, condensin-mediated long-range chromatin interactions contribute to shaping chromatin organization in interphase. The resulting structure confines chromatin mobility and protects the genome from transcription-induced DNA damage. This adds to the important roles of condensin in maintaining chromosome stability.
| S-EPMC7643427 | biostudies-literature
Project description:DNA sequence variation has been associated with quantitative changes in molecular phenotypes such as gene expression, but its impact on chromatin states is poorly characterized. To understand the interplay between chromatin and genetic control of gene regulation, we quantified allelic variability in transcription factor binding, histone modifications, and gene expression within humans. We found abundant allelic specificity in chromatin and extensive local, short-range, and long-range allelic coordination among the studied molecular phenotypes. We observed genetic influence on most of these phenotypes, with histone modifications exhibiting strong context-dependent behavior. Our results implicate transcription factors as primary mediators of sequence-specific regulation of gene expression programs, with histone modifications frequently reflecting the primary regulatory event.
| S-EPMC5502466 | biostudies-literature
Project description:To address the role of transient torsional stress in transcription, we have utilized the regulated expression of HO endonuclease in yeast to create double-strand breaks in DNA templates in vivo at preselected sites. Linearization of circular minichromosomes, either 2 kb upstream or immediately downstream of a lacZ reporter gene controlled by the yeast metallothionein gene (CUP1) promoter, did not alter the copper induction profile of lacZ RNA transcripts compared to that of nonlinearized controls. Constructs site-specifically integrated into yeast chromosome II gave similar results. In vivo cross-linking with psoralen as a probe for negative DNA supercoiling demonstrated that template linearization efficiently dissipated DNA supercoiling induced by transcription. Therefore, the efficient transcription of linearized, relaxed templates found here demonstrates that transient torsional tension is not required for transcription of chromatin templates in yeast.
| S-EPMC232134 | biostudies-other
Project description:DNA supercoiling is an inherent consequence of twisting DNA and is critical for regulating gene expression and DNA replication. However, DNA supercoiling at a genomic scale in human cells is uncharacterized. To map supercoiling, we used biotinylated trimethylpsoralen as a DNA structure probe to show that the human genome is organized into supercoiling domains. Domains are formed and remodeled by RNA polymerase and topoisomerase activities and are flanked by GC-AT boundaries and CTCF insulator protein-binding sites. Underwound domains are transcriptionally active and enriched in topoisomerase I, 'open' chromatin fibers and DNase I sites, but they are depleted of topoisomerase II. Furthermore, DNA supercoiling affects additional levels of chromatin compaction as underwound domains are cytologically decondensed, topologically constrained and decompacted by transcription of short RNAs. We suggest that supercoiling domains create a topological environment that facilitates gene activation, providing an evolutionary purpose for clustering genes along chromosomes.
| S-EPMC3689368 | biostudies-literature