Chromatin-dependent binding of the S. cerevisiae HMGB protein Nhp6A affects nucleosome dynamics and transcription [Affymetrix]
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ABSTRACT:
ORGANISM(S): Saccharomyces cerevisiae
PROVIDER: GSE23582 | GEO | 2010/09/15
SECONDARY ACCESSION(S): PRJNA133373
REPOSITORIES: GEO
Similar Datasets
Project description:The Saccharomyces cerevisiae protein Nhp6A is a model for the abundant and multifunctional HMGB family of chromatin-associated proteins. Nhp6A binds DNA in vitro without sequence-specificity and bends DNA sharply, but its role in chromosome biology is poorly understood. We show by whole genome ChIP-chip that Nhp6A is localized to specific regions of chromosomes that include about 23% of RNA polymerase II promoters. Nhp6A binding functions to stabilize positioned nucleosomes within promoter and 5' coding regions of these genes. Both genomic binding and transcript expression studies point to functionally-related groups of genes that are specifically bound by Nhp6A and whose transcription is altered by the absence of Nhp6. Genomic analyses of Nhp6A mutants specifically defective in DNA bending reveals a critical role of DNA bending for co-regulation of transcription but not for targeted binding by Nhp6A. We conclude that the chromatin environment, not DNA sequence recognition, localizes Nhp6A binding and that Nhp6A stabilizes chromatin structure and co-regulates transcription. Two amino acid residues within the DNA binding interface of Nhp6A are critical for bending DNA . Substitution of methionine 29 to alanine (M29A) reduces the formation of 98 bp microcircles by 6-fold in vitro, but equilibrium binding to linear DNA is only reduced 2-fold. The severe phenylalanine 48 to alanine (F48A) mutation abolishes formation of 98 bp microcircles, while again only lowering equilibrium binding to linear DNA by 2-fold (Masse et al. 2002; Dai et al. 2005). We used these bending mutants to address if Nhp6A bending activity is required for transcriptional regulation? Specifically, genome-wide binding and transcript analysis was performed on nhp6A-M29A ∆nhp6B, nhp6A-F48A ∆nhp6B, and nhp6A-P18A ∆nhp6B cells. Nhp6A-P18A was included to control for the modest decrease in DNA binding observed in the bending mutants because it also exhibits a 2-fold reduction of DNA binding but without a significant change of DNA bending (Yen et al. 1998; Allain et al. 1999). Transcription in four different genotypes (∆nhp6A ∆nhp6B, nhp6A-P18A ∆nhp6B, nhp6A-F48A ∆nhp6B, nhp6A-M29A ∆nhp6B) was compared to the same reference genotype (Nhp6A ∆nhp6B). Biological replicates were performed for each comparison.
2010-09-15 | E-GEOD-23607 | biostudies-arrayexpress
Project description:The Saccharomyces cerevisiae protein Nhp6A is a model for the abundant and multifunctional HMGB family of chromatin-associated proteins. Nhp6A binds DNA in vitro without sequence-specificity and bends DNA sharply, but its role in chromosome biology is poorly understood. We show by whole genome ChIP-chip that Nhp6A is localized to specific regions of chromosomes that include about 23% of RNA polymerase II promoters. Nhp6A binding functions to stabilize positioned nucleosomes within promoter and 5' coding regions of these genes. Both genomic binding and transcript expression studies point to functionally-related groups of genes that are specifically bound by Nhp6A and whose transcription is altered by the absence of Nhp6. Genomic analyses of Nhp6A mutants specifically defective in DNA bending reveals a critical role of DNA bending for co-regulation of transcription but not for targeted binding by Nhp6A. We conclude that the chromatin environment, not DNA sequence recognition, localizes Nhp6A binding and that Nhp6A stabilizes chromatin structure and co-regulates transcription. Two amino acid residues within the DNA binding interface of Nhp6A are critical for bending DNA . Substitution of methionine 29 to alanine (M29A) reduces the formation of 98 bp microcircles by 6-fold in vitro, but equilibrium binding to linear DNA is only reduced 2-fold. The severe phenylalanine 48 to alanine (F48A) mutation abolishes formation of 98 bp microcircles, while again only lowering equilibrium binding to linear DNA by 2-fold (Masse et al. 2002; Dai et al. 2005). We used these bending mutants to address if Nhp6A bending activity is required for transcriptional regulation? Specifically, genome-wide binding and transcript analysis was performed on nhp6A-M29A ∆nhp6B, nhp6A-F48A ∆nhp6B, and nhp6A-P18A ∆nhp6B cells. Nhp6A-P18A was included to control for the modest decrease in DNA binding observed in the bending mutants because it also exhibits a 2-fold reduction of DNA binding but without a significant change of DNA bending (Yen et al. 1998; Allain et al. 1999).
2010-09-15 | GSE23607 | GEO
Project description:The unicellular eukaryote Entamoeba histolytica is a human parasite that causes amebic dysentery and liver abscess. A genome-wide analysis of gene expression modulated by intestinal colonization and invasion identified an up-regulated transcript that encoded a putative high-mobility-group box (HMGB) protein, EhHMGB1. We tested if EhHMGB1 encoded a functional HMGB protein, and determined its role in control of parasite gene expression. Recombinant EhHMGB1 was able to bend DNA in vitro, a characteristic of HMGB proteins. Core conserved residues required for DNA bending activity in other HMGB proteins were demonstrated by mutational analysis to be essential for EhHMGB1 activity. EhHMGB1 was also able to enhance the binding of human p53 to its cognate DNA sequence in vitro, which is expected for an HMGB1 protein. Confocal microscopy, using antibodies against the recombinant protein, confirmed its nuclear localization. Overexpression of EhHMGB1 in HM1: IMSS trophozoites led to modulation of 33 transcripts involved in a variety of cellular functions. Of these, twenty were also modulated at either day one or day 29 in the mouse model of intestinal amebiasis. Notably, four transcripts with known roles in virulence, including two encoding Gal/GalNAc lectin light chains, were modulated in response to EhHMGB1 overexpression. We concluded that EhHMGB1 was a bona fide HMGB protein with the capacity to recapitulate part of the modulation of parasite gene expression seen during adaptation to the host intestine. 6 samples for two groups: 3M and Gir. Each groups contain 3 samples
2008-11-19 | E-GEOD-12204 | biostudies-arrayexpress
Project description:The unicellular eukaryote Entamoeba histolytica is a human parasite that causes amebic dysentery and liver abscess. A genome-wide analysis of gene expression modulated by intestinal colonization and invasion identified an up-regulated transcript that encoded a putative high-mobility-group box (HMGB) protein, EhHMGB1. We tested if EhHMGB1 encoded a functional HMGB protein, and determined its role in control of parasite gene expression. Recombinant EhHMGB1 was able to bend DNA in vitro, a characteristic of HMGB proteins. Core conserved residues required for DNA bending activity in other HMGB proteins were demonstrated by mutational analysis to be essential for EhHMGB1 activity. EhHMGB1 was also able to enhance the binding of human p53 to its cognate DNA sequence in vitro, which is expected for an HMGB1 protein. Confocal microscopy, using antibodies against the recombinant protein, confirmed its nuclear localization. Overexpression of EhHMGB1 in HM1: IMSS trophozoites led to modulation of 33 transcripts involved in a variety of cellular functions. Of these, twenty were also modulated at either day one or day 29 in the mouse model of intestinal amebiasis. Notably, four transcripts with known roles in virulence, including two encoding Gal/GalNAc lectin light chains, were modulated in response to EhHMGB1 overexpression. We concluded that EhHMGB1 was a bona fide HMGB protein with the capacity to recapitulate part of the modulation of parasite gene expression seen during adaptation to the host intestine.
2008-11-20 | GSE12204 | GEO
Project description:Retrotransposon Ty1 integration targets specifically positioned asymmetric nucleosomal DNA segments in tRNA hotspots
| PRJNA150613 | ENA
Project description:Identification of specifically activated angiogenic molecules in HMGB-1-induced angiogenesis
| PRJNA391577 | ENA
Project description:Background: Recently we characterised TRB1, a protein from a single-myb-histone family, as a structural and functional component of telomeres in Arabidopsis thaliana. TRB proteins, besides their ability to bind specifically telomeric DNA using their N-terminally positioned myb-like domain of the same type as in human TRF1 or TRF2 shelterin proteins, possess also histone-like domain which is involved in protein-protein interactions e.g., with POT1b. We set to investigate the genome-wide localization pattern of TRB1 to reveal its preferential mode of binding to chromatin in vivo and its potential functional roles in the genome-wide context. Results: Our results demonstrate that in addition to its roles at telomeres, TRB1 is preferentially associated with promoter regions of genes involved in ribosome biogenesis. This preference coincides with a frequent occurrence of telobox motifs in the upstream regions of genes in this category, but is not restricted to the telobox presence. Conclusions: We conclude that TRB1, in addition to its preferential telomeric localization, shows a specific genome-wide distribution pattern suggesting its role in regulation of genes involved in biogenesis of translational machinery. TRB1 DNA-binding activity investigated in 2 biological replicates (2 immunoprecipitation approaches) with controls; with technical replicates.
2015-12-21 | E-GEOD-69431 | biostudies-arrayexpress
Project description:The organization of nucleosomes influences transcriptional activity by controlling accessibility of DNA binding proteins to the genome. Genome-wide nucleosome binding profiles have identified a canonical nucleosome organization at gene promoters, where arrays of well-positioned nucleosomes emanate from nucleosome-depleted regions. The mechanisms of formation and the function of canonical promoter nucleosome organization remain unclear. Here we analyze the genome-wide location of nucleosomes during zebrafish embryogenesis and show that well-positioned nucleosome arrays appear on thousands of promoters during the activation of the zygotic genome. The formation of canonical promoter nucleosome organization is independent of DNA sequence preference, transcriptional elongation, and robust RNA polymerase II (Pol II) binding. Instead, canonical promoter nucleosome organization correlates with the presence of Histone H3 Lysine 4 trimethylation (H3K4me3) and affects future transcriptional activation. These findings reveal that genome activation is central to the organization of nucleosome arrays during early embryogenesis.
2013-10-29 | GSE51766 | GEO
Project description:The organization of nucleosomes influences transcriptional activity by controlling accessibility of DNA binding proteins to the genome. Genome-wide nucleosome binding profiles have identified a canonical nucleosome organization at gene promoters, where arrays of well-positioned nucleosomes emanate from nucleosome-depleted regions. The mechanisms of formation and the function of canonical promoter nucleosome organization remain unclear. Here we analyze the genome-wide location of nucleosomes during zebrafish embryogenesis and show that well-positioned nucleosome arrays appear on thousands of promoters during the activation of the zygotic genome. The formation of canonical promoter nucleosome organization is independent of DNA sequence preference, transcriptional elongation, and robust RNA polymerase II (Pol II) binding. Instead, canonical promoter nucleosome organization correlates with the presence of Histone H3 Lysine 4 trimethylation (H3K4me3) and affects future transcriptional activation. These findings reveal that genome activation is central to the organization of nucleosome arrays during early embryogenesis.
2013-10-18 | GSE44269 | GEO
Project description:High-mobility group box-1 (HMGB-1), a nonhistone chromosomal protein, is expressed in almost all types of cells with nucleus, and dysregulation of its expression correlates with pathological conditions such as inflammatory diseases, ischemia and cancers. Some of these conditions accompany abnormal angiogenesis induced by HMGB-1 mediated activation of downstream signaling pathways. So far, the underlying mechanism by which HMGB-1 induces angiogenesis remains largely unknown. In this study, we performed time-dependent gene expression microarray in endothelial cells (ECs) after HMGB-1 or VEGF treatment. By pathway analysis using each gene set up-regulated by HMGB-1 or VEGF, we found that most of HMGB-1 induced angiogenic pathways were also commonly activated by VEGF, while activation time and gene sets belonging to the pathways were different. In addition, HMGB-1 up-regulated some VEGFR signaling related conventional angiogenic factors including EGR1 and importantly, novel angiogenic factors such as ABL2, CEACAM1, KIT and VIPR1 which have been reported to independently promote angiogenesis in physiological and pathological conditions. Our gene expression profiling suggests that HMGB-1 is capable of independently inducing angiogenesis through activation of HMGB-1 specific angiogenic factors and also functions as an accelerator for VEGF mediated conventional angiogenesis according to physiological and pathological condition.
2017-12-29 | GSE100404 | GEO