Saccharomyces cerevisiae
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ABSTRACT:
PROVIDER: PRJNA210720 | ENA |
REPOSITORIES: ENA
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Project description:The ATP-dependent chromatin remodeling enzyme Fun30 represses transcription by sliding promoter proximal nucleosomes
| PRJNA210718 | ENA
Project description:The ATP-dependent chromatin remodeling enzyme Fun30 represses transcription by sliding promoter proximal nucleosomes [seq]
| PRJNA210719 | ENA
Project description:The evolutionarily conserved ATP-dependent chromatin remodeling enzyme Fun30 has recently been shown to play important roles in heterochromatin silencing and DNA repair. However, how Fun30 remodels nucleosomes is not clear. Here we report a nucleosome sliding activity of Fun30 and its role in transcriptional repression. We observed that Fun30 repressed the expression of genes involved in amino acid and carbohydrate metabolism, the stress response, and meiosis. In addition, Fun30 was localized at the 5′ and 3′ ends of genes and within the open reading frames of its targets. Consistent with its role in gene repression, we observed that Fun30-target genes lacked histone modifications often associated with gene activation and showed an increased level of ubiquitinated histone H2B. Furthermore, genome-wide nucleosome mapping analysis revealed that the length of the nucleosome-free region at the 5′ end of a subset of genes was changed in Fun30-depleted cells. In addition, the positions of the -1, +2 and +3 nucleosomes at the 5′ end of target genes were significantly shifted, while position of the +1 nucleosome remained largely unchanged in the fun30Δ mutant. Finally, we demonstrated that affinity purified single-component Fun30 exhibited nucleosome sliding activity in an ATP-dependent manner. These results define a role for Fun30 in regulation of transcription and indicate that Fun30 remodels chromatin at the 5′ end of genes by sliding promoter proximal nucleosomes.
2013-07-08 | GSE48570 | GEO
Project description:The evolutionarily conserved ATP-dependent chromatin remodeling enzyme Fun30 has recently been shown to play important roles in heterochromatin silencing and DNA repair. However, how Fun30 remodels nucleosomes is not clear. Here we report a nucleosome sliding activity of Fun30 and its role in transcriptional repression. We observed that Fun30 repressed the expression of genes involved in amino acid and carbohydrate metabolism, the stress response, and meiosis. In addition, Fun30 was localized at the 5′ and 3′ ends of genes and within the open reading frames of its targets. Consistent with its role in gene repression, we observed that Fun30-target genes lacked histone modifications often associated with gene activation and showed an increased level of ubiquitinated histone H2B. Furthermore, genome-wide nucleosome mapping analysis revealed that the length of the nucleosome-free region at the 5′ end of a subset of genes was changed in Fun30-depleted cells. In addition, the positions of the -1, +2 and +3 nucleosomes at the 5′ end of target genes were significantly shifted, while position of the +1 nucleosome remained largely unchanged in the fun30Δ mutant. Finally, we demonstrated that affinity purified single-component Fun30 exhibited nucleosome sliding activity in an ATP-dependent manner. These results define a role for Fun30 in regulation of transcription and indicate that Fun30 remodels chromatin at the 5′ end of genes by sliding promoter proximal nucleosomes.
2013-07-08 | GSE48562 | GEO
Project description:The evolutionarily conserved ATP-dependent chromatin remodeling enzyme Fun30 has recently been shown to play important roles in heterochromatin silencing and DNA repair. However, how Fun30 remodels nucleosomes is not clear. Here we report a nucleosome sliding activity of Fun30 and its role in transcriptional repression. We observed that Fun30 repressed the expression of genes involved in amino acid and carbohydrate metabolism, the stress response, and meiosis. In addition, Fun30 was localized at the 5′ and 3′ ends of genes and within the open reading frames of its targets. Consistent with its role in gene repression, we observed that Fun30-target genes lacked histone modifications often associated with gene activation and showed an increased level of ubiquitinated histone H2B. Furthermore, genome-wide nucleosome mapping analysis revealed that the length of the nucleosome-free region at the 5′ end of a subset of genes was changed in Fun30-depleted cells. In addition, the positions of the -1, +2 and +3 nucleosomes at the 5′ end of target genes were significantly shifted, while position of the +1 nucleosome remained largely unchanged in the fun30Δ mutant. Finally, we demonstrated that affinity purified single-component Fun30 exhibited nucleosome sliding activity in an ATP-dependent manner. These results define a role for Fun30 in regulation of transcription and indicate that Fun30 remodels chromatin at the 5′ end of genes by sliding promoter proximal nucleosomes. Data sets for each strain were generated from three biological replicates and experimental dye swap duplicates of each replicate. The six wildtype raw data files linked below were used to generate normalized, log2 (mutant/WT) ratios for all 3 Samples.
2013-07-08 | E-GEOD-48570 | biostudies-arrayexpress
Project description:The evolutionarily conserved ATP-dependent chromatin remodeling enzyme Fun30 has recently been shown to play important roles in heterochromatin silencing and DNA repair. However, how Fun30 remodels nucleosomes is not clear. Here we report a nucleosome sliding activity of Fun30 and its role in transcriptional repression. We observed that Fun30 repressed the expression of genes involved in amino acid and carbohydrate metabolism, the stress response, and meiosis. In addition, Fun30 was localized at the 5M-bM-^@M-2 and 3M-bM-^@M-2 ends of genes and within the open reading frames of its targets. Consistent with its role in gene repression, we observed that Fun30-target genes lacked histone modifications often associated with gene activation and showed an increased level of ubiquitinated histone H2B. Furthermore, genome-wide nucleosome mapping analysis revealed that the length of the nucleosome-free region at the 5M-bM-^@M-2 end of a subset of genes was changed in Fun30-depleted cells. In addition, the positions of the -1, +2 and +3 nucleosomes at the 5M-bM-^@M-2 end of target genes were significantly shifted, while position of the +1 nucleosome remained largely unchanged in the fun30M-NM-^T mutant. Finally, we demonstrated that affinity purified single-component Fun30 exhibited nucleosome sliding activity in an ATP-dependent manner. These results define a role for Fun30 in regulation of transcription and indicate that Fun30 remodels chromatin at the 5M-bM-^@M-2 end of genes by sliding promoter proximal nucleosomes. Micrococcal nuclease digested mononucleosome DNA from wild type and fun30D cells were sequenced by illumina Genome Analyzer. Genome-wide nucleosome positioning and occupancy were analyzed.
2013-07-08 | E-GEOD-48562 | biostudies-arrayexpress
Project description:Chromatin remodeling factors utilize ATP hydrolysis to modulate chromatin dynamics, and the Fun30-subfamily members in yeast and animals are a class of well-studied remodelers implicated in diverse biological processes. However, the molecular activity of plant Fun30 orthologues and their functions in plant growth still remain obscure yet. Compared with yeast and animal orthologues, Arabidopsis Fun30 possesses conserved ATP-dependent nucleosome sliding activity but loses the CUE domain functioning as protein adapter in evolution. Fun30 gene shows a tissue-specific expression pattern in vegetative meristems and various vascular tissues, and is functionally implicated in transcriptional repression of a large number of responsive genes under uninduced conditions. We focused on the interconnected phytohormones SA/JA pathways, and proved the Fun30 recruitment and changes of local nucleosome occupancy within chromatin regions of several key signaling and effector genes in each pathway. Besides SUVR2 involved in RdDM pathway, Fun30 also interacts with non-catalytic subunits of histone deacetylase complex, and Fun30-binding proteins exert in vitro TSA-inhibited histone deacetylase activity. In fun30 mutant, we detected increased H3 acetylation level within local chromatin regions of Fun30 target genes in vivo. Intriguingly, Fun30 transcription is severely inhibited by SA treatment, which thus releases its repression on SA-induced gene during the activation of the downstream SA pathway. Meanwhile, basal transcription level and JA-induced activation of key transcription factor MYC2 gene, as well as the consequent susceptibility to necrotrophic pathogen Botrytis cinerea, are abnormally increased in Fun30-deficient plants.
2020-08-25 | GSE156722 | GEO
Project description:Fun30 is the prototype of the Fun30-SMARCAD1-ETL sub-family of nucleosome remodelers involved in DNA repair and gene silencing. These proteins appear to act as single subunit nucleosome remodelers, but their molecular mechanisms are, at this point, poorly understood. Using multiple sequence alignment and structure prediction, we identify an evolutionarily conserved domain that is modeled to contain a SAM-like fold with one long, protruding helix, which we term SAM-key. Deletion of the SAM-key within budding yeast Fun30 leads to a defect in DNA repair and gene silencing similar to that of the fun30 mutant. In vitro, Fun30 protein lacking the SAM key is able to bind nucleosomes but is deficient in DNA-stimulated ATPase activity as well as nucleosome sliding and eviction. A structural model based on AlphaFold2 prediction and verified by crosslinking-MS indicates an interaction of the long SAM-key helix with protrusion I, a subdomain located between the two ATPase lobes that is critical for control of enzymatic activity. Mutation of the interaction interface phenocopies the domain deletion with a lack of DNA-stimulated ATPase activation and a nucleosome remodeling defect, thereby confirming a role of the SAM-key helix in regulating ATPase activity. Our data thereby demonstrate a central role of the SAM-key domain in mediating the activation of Fun30 catalytic activity, thus highlighting the importance of allosteric activation for this class of enzymes.
2023-07-18 | PXD037249 | Pride
Project description:Nucleosome remodeling factors regulate the occupancy and positioning of nucleosomes genome-wide through ATP-driven DNA translocation. While many nucleosomes are well- and consistently positioned, some nucleosomes and nucleosome-like structures are more sensitive to nuclease digestion or transitory in nature. To better understand the role of nucleosome remodeling factors in generating and clearing these alternative nucleosome structures, we depleted murine embryonic stem cells of the remodeler ATPases BRG1 and SNF2H then performed MNase-seq in murine embryonic stem cells. We performed MNase-seq under high- and low-MNase conditions to assess the effects of nucleosome remodeling factors on nuclease-sensitive or “fragile” nucleosome occupancy. In parallel, we gel-extracted MNase-digested fragments to enrich for another alternative nucleosome structure, the overlapping dinucleosome. Overlapping dinucleosomes are composed of two canonical nucleosomes, asymmetrically lacking one H2A:H2B dimer and wrapped by ~250 bp of DNA. In vitro studies of nucleosome remodeling have suggested that the collision of adjacent nucleosomes by nucleosome sliding can stimulate formation of overlapping dinucleosomes. Using these methods, we were able to identify fragile nucleosomes and overlapping dinucleosomes near transcription start sites and gene-distal DNaseI hypersensitive sites in mouse embryonic stem cells, among other loci. We find that BRG1 consistently stimulates occupancy of fragile nucleosomes but represses occupancy of overlapping dinucleosomes through its nucleosome remodeling function, while SNF2H expression slightly increases fragile nucleosome occupancy.
2023-03-14 | GSE216057 | GEO
Project description:During transcription, nucleosomes are evicted from regulatory and coding regions yet chromatin structure is stable. Restoration of chromatin structure involves concerted action of chromatin modifying activities. Our analysis demonstrates a genome wide function of the INO80 remodeling complex for stable repositioning of the nucleosome immediately proximal to the transcription initiation site. INO80 dependent remodeling of the promoter proximal nucleosomes has a global repressive role. Recruitment of INO80 to proximal nucleosomes overlaps with the elongating Polymerase II complex assembly. The amount of associated Polymerase II at start sites correlates with INO80 recruitment for inducible and constantly transcribed genes. Furthermore, at highly inducible promoters INO80 is required for repression of bidirectional transcription. Therefore, we suggest a function for INO80 after transcription initiation to achieve Polymerase II dependent reassembly of promoter proximal nucleosomes.
2016-12-24 | E-MTAB-1810 | biostudies-arrayexpress