Similar Datasets
Project description:DNA methylation is a conserved epigenetic modification that is typically associated with silencing of transposable elements and promoter methylated genes. However, some DNA-methylated loci are protected from silencing, allowing transcriptional flexibility in response to environmental and developmental cues. Through a genetic screen in Arabidopsis (Arabidopsis thaliana), we uncovered an antagonistic relationship between the MICRORCHIDIA (MORC) protein and the IMITATION SWITCH (ISWI) complex in regulating the DNA-methylated SUPPRESSOR OF DRM1 DRM2 CMT3 (SDC) reporter. We demonstrate that components of the plant-specific ISWI complex, including CHROMATIN REMODELING PROTEIN11 (CHR11), CHR17, DDT-RELATED PROTEIN4 (DDR4), and DDR5, function to partially derepress silenced genes and transposable elements (TEs), through their function in regulating nucleosome distribution. This action also requires the known transcriptional activator DNAJ proteins, providing a mechanistic link between nucleosome remodeling and transcriptional activation. Genome-wide studies revealed that DDR4 causes changes in nucleosome distribution at numerous loci, a subset of which is associated with changes in DNA methylation and/or transcription. Our work reveals a mechanism for balancing transcriptional flexibility and faithful silencing of DNA-methylated loci. As both ISWI and MORC family genes are widely distributed across plant and animal species, our findings may represent a conserved eukaryotic mechanism for fine-tuning gene expression under epigenetic regulation.
| S-EPMC10396365 | biostudies-literature
Project description:DNA methylation is a conserved epigenetic modification that usually functions to repress gene expression. However, not all DNA methylated loci are faithfully silenced, and genes bearing promoter DNA methylation often show varying levels of transcription. The flexibility in transcription allows for greater adaptability in response to environmental and developmental cues, the mechanisms of which are not fully understood. In this work, we demonstrate that a plant-specific ISWI complex, consisting of CHR11, CHR17, DDR4, and DDR5, functions to partially de-repress DNA methylated genes and TEs through chromatin relaxation. This action requires the known transcriptional activator DNAJ proteins, providing a mechanistic link between nucleosome remodeling and transcriptional activation. We also show that the anti-silencing effects of enhanced chromatin accessibility can be genetically uncoupled from that of DNA demethylation, and is antagonized by the chromatin compactor, MORC proteins. Our work reveals a mechanism for balancing between the needs of transcriptional flexibility and faithful silencing of DNA methylated loci. As both ISWI and MORC family genes are distributed widely across plant and animal species, the findings may represent a conserved eukaryotic mechanism for fine-tuning gene expression under epigenetic repression.
2023-05-08 | GSE202205 | GEO
Project description:DNA methylation is a conserved epigenetic modification that usually functions to repress gene expression. However, not all DNA methylated loci are faithfully silenced, and genes bearing promoter DNA methylation often show varying levels of transcription. The flexibility in transcription allows for greater adaptability in response to environmental and developmental cues, the mechanisms of which are not fully understood. In this work, we demonstrate that a plant-specific ISWI complex, consisting of CHR11, CHR17, DDR4, and DDR5, functions to partially de-repress DNA methylated genes and TEs through chromatin relaxation. This action requires the known transcriptional activator DNAJ proteins, providing a mechanistic link between nucleosome remodeling and transcriptional activation. We also show that the anti-silencing effects of enhanced chromatin accessibility can be genetically uncoupled from that of DNA demethylation, and is antagonized by the chromatin compactor, MORC proteins. Our work reveals a mechanism for balancing between the needs of transcriptional flexibility and faithful silencing of DNA methylated loci. As both ISWI and MORC family genes are distributed widely across plant and animal species, the findings may represent a conserved eukaryotic mechanism for fine-tuning gene expression under epigenetic repression.
2023-05-08 | GSE202270 | GEO
Project description:DNA methylation is a conserved epigenetic modification that usually functions to repress gene expression. However, not all DNA methylated loci are faithfully silenced, and genes bearing promoter DNA methylation often show varying levels of transcription. The flexibility in transcription allows for greater adaptability in response to environmental and developmental cues, the mechanisms of which are not fully understood. In this work, we demonstrate that a plant-specific ISWI complex, consisting of CHR11, CHR17, DDR4, and DDR5, functions to partially de-repress DNA methylated genes and TEs through chromatin relaxation. This action requires the known transcriptional activator DNAJ proteins, providing a mechanistic link between nucleosome remodeling and transcriptional activation. We also show that the anti-silencing effects of enhanced chromatin accessibility can be genetically uncoupled from that of DNA demethylation, and is antagonized by the chromatin compactor, MORC proteins. Our work reveals a mechanism for balancing between the needs of transcriptional flexibility and faithful silencing of DNA methylated loci. As both ISWI and MORC family genes are distributed widely across plant and animal species, the findings may represent a conserved eukaryotic mechanism for fine-tuning gene expression under epigenetic repression.
2023-05-08 | GSE227074 | GEO
Project description:DNA methylation is a conserved epigenetic modification that usually functions to repress gene expression. However, not all DNA methylated loci are faithfully silenced, and genes bearing promoter DNA methylation often show varying levels of transcription. The flexibility in transcription allows for greater adaptability in response to environmental and developmental cues, the mechanisms of which are not fully understood. In this work, we demonstrate that a plant-specific ISWI complex, consisting of CHR11, CHR17, DDR4, and DDR5, functions to partially de-repress DNA methylated genes and TEs through chromatin relaxation. This action requires the known transcriptional activator DNAJ proteins, providing a mechanistic link between nucleosome remodeling and transcriptional activation. We also show that the anti-silencing effects of enhanced chromatin accessibility can be genetically uncoupled from that of DNA demethylation, and is antagonized by the chromatin compactor, MORC proteins. Our work reveals a mechanism for balancing between the needs of transcriptional flexibility and faithful silencing of DNA methylated loci. As both ISWI and MORC family genes are distributed widely across plant and animal species, the findings may represent a conserved eukaryotic mechanism for fine-tuning gene expression under epigenetic repression.
2023-05-08 | GSE202204 | GEO
Project description:FACT (facilitates chromatin transcription) is a protein complex that allows RNA polymerase II (RNAPII) to overcome the nucleosome-induced barrier to transcription. While abundant in undifferentiated cells and many cancers, FACT is not abundant or is absent in most tissues. Therefore, we screened for additional proteins that might replace FACT upon differentiation. We identified two proteins, lens epithelium-derived growth factor (LEDGF) and hepatoma-derived growth factor 2 (HDGF2), each containing two high mobility group A (HMGA)-like AT-hooks and a methyl-lysine reading Pro-Trp-Trp-Pro (PWWP) domain that binds to H3K36me2 and H3K36me3.LEDGF and HDGF2 colocalize with H3K36me2/3 at genomic regions containing active genes. In myoblasts, LEDGF and HDGF2 are enriched on most active genes. Upon differentiation to myotubes, LEDGF levels decrease, while HDGF2 levels are maintained. Moreover, HDGF2 is required for their proper expression. HDGF2 knockout myoblasts exhibit an accumulation of paused RNAPII within the transcribed region of many HDGF2 target genes, indicating a defect in early elongation.
| S-EPMC6774727 | biostudies-literature
Project description:Transcriptional silencing in Saccharomyces requires specific nucleosome modifications promoted in part by a complex of Sir proteins that binds to the modified nucleosomes. Recent evidence suggests that modifications of both the histone amino termini and the core domain of nucleosomes contribute to silencing. We previously identified histone H4 mutations affecting residues in the core of the nucleosome that yield enhanced silencing at telomeres. Here we show that enhanced silencing induced by these mutations increases the proportion of cells in which telomeres and silent mating-type loci are in the silent state. One H4 mutation affects the expression of a subset of genes whose expression is altered by deletion of HTZ1, which encodes the histone variant H2A.Z, suggesting that the mutation may antagonize H2A.Z incorporation into nucleosomes. A second mutation causes the spread of silencing into subtelomeric regions that are not normally silenced in wild-type cells. Mechanistically, this mutation does not significantly accelerate the formation of silent chromatin but, rather, reduces the rate of decay of the silenced state. We propose that these mutations use distinct mechanisms to affect the dynamic interplay between activation and repression at the boundary between active and silent chromatin.
| S-EPMC549373 | biostudies-literature
Project description:Transcription initiation is a tightly regulated process that is crucial for many aspects of prokaryotic physiology. High-throughput transcription start site (TSS) mapping can shed light on global and local regulation of transcription initiation, which in turn may help us understand and predict microbial behavior. In this study, we used Capp-Switch sequencing to determine the TSS positions in the genomes of three model solventogenic clostridia: Clostridium acetobutylicum ATCC 824, C. beijerinckii DSM 6423, and C. beijerinckii NCIMB 8052. We first refined the approach by implementing a normalization pipeline accounting for gene expression, yielding a total of 12,114 mapped TSSs across the species. We further compared the distributions of these sites in the three strains. Results indicated similar distribution patterns at the genome scale, but also some sharp differences, such as for the butyryl-CoA synthesis operon, particularly when comparing C. acetobutylicum to the C. beijerinckii strains. Lastly, we found that promoter structure is generally poorly conserved between C. acetobutylicum and C. beijerinckii. A few conserved promoters across species are discussed, showing interesting examples of how TSS determination and comparison can improve our understanding of gene expression regulation at the transcript level. IMPORTANCE Solventogenic clostridia have been employed in industry for more than a century, initially being used in the acetone-butanol-ethanol (ABE) fermentation process for acetone and butanol production. Interest in these bacteria has recently increased in the context of green chemistry and sustainable development. However, our current understanding of their genomes and physiology limits their optimal use as industrial solvent production platforms. The gene regulatory mechanisms of solventogenesis are still only partly understood, impeding efforts to increase rates and yields. Genome-wide mapping of transcription start sites (TSSs) for three model solventogenic Clostridium strains is an important step toward understanding mechanisms of gene regulation in these industrially important bacteria.
| S-EPMC9045289 | biostudies-literature
Project description:Polycomb Group (PcG) proteins are part of an epigenetic cell memory system that plays essential roles in multicellular development, stem cell biology, X chromosome inactivation, and cancer. In animals, plants, and many fungi, Polycomb Repressive Complex 2 (PRC2) catalyzes trimethylation of histone H3 lysine 27 (H3K27me3) to assemble transcriptionally repressed facultative heterochromatin. PRC2 is structurally and functionally conserved in the model fungus Neurospora crassa, and recent work in this organism has generated insights into PRC2 control and function. To identify components of the facultative heterochromatin pathway, we performed a targeted screen of Neurospora deletion strains lacking individual ATP-dependent chromatin remodeling enzymes. We found the Neurospora homolog of IMITATION SWITCH (ISW) is critical for normal transcriptional repression, nucleosome organization, and establishment of typical histone methylation patterns in facultative heterochromatin domains. We also found that stable interaction between PRC2 and chromatin depends on ISW. A functional ISW ATPase domain is required for gene repression and normal H3K27 methylation. ISW homologs interact with accessory proteins to form multiple complexes with distinct functions. Using proteomics and molecular approaches, we identified three distinct Neurospora ISW-containing complexes. A triple mutant lacking three ISW accessory factors and disrupting multiple ISW complexes led to widespread up-regulation of PRC2 target genes and altered H3K27 methylation patterns, similar to an ISW-deficient strain. Taken together, our data show that ISW is a key component of the facultative heterochromatin pathway in Neurospora, and that distinct ISW complexes perform an apparently overlapping role to regulate chromatin structure and gene repression at PRC2 target domains.
| S-EPMC7848606 | biostudies-literature
Project description:Translocases such as DNA/RNA polymerases, replicative helicases, and exonucleases are involved in eukaryotic DNA transcription, replication, and repair. Since eukaryotic genomic DNA wraps around histone octamers and forms nucleosomes, translocases inevitably encounter nucleosomes. A previous study has shown that a nucleosome repositions downstream when a translocase collides with the nucleosome. However, the molecular mechanism of the downstream repositioning remains unclear. In this study, we identified the lane-switch mechanism for downstream repositioning with molecular dynamics simulations and validated it with restriction enzyme digestion assays and deep sequencing assays. In this mechanism, after a translocase unwraps nucleosomal DNA up to the site proximal to the dyad, the remaining wrapped DNA switches its binding lane to that vacated by the unwrapping, and the downstream DNA rewraps, completing downstream repositioning. This mechanism may have broad implications for transcription through nucleosomes, histone recycling, and nucleosome remodeling.
| S-EPMC8450081 | biostudies-literature