Evolutional heterochromatin condensation delineates chromocenter formation and retrotransposon constraint in plants
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA975586 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR24709427_1.fastq.gz | Fastqsanger.gz | |||
| SRR24709427_2.fastq.gz | Fastqsanger.gz | |||
| SRR24709428_1.fastq.gz | Fastqsanger.gz | |||
| SRR24709428_2.fastq.gz | Fastqsanger.gz | |||
| SRR24709429_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 100 |
Similar Datasets
Project description:Heterochromatic condensates (chromocenters) are critical for maintaining the silencing of heterochromatin. However, it is a riddle why the presence of chromocenters is variable across species. Here, we reveal that variations in the plant heterochromatin protein ADCP1 confer a diversity in chromocenter formation via phase separation. ADCP1 physically interacts with the high mobility group protein HMGA to form a complex and mediates heterochromatin condensation by multivalent interactions. The loss of intrinsically disordered regions (IDRs) in ADCP1 homologues during evolution has led to the absence of prominent chromocenter in various plant species, and introduction of IDR-containing ADCP1 with HMGA promotes heterochromatin condensation and retrotransposon silencing. Moreover, plants in the Cucurbitaceae group have evolved an IDR-containing chimera of ADCP1 and HMGA, which enables formation of chromocenters remarkably. Together, our work uncovers a coevolved mechanism of phase separation in packing heterochromatin and constraining retrotransposons.
2024-06-22 | GSE233265 | GEO
Project description:During interphase centromeres often coalesce into a small number of chromocenters, which can be visualized as distinct, DAPI dense nuclear domains. Intact chromocenters play a major role in maintaining genome stability as they stabilize the transcriptionally silent state of repetitive DNA while ensuring centromere function. Despite its biological importance, relatively little is known about the molecular composition of the chromocenter or the processes that mediate chromocenter formation and maintenance. To shed light on this, we performed confocal and super resolution microscopy and proximity based biotinylation experiments of three proteins associated with the chromocenter in Drosophila: the centromeric H3 variant dCenpA, the heterochromatin protein HP1a and the speciation factor HMR. Our work revealed an intricate internal structure of the chromocenter suggesting a complex multilayered structure of this intranuclear domain.
2020-01-01 | GSE137194 | GEO
Project description:Translation initiation factor eIF5A facilitates protein synthesis and impacts diverse biological processes, yet its role in transcriptional regulation is poorly understood. Here we find eIF5A highly expressed in diverse spermatogenic cell types. Conditional knockout of Eif5a (SKO) causes complete infertility in male mice due to round spermatid arrest. Interestingly, eIF5A deletion severely compromises chromocenter integrity in round spermatids. Proteomic profiling reveals widespread dysregulation in eIF5A-deficient round spermatids, downregulated proteins are enriched for chromatin-associated functions, likely contributing to chromocenter dysfunction. Notably, ATAC-seq analysis shows increased chromatin accessibility upon eIF5A depletion, accompanied by transcriptional dysregulation of genes critical for acrosome and manchette formation. Our data underscore that eIF5A not only regulates the translation of chromatin-organizing proteins required for chromocenter stability but also influences transcriptional regulation by modulating chromatin landscape. These findings illuminate a novel, germ cell-specific pathway coupling translational control and transcriptional regulation via chromatin reorganization.
2026-01-01 | GSE302912 | GEO
Project description:Translation initiation factor eIF5A facilitates protein synthesis and impacts diverse biological processes, yet its role in transcriptional regulation is poorly understood. Here we find eIF5A highly expressed in diverse spermatogenic cell types. Conditional knockout of Eif5a (SKO) causes complete infertility in male mice due to round spermatid arrest. Interestingly, eIF5A deletion severely compromises chromocenter integrity in round spermatids. Proteomic profiling reveals widespread dysregulation in eIF5A-deficient round spermatids, downregulated proteins are enriched for chromatin-associated functions, likely contributing to chromocenter dysfunction. Notably, ATAC-seq analysis shows increased chromatin accessibility upon eIF5A depletion, accompanied by transcriptional dysregulation of genes critical for acrosome and manchette formation. Our data underscore that eIF5A not only regulates the translation of chromatin-organizing proteins required for chromocenter stability but also influences transcriptional regulation by modulating chromatin landscape. These findings illuminate a novel, germ cell-specific pathway coupling translational control and transcriptional regulation via chromatin reorganization.
2026-01-01 | GSE302914 | GEO
Project description:Translation initiation factor eIF5A facilitates protein synthesis and impacts diverse biological processes, yet its role in transcriptional regulation is poorly understood. Here we find eIF5A highly expressed in diverse spermatogenic cell types. Conditional knockout of Eif5a (SKO) causes complete infertility in male mice due to round spermatid arrest. Interestingly, eIF5A deletion severely compromises chromocenter integrity in round spermatids. Proteomic profiling reveals widespread dysregulation in eIF5A-deficient round spermatids, downregulated proteins are enriched for chromatin-associated functions, likely contributing to chromocenter dysfunction. Notably, ATAC-seq analysis shows increased chromatin accessibility upon eIF5A depletion, accompanied by transcriptional dysregulation of genes critical for acrosome and manchette formation. Our data underscore that eIF5A not only regulates the translation of chromatin-organizing proteins required for chromocenter stability but also influences transcriptional regulation by modulating chromatin landscape. These findings illuminate a novel, germ cell-specific pathway coupling translational control and transcriptional regulation via chromatin reorganization.
2026-01-01 | GSE302913 | GEO
Project description:Breaking constraint of mammalian axial formulae
| PRJNA660363 | ENA
Project description:In higher eukaryotes centromeres often coalesce into a large intranuclear domain called the chromocenter. Chromocenters are important for the organization of pericentric heterochromatin and a disturbance of their formation results in an upregulation of repetitive elements and causes defects in chromosome segregation. Mutations in the gene encoding for the centromere associated Drosophila speciation factor HMR show very similar phenotypes suggesting a role of HMR in chromocenter architecture and function. We performed confocal and super resolution microscopy as well as proximity based biotinylation experiments of HMR, centromeric protein dCenpA and heterochromatic protein HP1a to generate a molecular map of HMR, dCenpA and HP1a bound chromatin. Our work reveals an intricate internal structure of the centromeric chromatin region, which suggests a role of HMR in separating heterochromatin from centromeric chromatin.
2020-03-23 | PXD012551 | Pride
Project description:Histone variants play crucial roles in gene expression, genome integrity and chromosome segregation. However, to what extent histone variants control chromatin architecture remains largely unknown. Here, we show that the previously uncharacterized histone variant H2A.W plays a crucial role in condensation of heterochromatin. Genome-wide profiling of all four types of H2A variants in Arabidopsis shows that H2A.W specifically associates with heterochromatin. H2A.W recruitment is independent of heterochromatic marks H3K9me2 and DNA methylation. Genetic interactions show that H2A.W acts in synergy with CMT3 mediated methylation to maintain genome integrity. In vitro, H2A.W enhances chromatin condensation through a higher propensity to make fiber-to-fiber interactions via its conserved C-terminal motif. In vivo, elimination of H2A.W causes decondensation of heterochromatin and conversely, ectopic expression of H2A.W promotes heterochromatin condensation. These results demonstrate that H2A.W plays critical roles in heterochromatin by promoting higher order chromatin condensation. Since similar H2A.W C-terminal motifs are present in other variant found in mammals and other organisms our findings impact our understanding of heterochromatin condensation in a wide variety of eukaryotic organisms. Two mRNA-seq samples, two bisulfite-seq samples, six ChIP-seq samples.
2014-07-05 | E-GEOD-50942 | biostudies-arrayexpress
Project description:Amyotrophic Lateral Sclerosis (ALS) is a rare neurodegenerative disease characterized by motor neuron dysfunction and loss, leading to progressive paralysis and death. A portion of ALS cases is caused by mutation of the proteasome shuttle factor Ubiquilin 2 (UBQLN2), but the molecular pathway leading from UBQLN2 dysfunction to neurodegenerative disease remains unclear. Here, we demonstrate a major function of UBQLN2 in regulating activity of the domesticated gag-pol retrotransposon ‘paternally expressed gene 10’ (PEG10) in human cells and tissues. UBQLN2 exclusively facilitates degradation of the frameshifted gag-pol form of PEG10 through recognition of a unique polyproline repeat. In cells, the PEG10 gag-pol protein cleaves itself in a mechanism reminiscent of retrotransposon self-processing to generate a liberated ‘nucleocapsid’ fragment, which uniquely localizes to the nucleus. Overexpression of the nucleocapsid fragment upregulates transcription of neuronal genes involved in axon remodeling, which were also affected in sporadic ALS (sALS) patient tissues. Finally, proteomics of spinal cords from ALS patients revealed that PEG10 gag-pol is significantly elevated in disease compared to healthy controls. These findings implicate the retrotransposon-like activity of PEG10 as a contributing mechanism in ALS through regulation of neuronal gene expression, and restraint of PEG10 as a primary function of UBQLN2.
2023-03-24 | PXD031964 | Pride
Project description:Coactivator condensation drives lineage specification
| PRJNA988048 | ENA