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Extensive long-range polycomb interactions and weak compartmentalization are hallmarks of human neuronal 3D genome

ABSTRACT: Extensive long-range polycomb interactions and weak compartmentalization are hallmarks of human neuronal 3D genome

PROVIDER: PRJNA956258 | ENA |

REPOSITORIES: ENA

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Extensive long-range polycomb interactions and weak compartmentalization are hallmarks of human neuronal 3D genome

Project description:Chromatin architecture regulates gene expression and shapes cellular identity, particularly in neuronal cells. Specifically, polycomb group (PcG) proteins enable establishment and maintenance of neuronal cell type by reorganizing chromatin into repressive domains that limit the expression of fate-determining genes and sustain distinct gene expression patterns in neurons. Here, we map the 3D genome architecture in neuronal and non-neuronal cells isolated from the Wernicke's area of four human brains and comprehensively analyze neuron-specific aspects of chromatin organization. We find that genome segregation into active and inactive compartments is greatly reduced in neurons compared to other brain cells. Furthermore, neuronal Hi-C maps reveal strong long-range interactions, forming a specific network of PcG-mediated contacts in neurons that is nearly absent in other brain cells. These interacting loci contain developmental transcription factors with repressed expression in neurons and other mature brain cells. But only in neurons, they are rich in bivalent promoters occupied by H3K4me3 histone modification together with H3K27me3, which points to a possible functional role of PcG contacts in neurons. Importantly, other layers of chromatin organization also exhibit distinct structure in neurons, which corroborates with increased cohesin levels in neurons and therefore might be attributed to elevated neuronal loop extrusion activity.

2024-03-26 | GSE229816 | GEO

Attenuated chromatin compartmentalization in meiosis and its maturation in sperm development

Project description:Germ cells manifest a unique gene expression program and regain totipotency in the zygote. Here, we perform Hi-C analysis to examine 3D chromatin organization in male germ cells during spermatogenesis. We show that the highly compartmentalized 3D chromatin organization characteristic of interphase nuclei is attenuated in meiotic prophase. Meiotic prophase is predominated by short-range intrachromosomal interactions that represent a condensed form akin to that of mitotic chromosomes. However, unlike mitotic chromosomes, meiotic chromosomes display weak genomic compartmentalization, weak topologically associating domains, and localized point interactions in prophase. In postmeiotic round spermatids, genomic compartmentalization increases and gives rise to the strong compartmentalization seen in mature sperm. The X chromosome lacks domain organization during meiotic sex-chromosome inactivation. We propose that male meiosis occurs amid global reprogramming of 3D chromatin organization and that strengthening of chromatin compartmentalization takes place in spermiogenesis to prepare the next generation of life.

2019-02-18 | GSE119805 | GEO

A molecular mechanism for compartmentalization and silencing of chromatin domains at the nuclear lamina

Project description:This SuperSeries is composed of the following subset Series: GSE35777: A molecular mechanism for compartmentalization and silencing of chromatin domains at the nuclear lamina [Tiling Array] GSE36048: A molecular mechanism for compartmentalization and silencing of chromatin domains at the nuclear lamina [ChIP-seq] Refer to individual Series

2012-02-24 | E-GEOD-36049 | biostudies-arrayexpress

Polycomb-dependent differential chromatin compartmentalization determines gene co-regulation in Arabidopsis

Project description:Polycomb-dependent differential chromatin compartmentalization determines gene co-regulation in Arabidopsis

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Effect of extremely low frequency weak magnetic fields

Project description:We used AML12 cells exposured with pulsed extremely low frequency weak magnetic fields for 4 msec at increasing frequency of 1, 2, 3, 4, 5, 6, 7, and 8 Hz for 1 sec each. The 1-to-8 Hz pulses over 8 sec were repeated indefinitely. Peak magnetic intensity was 100 mG. AML12 cells were incubated for 1 h under extremely low frequency weak magnetic fields.

2022-05-05 | GSE166811 | GEO

Transcriptional response to weak organic acids in chemostat cultures of Saccharomyces cerevisiae

Project description:Raw expression values (CHP data) for transcriptional profiling of the response of Saccharomyces cerevisiae to challenges with various weak organic acids Keywords: response to weak organic acids

2007-02-27 | GSE5926 | GEO

RNA damage compartmentalization by DHX9 granules

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Effect of extremely low frequency weak magnetic fields

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Prp4 Kinase Grants the License to Splice: Control of Weak Splice Sites during Spliceosome Activation

Project description:The genome of the fission yeast Schizosaccharomyces pombe encodes 17 kinases that are essential for cell growth. These include the cell-cycle regulator Cdc2, as well as several kinases that coordinate cell growth, polarity, and morphogenesis during the cell cycle. In this study, we further characterized another of these essential kinases, Prp4, and showed that the splicing of many introns is dependent on Prp4 kinase activity. For detailed characterization, we chose the genes res1 and ppk8, each of which contains one intron of typical size and position. Splicing of the res1 intron was dependent on Prp4 kinase activity, whereas splicing of the ppk8 intron was not. Extensive mutational analyses of the 5’ splice site of both genes revealed that proper transient interaction with the 5’ end of snRNA U1 governs the dependence of splicing on Prp4 kinase activity. Proper transient interaction between the branch sequence and snRNA U2 was also important. Therefore, the Prp4 kinase is required for recognition and efficient splicing of introns displaying weak exon1/5’ splice sites and weak branch sequences.

2015-12-01 | GSE75517 | GEO

Spatial Compartmentalization at the Nuclear Periphery Characterized by Genome-wide Mapping

Project description:How gene positioning to the nuclear periphery regulates transcription remains largely unclear. We have previously observed the differential compartmentalization of transcription factors and histone modifications at the nuclear periphery in mouse C2C12 myoblasts. Here, we have integrated high throughput DNA sequencing into the DNA adenine methyltransferase identification (DamID) assay, and have identified ~15, 000 sequencing-based Lamina-Associated Domains (sLADs) in mouse 3T3 fibroblasts and C2C12 myoblasts. These genomic regions range from a few kb to over 1 Mb and cover ~30% of the genome, and are spatially proximal to the nuclear lamina (NL). Active histone modifications such as H3K4me2, H3K9Ac, H3K36me3 and H3K79me2 are all localized away from the nuclear periphery microscopically, and distributed predominantly out of sLADs genome-wide. Therefore, the spatial compartmentalization of active histone modifications likely characterizes a major portion of chromatin at the nuclear periphery in mammalian cells. Genomic regions around transcription start sites of expressed sLAD genes display reduced associations with the NL and possess active histone modifications; in contrast, gene bodies of expressed sLAD genes possess very low levels of active histone modifications. Our genome-wide analyses of NL-associated chromatin have enabled functional and mechanistic dissections of gene positioning on transcription regulation. generate DamID maps of genome-NL interaction for mouse 3T3 fibroblasts and C2C12 myoblasts

2013-10-30 | E-GEOD-41583 | biostudies-arrayexpress

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