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Nucleoporin Elys attaches peripheral chromatin to the nuclear pores in interphase nuclei

ABSTRACT: Nucleoporin Elys attaches peripheral chromatin to the nuclear pores in interphase nuclei

PROVIDER: PRJNA907263 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR22478785_1.fastq.gz	Fastqsanger.gz
	SRR22478785_2.fastq.gz	Fastqsanger.gz
	SRR22478786_1.fastq.gz	Fastqsanger.gz
	SRR22478786_2.fastq.gz	Fastqsanger.gz
	SRR22478787_1.fastq.gz	Fastqsanger.gz

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Nucleoporin Elys attaches peripheral chromatin to the nuclear pores in interphase nuclei

Project description:Nucleoporin Elys attaches peripheral chromatin to the nuclear pores in interphase nuclei

| PRJNA906081 | ENA

Nucleoporin Elys attaches peripheral chromatin to the nuclear pores in interphase nuclei

Project description:Transport of macromolecules through the nuclear envelope (NE) is mediated by nuclear pore complexes (NPCs) consisting of nucleoporins (Nups). Elys/Mel-28 is the Nup that binds and connects the decondensing chromatin with the reassembled NPCs at the end of mitosis. Whether Elys links chromatin with the NE during interphase is unknown. Using DamID-seq, we identified Elys binding sites in Drosophila late embryos and divided them into those associated with nucleoplasmic or with NPC-linked Elys. These Elys binding sites are located within active or inactive chromatin, respectively. Strikingly, Elys knockdown in S2 cells results in peripheral chromatin displacement from the NE, in decondensation of NE-attached chromatin, and in derepression of genes within. It also leads to slightly more compact active chromatin regions. Our findings indicate that NPC-linked Elys, together with the nuclear lamina, anchors peripheral chromatin to the NE, whereas nucleoplasmic Elys decompacts active chromatin.

2024-06-28 | GSE218886 | GEO

Nucleoporin Elys attaches peripheral chromatin to the nuclear pores in interphase nuclei

Project description:Transport of macromolecules through the nuclear envelope (NE) is mediated by nuclear pore complexes (NPCs) consisting of nucleoporins (Nups). Elys/Mel-28 is the Nup that binds and connects the decondensing chromatin with the reassembled NPCs at the end of mitosis. Whether Elys links chromatin with the NE during interphase is unknown. Using DamID-seq, we identified Elys binding sites in Drosophila late embryos and divided them into those associated with nucleoplasmic or NPC-linked Elys. These Elys binding sites are located within active or inactive chromatin, respectively. Strikingly, Elys knockdown in S2 cells results in peripheral chromatin displacement from the NE, in decondensation of NE-attached chromatin, and in derepression of genes within. It also leads to slightly more compact active chromatin regions. Our findings indicate that NPC-linked Elys, together with the nuclear lamina, anchors peripheral chromatin to the NE, whereas nucleoplasmic Elys decompacts active chromatin.

2024-07-01 | GSE219152 | GEO

Deletion of nucleoporin Seh1 impaired neurogenesis through transcriptional regulation

Project description:Nucleoporin Seh1 has been involved in gene regulation. To dissect nucleoporin's direct regulated genes, we performed chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for nucleoporin Seh1 in neural stem cells.

2022-06-09 | GSE205508 | GEO

Deletion of nucleoporin Seh1 impaired neurogenesis through transcriptional regulation (ChIP-Seq)

Project description:Nucleoporin Seh1 and chromodomain helicase DNA binding protein 4 have been involved in gene regulation. To dissect direct regulated genes, we performed chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for nucleoporin Seh1 or chromodomain helicase DNA binding protein 4 in neural stem cells.

2023-05-29 | GSE233613 | GEO

Nuclear Pores Assemble from Nucleoporin Condensates During Oogenesis.

Project description:The molecular events that direct nuclear pore complex (NPC) assembly toward nuclear envelopes have been conceptualized in two pathways that occur during mitosis or interphase, respectively. In gametes and embryonic cells, NPCs also occur within stacked cytoplasmic membrane sheets, termed annulate lamellae (AL), which serve as NPC storage for early development. The mechanism of NPC biogenesis at cytoplasmic membranes remains unknown. Here, we show that during Drosophila oogenesis, Nucleoporins condense into different precursor granules that interact and progress into NPCs. Nup358 is a key player that condenses into NPC assembly platforms while its mRNA localizes to their surface in a translation-dependent manner. In concert, Microtubule-dependent transport, the small GTPase Ran and nuclear transport receptors regulate NPC biogenesis in oocytes. We delineate a non-canonical NPC assembly mechanism that relies on Nucleoporin condensates and occurs away from the nucleus under conditions of cell cycle arrest.

| S-EPMC6838685 | biostudies-literature

Chromatin associations in Arabidopsis interphase nuclei.

Project description:The arrangement of chromatin within interphase nuclei seems to be caused by topological constraints and related to gene expression depending on tissue and developmental stage. In yeast and animals it was found that homologous and heterologous chromatin association are required to realize faithful expression and DNA repair. To test whether such associations are present in plants we analyzed Arabidopsis thaliana interphase nuclei by FISH using probes from different chromosomes. We found that chromatin fiber movement and variable associations, although in general relatively seldom, may occur between euchromatin segments along chromosomes, sometimes even over large distances. The combination of euchromatin segments bearing high or low co-expressing genes did not reveal different association frequencies probably due to adjacent genes of deviating expression patterns. Based on previous data and on FISH analyses presented here, we conclude that the global interphase chromatin organization in A. thaliana is relatively stable, due to the location of its 10 centromeres at the nuclear periphery and of the telomeres mainly at the centrally localized nucleolus. Nevertheless, chromatin movement enables a flexible spatial genome arrangement in plant nuclei.

| S-EPMC4230181 | biostudies-literature

Distribution of Drosophila insulator proteins during interphase and mitosis

Project description:Here we compare the distribution of insulator proteins during interphase and mitosis. We performed ChIP-seq analysis on purified populations of interphase and mitotic Kc cells, using antibodies against CP190, dCTCF, BEAF, and Su(Hw). Examination of 4 different insulator proteins during interphase and mitosis

2013-01-21 | E-GEOD-32584 | biostudies-arrayexpress

Condensin plays a role in both interphase nuclei and premature chromosome condensation

Project description:Purpose: to identify how condensin I removal affects gene expression globally. Methods: Chicken DT40 CAP-H KO cells were treated with or without dox for 36 h. Total RNA samples were extracted and subjected to sequencing using an Illumina Hiseq2000 platform. Library preparation and Illumina sequencing were performed by Macrogen (South Korea). The sequence tags were spliced-mapped onto the chicken genome galGal4 using Tophat and Bowtie2 following quality test using FASTQC. Differential expression of genes was analyzed using the Bioconductor v2.3 package edgeR v3.2.3. Tag enrichment in NCBI RefSeq genes was calculated between dox-treated and untreated cells using edgeR exact test with tag-wise dispersion estimation. Results: We identified a total of 3798 genes to be differentially expressed in G1 condensin I-depleted chicken DT40 cells: 2495 down regulated and 1303 up regulated. Conclusions: Removal of CAP-H leads to significant misregulation of gene expression, suggesting a key role for condensin I in transcription during interphase. Total RNA profiles of CAP-H KO cells with or without Dox were generated by sequencing using Illumina Hiseq2000 platform.

2017-05-03 | E-GEOD-74892 | biostudies-arrayexpress

Distribution of Drosophila insulator proteins during interphase and mitosis

2013-01-21 | GSE32584 | GEO