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Phase-separated nuclear bodies of nucleoporin fusions promote condensation of MLL1/CRM1 and rearrangement of 3D genome structure

ABSTRACT: Phase-separated nuclear bodies of nucleoporin fusions promote condensation of MLL1/CRM1 and rearrangement of 3D genome structure

PROVIDER: PRJNA917305 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR22951837_1.fastq.gz	Fastqsanger.gz
	SRR22951837_2.fastq.gz	Fastqsanger.gz
	SRR22951838_1.fastq.gz	Fastqsanger.gz
	SRR22951838_2.fastq.gz	Fastqsanger.gz
	SRR22951839_1.fastq.gz	Fastqsanger.gz

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Phase-separated nuclear bodies of nucleoporin fusions promote condensation of MLL1/CRM1 and rearrangement of 3D genome structure

Project description:We performed Hi-C to analyze the effect of NUP98-HOXA9 fusion on 3D chromatin structure of mouse embryonic stem cells (mESCs). Our analysis revealed that NUP98-HOXA9 induced a drastic alteration of high-order genome structure in a phase separation-dependent manner.

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Genome-wide mapping of MLL1, CRM1, and NUP-fusion derivatives in human leukemia or mouse ES cell lines

Project description:We used ChIP-seq to examine the genome-wide binding of MLL1, CRM1, and NUP-fusions in human leukemia or mouse ES cell lines. Our analysis revealed that MLL1, CRM1, and NUP-fusions are preferentially co-localized on the genome.

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Gene expression profiling of human DLD-1 cells after block of CRM1 receptor with Leptomycin B inhibitor.

Project description:We used RNA-seq approach to define a contribution of mammalian export receptor CRM1 (Chromosomal Maintenance 1 or Exportin 1) into Tpr-dependent export of RNA molecules from the nucleus to the cytoplasm. Basket nucleoporin Tpr was AID-tagged and depleted through Auxin Induced Degradation system. Loss of Tpr led to rapid changes in gene expression profile, and gene expression changes were compared to GANP, NXF1, RanGAP1 (GSE132363) and CRM1 loss and inhibition, respectively. Altogether, we found a minimal subset of RNAs that are controlled both by Tpr nucleoporin and CRM1 receptor.

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Project description:RIME/ChIP-MS analysis for Nucleoporin, Nup214 and CRM1. Rapid Immunoprecipitation Mass spectrometry of Endogenous proteins was used.

2023-07-26 | PXD042027 | JPOST Repository

Genome-wide mapping of Nup98HoxA9- and Crm1-binding sites in ES cell lines.

Project description:We used ChIP-seq to examine the genome-wide binding of Nup98-HoxA9 and Crm1 in ES cells. Our analysis revealed that Nup98-HoxA9 is highly and preferentially targeted to specific chromatin sites, particularly near Hox cluster regions where the export factor Crm1 is originally prebound. chromatin immunoprecipitation

2016-01-04 | E-GEOD-68783 | biostudies-arrayexpress

Exportin Crm1 is repurposed as a docking protein to generate microtubule organizing centers at the nuclear pore

Project description:Non-centrosomal microtubule organizing centers (MTOCs) are important for microtubule organization in many cell types. In fission yeast Schizosaccharomyces pombe, the protein Mto1, together with partner protein Mto2 (Mto1/2 complex), recruits the g-tubulin complex to multiple non-centrosomal MTOCs, including the nuclear envelope (NE). Here, we develop a comparative-interactome mass spectrometry approach to determine how Mto1 localizes to the NE. Surprisingly, we find that Mto1, a constitutively cytoplasmic protein, docks at nuclear pore complexes (NPCs), via interaction with exportin Crm1 and cytoplasmic FG-nucleoporin Nup146. Although Mto1 is not a nuclear export cargo, it binds Crm1 via a nuclear export signal-like sequence, and docking requires both Ran in the GTP-bound state and Nup146 FG repeats. In addition to determining the mechanism of MTOC formation at the NE, our results reveal a novel role for Crm1 and the nuclear export machinery in the stable docking of a cytoplasmic protein complex at NPCs.

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Expression analysis on Mll1+/+ and Mll1-/- MEFs

Project description:Global analysis of H3K4 methylation defines MLL family member targets and points to a role for MLL1-mediated H3K4 methylation in the regulation of transcriptional initiation by RNA polymerase II A common landmark of activated genes is the presence of trimethylation on lysine 4 of histone H3 (H3K4) at promoter regions. The Set1/COMPASS was the founding member and the only H3K4 methylases in S. cerevisiae, however, in mammals at least six H3K4 methylases Set1A/B and MLL1-4 are found in COMPASS-like complexes capable of methylating H3K4. To gain further insight into the different roles and functional targets for the H3K4 methylases, we have undertaken a genome-wide analysis of H3K4 methylation pattern in wild-type Mll1+/+ and Mll1-/- mouse fibroblasts (MEFs). We found that Mll1 is required for the H3K4 trimethylation of less than 5% of promoters carrying this modification. Many of these genes, which include developmental regulators such as Hox genes show decreased levels of RNA polymerase II recruitment and expression concomitant with the loss of H3K4 methylation. Although Mll1 is only required for the methylation of a subset of Hox genes, Menin, a component of the Mll1 and Mll2 complexes, is required for the overwhelming majority of H3K4 methylation at Hox loci. However, the loss of MLL3/4 and/or the Set1 complexes have little to no effect on the Hox loci H3K4 methylation or expression levels in these MEFs. Together these data provide insight into redundancy and specialization of COMPASS-like complexes in mammals and provide evidence on a possible role for Mll1-mediated H3K4 methylation in the regulation of transcriptional initiation. Expression arrays were done with Mll1+/+ and Mll1-/- mouse embryonic fibroblasts. Four replicates were done (dyes were swapped). DNA was hybridized to Agilent Mouse Whole Genome Expression Arrays (4x44k).

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Project description:Genome-wide mapping of MLL1, CRM1, and NUP-fusion derivatives in human leukemia or mouse ES cell lines

| PRJNA837475 | ENA

Genome-wide mapping of Nup98HoxA9- and Crm1-binding sites in ES cell lines.

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CRM1 Exportome and nucleocytoplasmic partition

Project description:CRM1 mediates one of the major nuclear export pathways with the broadest range of cargoes. So far, more than 100 structurally and functionally diverse CRM1 cargoes have been described. We employed affinity purification mass spectrometry for in depth characterization of CRM1 "exportome" in three model systems and we identified surprisingly large numbers, namely >700 export substrates from the yeast S. cerevisiae, ≈ 1000 from Xenopus oocytes and >1050 from human cells.I. Futher, we quantified the partitioning of ≈9600 proteoforms between nucleus and cytoplasm of Xenopus oocytes.

2016-01-04 | PXD002899 | Pride

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