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Mitotic chromosome scaffold

ABSTRACT: Quantitative proteomics analysis of mitotic chromosome scaffold based on SILAC

ORGANISM(S): Gallus Gallus

SUBMITTER: Shinya Ohta

PROVIDER: PXD007269 | JPOST Repository | Sun Oct 07 00:00:00 BST 2018

REPOSITORIES: jPOST

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Dataset's files

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			Action	DRS
	,Arg10,Lys8_0.allSpectra.CID.ITMS.iso_0.apl	Other
	,Arg10,Lys8_0.allSpectra.CID.ITMS.iso_1.apl	Other
	,Arg10,Lys8_0.allSpectra.CID.ITMS.iso_2.apl	Other
	,Arg10,Lys8_0.allSpectra.CID.ITMS.iso_3.apl	Other
	,Arg10,Lys8_0.allSpectra.CID.ITMS.iso_4.apl	Other

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Publications

Quantitative Proteomics of the Mitotic Chromosome Scaffold Reveals the Association of BAZ1B with Chromosomal Axes.

Ohta Shinya S Taniguchi Takako T Sato Nobuko N Hamada Mayako M Taniguchi Hisaaki H Rappsilber Juri J

Molecular & cellular proteomics : MCP 20180928 2

In mitosis, chromosomes achieve their characteristic shape through condensation, an essential process for proper segregation of the genome during cell division. A classical model for mitotic chromosome condensation proposes that non-histone proteins act as a structural framework called the chromosome scaffold. The components of the chromosome scaffold, such as DNA topoisomerase IIα (TOP2A) and structural maintenance of chromosomes protein 2 (SMC2), are necessary to generate stable mitotic chromo ...[more]

PMID: 30266865

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mitotic chromosome scaffold SMC2ON vs OFF

Project description:Quantitative proteomics analysis of mitotic chromosome scaffold based on SILAC

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Podocyte injury in Fabry nephropathy

Project description:Current therapies for Fabry disease are based on reversing intra-cellular accumulation of globotriaosylceramide (Gb3) by enzyme replacement (ERT) or chaperone mediated stabilization, thereby alleviating lysosome dysfunction. However, the therapeutic effect in the regression of end-organ damage (ie. kidney damage) is limited. Ultrastructural analysis of serial human kidney biopsies showed that long-term use of ERT reduced Gb3 accumulation in podocytes but did not alter podocyte injury. A novel CRISPR-/CAS9-mediated -Galactosidase knockout podocyte cell line confirmed ERT-mediated reversal of Gb3 accumulation without resolution of lysosomal dysfunction. Transcriptomic-based connectivity mapping and SILAC-based quantitative proteomics identified alpha-synuclein (SNCA) accumulation as a key event mediating podocyte injury.

2023-04-10 | GSE186258 | GEO

Project description:Quantitative catalogue of mammalian mitotic chromosome-associated RNAs

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pSILAC mass spectrometry reveals ZFP91 as novel IMiD dependent substrate of the CRL4CRBN ligase

Project description:Thalidomide and its derivatives lenalidomide and pomalidomide (IMiDs) are effective treatments of hematologic malignancies. It was shown that IMiDs impart gain of function properties to the CUL4-RBX1-DDB1-CRBN (CRL4CRBN) ubiquitin ligase that enable binding, ubiquitination and degradation of key therapeutic targets such as IKFZ1, IKZF3 and CSNK1A1. While these substrates have been implicated as efficacy targets in multiple myeloma (MM) and 5q deletion associated myelodysplastic syndrome (del(5q)-MDS), other targets likely exist. Using a pulse-chase SILAC mass spectrometry-based proteomics approach, we demonstrate that lenalidomide induces the ubiquitination and degradation of ZFP91. We establish that ZFP91 is a bona fide IMiD dependent CRL4CRBN substrate and further show that ZFP91 harbors a zinc finger (ZnF) motif, related to the IKZF1/3 ZnF, critical for IMiD dependent CRBN binding. These findings demonstrate that single time point pulse-chase SILAC mass spectrometry-based proteomics (pSILAC-MS) is a sensitive approach for target identification of small molecules inducing selective protein degradation.

2017-03-01 | GSE94728 | GEO

IDENTIFICATION OF SUMO-2/3 MODIFIED PROTEINS ASSOCIATED WITH MITOTIC CHROMOSOMES

Project description:Sumoylation is essential for progression through mitosis, but the specific protein targets and functions remain poorly understood. In this study, we used chromosome spreads to more precisely define the localization of SUMO-2/3 to the inner-centromere and protein scaffold of mitotic chromosomes. We also developed methods to immune-purify proteins modified by endogenous, untagged SUMO-2/3 from mitotic chromosomes. Using these methods we identified 149 chromosome associated SUMO-2/3 substrates by nLC-ESI-MS/MS. Approximately one-third of the identified proteins have reported functions in mitosis. Consistent with SUMO-2/3 immunolocalization, we identified known centromere and kinetochore associated proteins, as well as chromosome scaffold associated proteins. Notably, >30 proteins involved in chromatin modification or remodeling were identified. Our results provide insights into the roles of sumoylation as a regulator of chromatin structure and other diverse processes in mitosis. Furthermore, our purification and fractionation methodologies represent an important compliment to existing approaches to identify sumoylated proteins using exogenously expressed and tagged SUMOs.

2014-10-07 | MSV000078890 | MassIVE

Comparison of Nuclear Matrix and Mitotic Chromosome Scaffold proteins in Drosophila S2 cells – Transmission of hallmarks of nuclear organization through mitosis

Project description:During open mitosis chromatin condenses to form chromosomes and decondenses post-mitotically to re-occupy their designated nuclear territory in a precisely lineage specific manner. This necessitates that features of nuclear architecture persist through mitosis. Here we present a proteomic study, which shows that the features of nuclear architecture in interphase nucleus are retained on the mitotic chromosome. Proteomic comparison was made between nuclease and high salt resistant fraction of interphase nucleus known as nuclear matrix (NuMat) and an identical biochemical fraction in the mitotic chromosome known as mitotic chromosome scaffold (MiCS). Our study elucidates that a large graction of the NuMat proteins are retained in the MiCS and possibly play an important role in maintenance of cell lineage specific features of nuclear architecture during cell division and thereby serve as components of cellular memory.

2018-07-17 | PXD008404 | Pride

E-PROT-103

Project description:Quantitative proteomics analysis of paired colorectal cancer and non-tumorigenic tissues

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Dynamic profiling of the protein life cycle in response to pathogens (protein)

Project description:Protein expression is regulated by production and degradation of mRNAs and proteins, but their specific relationships remain unknown. We combine measurements of protein production and degradation and mRNA dynamics to build a quantitative genomic model of the differential regulation of gene expression in LPS stimulated mouse dendritic cells. Changes in mRNA abundance play a dominant role in determining most dynamic fold changes in protein levels. Conversely, the preexisting proteome of proteins performing basic cellular functions is remodeled primarily through changes in protein production or degradation, accounting for over half of the absolute change in protein molecules in the cell. Thus, the proteome is regulated by transcriptional induction of novel cellular functions and remodeling of preexisting functions through the protein life cycle. Mouse primary dendritic cells were treated with LPS or mock stimulus and profiled over a 12-hour time course. Cells were grown in M-labeled SILAC media, which was replaced with H-labeled SILAC media at time 0. Aliquots were taken at 0, 0.5, 1, 2, 3, 4, 5, 6, 9, and 12 hours post-stimulation and added to equal volumes of a master mix of unlabeled (L) cells for the purpose of normalization. RNA-Seq was performed at 0, 1, 2, 4, 6, 9, and 12 hours post-stimulation.

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