Dataset Information

Interactome of Flag-TDP-43, Flag-SUMO2-TDP-43 and Flag-4xSUMO2-TDP-43

ABSTRACT: Identifications of proteins interacting with TDP-43 or linear fusions of mono- or tetra-SUMO2 with TDP-43.

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Epithelial Cell, Kidney

SUBMITTER: Jan Keiten-Schmitz

LAB HEAD: Stefan Müller

PROVIDER: PXD050322 | Pride | 2025-09-08

REPOSITORIES: Pride

ACCESS DATA

Dataset's files

Source:

			Action	DRS
	20220128_MAA_KW_EX594_Flag_IP_PCI_1.raw	Raw
	20220128_MAA_KW_EX594_Flag_IP_PCI_2.raw	Raw
	20220128_MAA_KW_EX594_Flag_IP_PCI_3.raw	Raw
	20220128_MAA_KW_EX594_Flag_wt_1xSumo2_Flag_1.raw	Raw
	20220128_MAA_KW_EX594_Flag_wt_1xSumo2_Flag_2.raw	Raw

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Publications

Induced proximity to PML protects TDP-43 from aggregation via SUMO-ubiquitin networks.

Wagner Kristina K Keiten-Schmitz Jan J Adhikari Bikash B Patra Upayan U Husnjak Koraljka K McNicoll François F Dormann Dorothee D Müller-McNicoll Michaela M Tascher Georg G Wolf Elmar E Müller Stefan S

Nature chemical biology 20250417 9

The established role of cytosolic and nuclear inclusions of TDP-43 in the pathogenesis of neurodegenerative disorders has multiplied efforts to understand mechanisms that control TDP-43 aggregation and has spurred searches for approaches limiting this process. Formation and clearance of TDP-43 aggregates are controlled by an intricate interplay of cellular proteostasis systems that involve post-translational modifications and frequently rely on spatial control. We demonstrate that attachment of ...[more]

PMID: 40246979

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Project description:Mutations in TDP-43 (an RNA binding protein) are known to cause amyotrophic lateral sclerosis (ALS). Previously, our group and several other studies showed that TDP-43 binds to several RNA targets in the mammalian CNS. ALS causing mutations in the C-terminal region of TDP-43 that is involved in splicing regulation may lead to aberrant splicing of several RNA transcripts. The main aim of this study is to identify the effect of an ALS causing mutation on the splicing regulation of previously known targets of TDP-43. Mice overexpressing a mutant human TDP-43 (hTDP-43) gene were obtained from The Jackson Laboratory (strain name - B6;CB-Tg(Prnp-TARDBP*A315T) 95Balo/J; Stock no:010700). Mutant hTDP43 was expressed under the control of a prion protein promoter that drives the expression mainly in the mouse CNS and the male transgenic mice developed symptoms around 12 weeks of age while the female mice develop symptoms approximately 20 weeks of age. Therefore, Tg animals that are 50 days old were considered pre-symptomatic and 100 days old (Tg) animals were considered to be in the post-symptomatic stages of the disease for exon array experiments. Age and sex matched pre and post-symptomatic transgenic animals and their wild type littermates were euthanised by cervical dislocation and tissues (brain and spinal cord) were harvested immediately for total RNA isolation experiments (n=3 per group). 200 ng of total RNA from transgenic TDP-43 mice and wild type animals was converted to cDNA and then amplified using the Applause WT-Amp Plus ST kit (NuGEN). Amplified cDNA was then fragmented and biotin labeled using the Encore Biotin Module kit (NuGEN) according to the manufacturer's instruction manual. Labelled cDNA was then hybridised onto Affymetrix GeneChip Exon 1.0 ST arrays in a hybridisation oven at 45 degrees C for 20 hours at 60rpm. After hybridization, washing and staining of the arrays were carried out using Affymetrix fluidics station 450 followed by scanning using GeneChip scanner. GeneChip Command Console Software (AGCC) controlled both the fluidics station and the scanner. CEL files generated by AGCC were uploaded onto Partek software and the data analysis was carried out using the exon array analysis workflow. Exon 1.0 ST arrays contain many more probes, which are classified into three major types based on their source. They are Core, extended and full probe set annotation. Core annotation refers the probe sets that are the most reliable of the three and is derived based on evidences from Refseq and GenBank. Extended annotations refer to probe sets that are generated based on EST sequences, ENSEMBL gene collections and other databases including those used for generating core probe sets. The full annotation refers to probe sets that are purely based on computational predictions. Core probe set annotation, unlike the extended or full annotation excludes the speculative probes reducing the incidence of false positives and was employed for exon array analysis. Alt-splice Anova, a statistical tool available in Partek was used for identifying novel alternative splicing events.