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Identification of RPA1 interactome in mouse liver tissue

ABSTRACT: To examine the molecular mechanisms by which RPA1 regulates transcription in liver, we conducted immunoprecipitation followed by mass spectrometry to characterize RPA1-associated proteins in mouse liver.

INSTRUMENT(S): LTQ Orbitrap Elite

ORGANISM(S): Mus Musculus (mouse)

TISSUE(S): Liver

SUBMITTER: Qi Yin

LAB HEAD: Yuxin Yin

PROVIDER: PXD021529 | Pride | 2022-07-19

REPOSITORIES: Pride

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			Action	DRS
	CTR_M2_64.raw	Raw
	CTR_M2_65.raw	Raw
	Multiconsensusfrom4Reports.xlsx	Xlsx
	RPA1_M2_64.raw	Raw
	RPA1_M2_65.raw	Raw

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Publications

RPA1 controls chromatin architecture and maintains lipid metabolic homeostasis.

Yin Qi Q Li Yang Y Zhou Zhe Z Li Xiang X Li Minghao M Liu Chengyang C Dong Di D Wang Guangxi G Zhu Minglu M Yang Jingyi J Jin Yan Y Guo Limei L Yin Yuxin Y

Cell reports 20220701 2

Non-alcoholic fatty liver disease (NAFLD) is the most common liver disease, with a prevalence of 25% worldwide. However, the underlying molecular mechanism involved in the development and progression of the NAFLD spectrum remains unclear. Single-stranded DNA-binding protein replication protein A1 (RPA1) participates in DNA replication, recombination, and damage repair. Here, we show that Rpa1<sup>+/-</sup> mice develop fatty liver disease during aging and in response to a high-fat diet. Liver-sp ...[more]

PMID: 35830798

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Identification of PAC1 interactome in activated T cells

Project description:To examine the molecular mechanisms by which PAC1 suppresses T cell response to antigen, we conducted immunoprecipitation followed by mass spectrometry to characterize PAC1-associated proteins in activated T cells

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Antagonistic roles of canonical and alternative-RPA in disease-associated tandem CAG repeat instability

Project description:Ongoing CAG expansions in Spinocerebellar ataxia type 1 (SCA1) and Huntington disease (HD) brains exacerbate disease. Expansions involve aberrant repair of mutagenic slipped-DNAs, formed from single-stranded DNAs. Whether singlestranded DNA-binding proteins prevent or facilitate expansions is unknown. We assessed canonical RPA (RPA1-RPA2-RPA3) and Alternative-RPA (RPA1-RPA4- RPA3), containing primate-specific RPA4. RPA is essential for all DNA metabolism. Alt-RPA has undefined functions. Alt-RPA is upregulated 10-fold in HD and SCA1 patient brains. RPA enhances, while Alt-RPA blocks, correct repair of slipped-CAGs. RPA, but not Alt-RPA, efficiently binds and melts slipped-DNAs. RPA enhances, while Alt-RPA blocks, removal of excess slipped-DNAs by FAN1 nuclease. Protein-protein interactomes reveal unique and shared partners of RPA and Alt-RPA, including expansion-driving proteins. RPA-overexpression in SCA1 mice inhibits CAG expansions in brains, rescuing neuron morphology and motor phenotypes. Modulating repeat mutations is one example involving antagonistic Alt-RPA↔RPA interactions, illuminating questions as to which RPA-mediated processes are also modulated by AltRPA.

2023-10-13 | PXD044158 | Pride

Human SMARCA5 interactome in transgenic SMARCA5 mouse model

Project description:We hypothesize that the ISWI ATPase Smarca5 plays a role in hematopoietic stem cell development via its interaction partners, and to study the role, we used a mouse model with transgenic expression of SMARCA5 coupled with mass spectrometry analysis. The study uses transgenic SMARCA5 mouse model with conditional hypomorphic allele (lower expression on protein level compared to controls) incorporated into Rosa26 locus, transgenic allele uses endogenous Rosa26 promoter. The transgenic human SMARCA5 protein has a FLAG tag at its C-terminus, which allows specific immunoprecipitation and also differentiation from the endogenous protein (human and mouse SMARCA5 are almost identical at the protein level). To ensure the highest possible expression of the transgenic allele, we used a model that also had one endogenous Smarca5 allele deleted. Various organs (thymus, spleen, brain, kidney, liver, testes, muscle, fetal liver) were isolated from transgenic mice, lysed and then immunoprecipitated using anti-FLAG antibody. The immunoprecipitates were then analyzed using mass spectrometry to determine SMARCA5 interactomes in various tissues. Transgenic human SMARCA5 was confirmed to form all the expected complexes and capable of replacing the functions of the mouse protein. For details, see the publication of Turkova et al. 2024 in Communications Biology.

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RPA1 controls chromatin architecture and maintains lipid metabolic homeostasis

Project description:Replication protein A1 (RPA1) is a single-stranded DNA binding protein that is known to participate in DNA replication, recombination and damage repair. However, little is known about RPA1’s role in controlling chromatin architecture and gene transcription. Further, physiological functions of RPA1 in mouse tissues still remain exclusive. Here we show that Rpa1 heterozygous mice developed age-depended fatty liver disease and are more susceptible to hepatic steatosis in response to high-fat diet. Liver specific deletion of Rpa1 impairs fatty acid oxidation, leading to hepatic steatosis and high incidence of hepatocellular carcinoma. Transcriptome analysis identified down-regulation of fatty acid oxidation related genes. Cleavage Under Targets and Tagmentation (CUT&Tag) and Assay for transposase-accessible chromatin using sequencing (ATAC-seq) revealed that RPA1 binds and regulates chromatin accessibility in regulatory regions of a group of genes involved in lipid metabolism in liver. Further, down-regulation of RPA1 was found in patients with fatty liver disease. Thus, our results not only established that RPA1 is critical controller of chromatin architecture and regulator of gene transcription, but also provided new insights into the epigenetic mechanism of fatty liver disease, which could inform future therapy.

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Dual Binding of Chromomethylase Domains to H3K9me2-containing Nucleosomes Mediates DNA Methylation in PlantsM-BM-

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Identification of proteins that form complexes with SerpinA1 by LC-MS/MS

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