Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

13 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Expression data from control and Mbd4 KO CH12 cells that were activated with CIT for 24 hours.

ABSTRACT: AID-dependent U/G mismatches in S DNA are converted by BER and MMR DNA pathways into double-stranded breaks that are required for optimal CSR in activated B cells. Deficits in MMR proteins, MSH2, MLH1, and PMS2 result in lower CSR frequencies that are coupled with impaired DSB formation. MBD4 interacts with MLH1 and has been postulated to coordinate mismatch repair of U/G. Deletions of Mbd4 targeting the 5' end of the gene in mice do not affect CSR . However, Mbd4 transcription is complex, with the propensity to create alternative transcripts, including residual transcription leading to to truncated protein expression that complicates ananlysis in these mice. We describe a novel function of MBD4 housed in the C-terminus that is critical for DSB formation, which shares several characteristics with MMR . We conclude that the 3' end of the Mbd4 gene positively contributes to CSR and likely intersects the MMR pathway. 2 independent samples for each control and Mbd4 KO group

ORGANISM(S): Mus musculus

SUBMITTER: Amy Kenter

PROVIDER: E-GEOD-51559 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Expression data from control and Mbd4 KO CH12 cells that were activated with CIT for 24 hours.

Project description:AID-dependent U/G mismatches in S DNA are converted by BER and MMR DNA pathways into double-stranded breaks that are required for optimal CSR in activated B cells. Deficits in MMR proteins, MSH2, MLH1, and PMS2 result in lower CSR frequencies that are coupled with impaired DSB formation. MBD4 interacts with MLH1 and has been postulated to coordinate mismatch repair of U/G. Deletions of Mbd4 targeting the 5' end of the gene in mice do not affect CSR . However, Mbd4 transcription is complex, with the propensity to create alternative transcripts, including residual transcription leading to to truncated protein expression that complicates ananlysis in these mice. We describe a novel function of MBD4 housed in the C-terminus that is critical for DSB formation, which shares several characteristics with MMR . We conclude that the 3' end of the Mbd4 gene positively contributes to CSR and likely intersects the MMR pathway.

2013-12-19 | GSE51559 | GEO

Gene expression analysis of B cell lymphomas from representative IÂµHABcl6, IÂµHABcl6 Ung-/- Msh2-/-, and IÂµHABcl6 Msh2-/- mouse models.

Project description:Somatic hypermutation (SHM) and class switch recombination (CSR) of immunoglobulin (Ig) genes are genomic modification events that occur in germinal center (GC) B cells and are initiated through deamination of cytidine to uracil by activation induced cytidine deaminase (AID). Resulting uracil-guanine (U-G) mismatches are subsequently processed by low-fidelity base-excision (BER) and mismatch repair (MMR) pathways to yield mutations and DNA strand lesions. Although off-target AID activity also contributes to oncogenic point mutations and chromosome translocations associated with B cell lymphomas, the role of downstream AID-associated DNA repair pathways in the pathogenesis of these lymphomas is unknown. Here, we show that simultaneous BER and MMR deficiency causes genomic instability and a shorter latency to the development of a BCL6-driven GC B cell lymphoma. In contrast, loss of BER alone is highly protective against B cell transformation while loss of MMR fosters the development of a variety of malignancies. These findings lend insight into a complex interplay between AID-associated BER and MMR pathways that produces a net protective effect against GC B cell lymphomagenesis. Representative B cell lymphomas from 3 IÂµHABcl6, 6 IÂµHABcl6 Ung-/- Msh2-/-, and 5 IÂµHABcl6 Msh2-/- mice were analyzed in this study. Total RNA was extracted from frozen tumor cells and processed according to Illumina standard protocols.

2015-12-08 | E-GEOD-48304 | biostudies-arrayexpress

MBD4 loss results in global reactivation of promoters and retroelements with low methylated CpG density.

Project description:Inherited defects in the base-excision repair gene MBD4 predispose individuals to adenomatous polyposis and colorectal cancer, which is characterized by an accumulation of C>T transitions resulting from spontaneous deamination of 5’-methylcytosine. Despite its significance, this DNA repair pathway is still poorly understood. Here we show that the protein MBD4 is required for DNA methylation maintenance and G/T mismatch repair. Transcriptome and methylome analyses reveal a genome-wide hypomethylation of promoters, gene bodies and repetitive elements in the absence of MBD4 in vivo. Methylation mark loss is accompanied by a broad transcriptional derepression phenotype affecting promoters and retroelements with low methylated CpG density. MBD4 in vivo forms a complex with the mismatch repair proteins (MMR), which exhibits high bi-functional glycosylase/AP-lyase endonuclease specific activity towards methylated DNA substrates containing a G/T mismatch. Experiments using recombinant proteins reveal that the association of MBD4 with the MMR protein MLH1 is required for this activity. The described data identify MBD4 as an enzyme specifically designed to repair deaminated 5-methylcytosines and illustrates how MBD4 functions in normal and pathological conditions.

2022-01-10 | GSE84497 | GEO

MBD4 loss results in global reactivation of promoters and retroelements with low methylated CpG density.

2022-01-10 | GSE84319 | GEO

MBD4 loss results in global reactivation of promoters and retroelements with low methylated CpG density.

2022-01-10 | GSE84318 | GEO

Gene expression analysis of B cell lymphomas from representative IµHABcl6, IµHABcl6 Ung-/- Msh2-/-, and IµHABcl6 Msh2-/- mouse models.

2015-12-08 | GSE48304 | GEO

DNA mismatch repair activity of MutLα is regulated by CK2-dependent phosphorylation of MLH1 (S477)

Project description:MutLα, a heterodimer consisting of MLH1 and PMS2, is a key player of DNA mismatch repair (MMR), yet little is known about its regulation. In this study, we used mass spectrometry to identify phosphorylated residues within MLH1 and PMS2. The most frequently detected phosphorylated amino acid was serine 477 of MLH1. Isolation of nuclear and cytoplasmic fractions showed that p-MLH1S477 remains predominantly in the cytoplasm. Pharmacological treatment indicates that Casein Kinase II (CK2) could be responsible for the phosphorylation of MLH1 at serine 477 in vivo. In vitro kinase assay verified MLH1 as a substrate of CK2. Most importantly, using in vitro MMR assay we could demonstrate that p-MLH1S477 lost MMR activity while the activity of MLH1S477A, which could not be phosphorylated at position S477, was not modified. In summary, we identified that post-translational phosphorylation of MLH1 by CK2 at amino acid position 477 can switch off MMR activity in vitro. Since CK2 is overexpressed in many tumors and is able to inactivate MMR by phosphorylation of MLH1, the new mechanism here described could have an important impact on tumors overactive in CK2.

2018-08-28 | PXD009524 | Pride

DNA mismatch repair activity of MutLalpha is regulated by CK2-dependent phosphorylation of MLH1

Project description:Mass spectrometry based PTM phosphorylation analysis to study regulation mechanism of MUTL alpha, a heterodimer consisting of MLH1 and PMS2 and a key player in DNA mismatch repair (MMR). It could be demonstrated that phosphorylation of MLH1 by Casein Kinase II (CK2) at amino acid position 477 can switch off MMR activity in vitro.

2018-08-29 | PXD009026 | Pride

The MLH1 c.-27C>A and c.85G>T variants are borne on a European ancestral haplotype which underlies an autosomal dominant form of MLH1 epimutation.

Project description:Lynch syndrome, caused by germline heterozygous mutations of the DNA mismatch repair genes MLH1, MSH2, MSH6 and PMS2, or deletions affecting the EPCAM gene upstream of MSH2, is characterized by a predisposition to early-onset colorectal and additional extracolonic cancers. An alternative but rare cause of Lynch syndrome is a constitutional epimutation of MLH1, which is characterized by promoter methylation and transcriptional silencing of a single allele in normal tissues. Worldwide, five families with autosomal dominant transmission of a constitutional MLH1 epimutation linked to an MLH1 haplotype with two single nucleotide variants (c.-27C>A and c.85G>T) have been identified. Array-based genotyping using Affymetrix SNP 6.0 data in four of these families revealed a shared haplotype extending across a ≤2.6 Mb region of chromosome 3p22 encompassing MLH1 and additional flanking genes, indicating common ancestry. Genomic DNA from 5 carriers of the c.-27C>A and c.85G>T variants was hybridized on Affymetrix SNP6.0 array according to manufacturer's procedures

2013-04-01 | E-GEOD-45149 | biostudies-arrayexpress

Loss of Msh2 and a single-radiation hit induce common, genome-wide, and persistent epigenetic changes in the intestine

Project description:Background: Mismatch repair (MMR)-deficiency increases the risk of colorectal tumorigenesis. To determine whether the tumors develop on a normal or disturbed epigenetic background and how radiation affects this, we determined genome-wide histone H3 methylation profiles in macroscopic normal intestinal tissue of young radiated and untreated MMR-deficient VCMsh2LoxP/LoxP (Msh2−/−) mice months before tumor onset. Results: Histone H3 methylation increases in Msh2−/− compared to control Msh2+/+ mice. Activating H3K4me3 and H3K36me3 histone marks frequently accumulate at genes that are H3K27me3 or H3K4me3 modified in Msh2+/+ mice, respectively. The genes recruiting H3K36me3 enrich in gene sets associated with DNA repair, RNA processing, and ribosome biogenesis that become transcriptionally upregulated in the developing tumors. A similar epigenetic effect is present in Msh2+/+ mice 4 weeks after a single-radiation hit, whereas radiation of Msh2−/− mice left their histone methylation profiles almost unchanged. Conclusions: MMR deficiency results in genome-wide changes in histone H3 methylation profiles preceding tumor development. Similar changes constitute a persistent epigenetic signature of radiation-induced DNA damage.

2019-03-26 | GSE128842 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data