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Genome binding/occupancy profiling of transferred WT or Mek1/2-tKO CD45.2+OT-II T cells.

ABSTRACT: The purpose of this study was to elucidate the molecular mechanisms of Mek1/2 deficiency-mediated Tfh development, we established the adoptive transfer OVA/CFA immunization model and isolated transferred WT or Mek1/2-tKO CD45.2+OT-II T cells from dLNs for ATAC sequencing.

ORGANISM(S): Mus musculus

PROVIDER: GSE299628 | GEO | 2026/05/05

REPOSITORIES: GEO

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Transcriptomic profile of transferred WT or Mek1/2_tKO CD45.2+OT-II T cells.

Project description:The purpose of this study was to elucidate the molecular mechanisms of Mek1/2 deficiency-mediated Tfh development, we established the adoptive transfer OVA/CFA immunization model and isolated transferred WT or Mek1/2_tKO CD45.2+OT-II T cells from dLNs for RNA sequencing.

2026-05-05 | GSE299522 | GEO

Histone H3 threonine 11 phosphorylation is catalyzed directly by the meiosis-specific kinase Mek1 and provides a molecular readout of Mek1 activity in vivo

Project description:Saccharomyces cerevisiae Mek1 is a CHK2/Rad53-family kinase that regulates meiotic recombination and progression upon its activation in response to DNA double-strand breaks (DSBs). The full catalog of direct Mek1 phosphorylation targets remains unknown. Here, we show that phosphorylation of histone H3 on threonine 11 (H3 T11ph) is induced by meiotic DSBs in S. cerevisiae and Schizosaccharomyces pombe. Molecular genetic experiments in S. cerevisiae confirmed that Mek1 is required for H3 T11ph and revealed that phosphorylation is rapidly reversed when Mek1 kinase is no longer active. Reconstituting histone phosphorylation in vitro with recombinant proteins demonstrated that Mek1 directly catalyzes H3 T11 phosphorylation. Mutating H3 T11 to nonphosphorylatable residues conferred no detectable meiotic defects, indicating that H3 T11ph is dispensable for Mek1 functions in controlling recombination. However, H3 T11ph provides an excellent marker of ongoing Mek1 kinase activity in vivo. Anti-H3 T11ph chromatin immunoprecipitation followed by deep sequencing demonstrated that H3 T11ph was highly enriched at presumed sites of attachment of chromatin to chromosome axes, gave a more modest signal along chromatin loops, and was present at still lower levels immediately adjacent to DSB hotspots. These localization patterns closely tracked the distribution of Red1 and Hop1, axis proteins required for Mek1 activation. These findings provide insight into the spatial disposition of Mek1 kinase activity and the higher order organization of recombining meiotic chromosomes.

2017-10-17 | GSE103823 | GEO

Transcriptomic profile of polarized WT or Mek1/2_tKO CD4+ T cells

Project description:MEK1/2 are required for proper Tfh cell differentiation. To more specifically define the function of MEK1/2 signaling in Tfh cell development, we performed RNA-seq analysis.

2026-05-05 | GSE299327 | GEO

Single cell SMART RNAseq on WT and TKO E14 EpiLCs

Project description:We investigate how DNA methylation absence impact transcriptionnal regulation during epiblast differentiation. More specifically, how synchronous is the naïve to primed transitioning in TKO cells compared to WT, and if there is a "germline-competent" TKO subpopulation of EpiLCs. To this end, we used in vitro Epiblast-like cell (EpiLC) differentiation WT and TKO at D0, D1, D2 and D4. We next performed single-cell SMARTseq2 RNA sequencing.

2023-10-09 | GSE214462 | GEO

A web-based search tool for visualizing instrument performance using the Triple Knockout (TKO) proteome standard

Project description:Multiplexing strategies are at the forefront of mass spectrometry-based proteomics, with SPS-MS3 methods becoming increasingly commonplace. A known caveat of isobaric multiplexing is interference resulting from co-isolated and co-fragmented ions that do not originate from the selected precursor of interest. The triple knockout (TKO) standard was designed to benchmark data collection strategies to minimize interference. However, a limitation to its widespread use has been the lack of an automated analysis platform. Here, we present a TKO Visualization Tool (TVT). The TVT viewer allows for automated, web-based, database searching of the TKO standard, returning traditional figures of merit, such as peptide and protein counts, scan-specific ion accumulation times, as well as the TKO-specific metric, the IFI (interference-free index). Moreover, the TVT viewer allows for plotting of multiple TKO standards to assess protocol optimizations, compare instruments, or measure degradation of instrument performance over time. To showcase the TVT viewer, we investigated the selection of 1) stationary phase resin, 2) MS2 isolation window width, and 3) number of SPS ions for SPS-MS3 analysis. Using the TVT viewer will allow the proteomics community to search and compare TKO results to optimize user-specific data collection workflows.

2018-12-04 | PXD011654 | Pride

Spo11-oligo mapping in S. cerevisiae red1, hop1, mek1 mutants

Project description:Meiotic recombination starts with the formation of DNA double-strand breaks (DSBs) made by Spo11. In Saccharomyces cerevisiae, the nonrandom distribution of meiotic DSBs along the genome can be attributed to the combined influence of multiple factors on Spo11 cleavage. One factor is higher-order chromatin structure, particularly the loop-axis organization of meiotic chromosomes. Axial element proteins Red1 and Hop1 provide the basis for meiotic loop-axis organization and are implicated in diverse aspects of meiotic recombination. Mek1 is a meiotic-specific kinase associated with Red1 and Hop1. Red1, Hop1, and Mek1 are required for normal DSB levels, but their effects on the DSB distribution has not been examined, and exactly how these proteins influence DSB levels and distribution is unknown. Here, we examined the contributions of Red1, Hop1, and Mek1 to the DSB distribution by deep sequencing and mapping Spo11-associated oligonucleotides from red1, hop1, and mek1 mutant strains, thereby generating genome-wide meiotic DSB maps.

2018-09-01 | GSE84859 | GEO

MEK1/2 inhibitors unlock the constrained interferon response in macrophages through IRF1 signaling

Project description:Analysis of bone-marrow derived macrophages (BMDMs) stimulated with single or combinatorial TLR agonist and MEK1/2 inhibitor in wild-type and Irf1-/- macrophages. Results provide insights into the versatile but yet uncharacterized roles of IRF1 in TLR-MEK1/2-ERK MAPK signaling.

2018-12-28 | GSE123512 | GEO

Tracing the lineage of replicative RNAs carrying MEK1 in the evolution of drug resistance

Project description:Drug resistance poses a significant clinical challenge, and comprehending the mechanisms underlying this resistance can facilitate the design of novel inhibitors and advance cancer treatment. The REPLACE system was employed to examine resistance mutations in MEK1 during the administration of 3 allosteric inhibitors. To explore the accumulation of mutations in various RNAs during the MEK1 evolution experiment, we established a barcoded library and conducted lineage tracing of replicative RNAs carrying MEK1 throughout the drug resistance evolution process.

2024-09-30 | GSE271875 | GEO

Transcriptomic and epigenomic profiling of Tet TKO neural stem cells to study NSC specification and multipotency

Project description:In this study we: (1) identify genes deregulated in wildtype (WT) and Tet triple knockout (TKO) mouse embryonic stem cells (ESC) and neural stem cells (NSC). (2) Profile genome-wide changes in DNA methylation in WT and TKO ESCs and NSCs. (3) Map histone marks H3K4me1 and H3K27ac in WT and TKO ESCs and NSCs. (4) Identify promoter-interacting chromatin loops in WT and TKO NSCs.

2024-07-23 | GSE248933 | GEO

RNA seq of CD45.2+ Neo1 deficient or wildtype Hematopoietic stem cells, 4 or 15 month after stem cell transplantation

Project description:To study the role of the receptor Neo1 in Hematopoietic stem cells (HSC) we transplanted Neo1 deficient bone marrow and wildtype controls on a CD45.2 background into lethally irradiated CD45.1 recipients. Either 4 or 15 months after transplantation we isolated HSC (Lineage -, Sca-1+, c-Kit+, Cd150+, CD48-, CD34-, CD45.2+) to identify molecular differences due to Neo1 deficiency and found a loss of HSC quiescence and signatures associated with decreased stem cell function.

2020-07-22 | E-MTAB-7902 | biostudies-arrayexpress

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