8 research outputs found
MS1-Based Label-Free Proteomics Using a Quadrupole Orbitrap Mass Spectrometer
Presented is a data set for benchmarking
MS1-based label-free quantitative
proteomics using a quadrupole orbitrap mass spectrometer. Escherichia coli digest was spiked into a HeLa digest
in four different concentrations, simulating protein expression differences
in a background of an unchanged complex proteome. The data set provides
a unique opportunity to evaluate the proteomic platform (instrumentation
and software) in its ability to perform MS1-intensity-based label-free
quantification. We show that the presented combination of informatics
and instrumentation produces high precision and quantification accuracy.
The data were also used to compare different quantitative protein
inference methods such as iBAQ and Hi-<i>N</i>. The data
can also be used as a resource for development and optimization of
proteomics informatics tools, thus the raw data have been deposited
to ProteomeXchange with identifier PXD001385
Development of APE1 enzymatic DNA repair assays: low APE1 activity is associated with increase lung cancer risk
Neutralizing Gatad2a-Chd4-Mbd3/NuRD Complex Facilitates Deterministic Induction of Naive Pluripotency
Mbd3, a member of nucleosome remodeling and deacetylase (NuRD) co-repressor complex, was previously identified as an inhibitor for deterministic induced pluripotent stem cell (iPSC) reprogramming, where up to 100% of donor cells successfully complete the process. NuRD can assume multiple mutually exclusive conformations, and it remains unclear whether this deterministic phenotype can be attributed to a specific Mbd3/NuRD subcomplex. More-over, since complete ablation of Mbd3 blocks somatic cell proliferation, we aimed to explore functionally relevant alternative ways to neutralize Mbd3-dependent NuRD activity. We identify Gatad2a, a NuRD-specific subunit, whose complete deletion specifically disrupts Mbd3/NuRD repressive activity on the pluripotency circuitry during iPSC differentiation and reprogramming without ablating somatic cell proliferation. Inhibition of Gatad2a facilitates deterministic murine iPSC reprogramming within 8 days. We validate a distinct molecular axis, Gatad2a-Chd4-Mbd3, within Mbd3/NuRD as being critical for blocking reestablishment of naive pluripotency and further highlight signaling-dependent and post-translational modifications of Mbd3/NuRD that influence its interactions and assembly