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ProteomicsA lineage master regulator and cancer-selective partner transcription factor reprogram 3D chromatin topology to establish tumor-specific gene control
Lineage-determining transcription factors (TFs), such as p63 in epithelial tissues, establish normal tissue identity but can also drive carcinogenesis. The epigenetic basis for these divergent effects, however, is unclear. Here, we show that p63 reorganizes three-dimensional (3D) chromatin topology ...
ORGANISM(S): Homo sapiens (Human) 
2026-09-14 | PXD073599 | Pride
P63 foxk1 
GenomicsMITF ChIP-seq in primary melanocyte and melanoma as a function of oncogenic BRAF
Thousands of enhancers are characterized in the human genome, yet few have been shown important in cancer. Inhibiting oncokinases, such as EGFR, ALK, HER2, and BRAF, is a mainstay of current cancer therapy but is hindered by innate drug resistance mediated by upregulation of the HGF receptor, MET. T...
ORGANISM(S): Homo sapiens 
2014-01-14 | E-GEOD-50681 | biostudies-arrayexpress
ProteomicsirCLIP-RNP reveals patterns of dynamic protein associations on RNA
RNA binding proteins (RBPs) interact with RNA targets to control an array of processes, including RNA splicing, stability, transport, and translation1-3. Dysfunctional RNA-RBP interactions contribute to pathogenesis of a plethora of human diseases1,4,5, underscoring the need for a greater understand...
ORGANISM(S): Homo sapiens (Human) 
2025-01-28 | PXD053494 | Pride
Mass spectrometry Ms Crisslinking immunoprecipitation Rna binding proteins Clip Rbp 
TranscriptomicsModeling Inducible Human Tissue Neoplasia Identifies an ECM Interaction Network Involved in Cancer Progression
To elucidate mechanisms of cancer progression, we generated inducible human neoplasia in 3-dimensionally intact epithelial tissue. Gene expression profiling of both epithelia and stroma at specific time points during tumor progression revealed sequential enrichment of genes mediating discrete biolog...
ORGANISM(S): Mus musculus 
2009-06-02 | E-GEOD-15299 | biostudies-arrayexpress
TranscriptomicsDepletion of Erk1 and Erk2 MAP kinases in primary human keratinocytes
We assessed the effect of RNAi-mediated MAP kinase cascade signaling blockade in primary human keratinocytes. Two sets of siRNA targeting different regions of the Erk1/2 genes were used, enabling identification of off-target siRNA effects. Primary human keratinocytes were electroporated with scra...
ORGANISM(S): Homo sapiens 
2009-05-03 | E-GEOD-15417 | biostudies-arrayexpress
ProteomicsPROBER Identifies Proteins Associated with Programable Sequence-Specific DNA in Living Cells
DNA-protein interactions mediate physiologic gene regulation and may be altered by DNA variants linked to polygenic disease. To enhance the speed and signal-to-noise ratio (SNR) of identifying and quantifying proteins that associate with specific DNA sequences in living cells, we developed proximal ...
ORGANISM(S): Homo sapiens (Human) 
2022-07-27 | PXD029470 | Pride
Basu Bqtl Tert Snp Probe Bioid 
ProteomicsPROBER Identifies Proteins Associated with Sequence-Specific DNA in Living Cells
DNA-protein interactions mediate physiologic gene regulation and may be altered by DNA variants linked to polygenic disease. To enhance the speed and signal-to-noise ratio (SNR) of identifying and quantifying proteins that associate with specific DNA sequences in living cells, we developed proxim...
ORGANISM(S): Homo sapiens (Human) 
2022-07-27 | PXD032726 | Pride
Dna-protein tnteraction Prober Lc-ms/ms 
ProteomicsPROBER Identifies Proteins Associated with Sequence- Specific DNA in Living Cells
Specific DNA-protein interactions mediate physiologic gene regulation and may be altered by DNA variants linked to polygenic disease. To enhance the speed and signal-to-noise ratio (SNR) of identifying and quantifying proteins associating with specific DNA sequences in living cells, we developed pro...
ORGANISM(S): Homo sapiens (Human) 
2022-07-27 | PXD023732 | Pride
Dna-protein interaction Prober Lc-ms/ms 
TranscriptomicsDNMT1 Maintains Progenitor Function in Self-Renewing Somatic Tissue
Progenitor cells maintain self-renewing tissues throughout life by sustaining their capacity for proliferation while suppressing cell cycle exit and terminal differentiation. DNA methylation provides a potential epigenetic mechanism for the cellular memory needed to preserve the somatic progenitor s...
ORGANISM(S): Homo sapiens 
2010-06-23 | E-GEOD-18590 | biostudies-arrayexpress
GenomicsZNF750 Interacts with KLF4 and Specific Chromatin Regulators to Control Epidermal Differentiation
Here we find that ZNF750 activates epidermal differentiation genes and represses progenitor genes as part of two distinct protein complexes Identified genomic binding sites of ZNF750 and its interacting proteins
ORGANISM(S): Homo sapiens 
2014-09-11 | E-GEOD-57702 | biostudies-arrayexpress
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