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Article
Open AccessSMARCB1 loss activates patient-specific distal oncogenic enhancers in malignant rhabdoid tumors
Malignant rhabdoid tumor (MRT) is a highly malignant and often lethal childhood cancer. MRTs are genetically defined by bi-allelic inactivating mutations in SMARCB1, a member of the BRG1/BRM-associated factors (B...
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Article
Open AccessCTCF and cohesin promote focal detachment of DNA from the nuclear lamina
Lamina-associated domains (LADs) are large genomic regions that are positioned at the nuclear lamina. It has remained largely unclear what drives the positioning and demarcation of LADs. Because the insulator ...
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Article
Open AccessCBX2 shapes chromatin accessibility promoting AML via p38 MAPK signaling pathway
The dynamic epigenome and proteins specialized in the interpretation of epigenetic marks critically contribute to leukemic pathogenesis but also offer alternative therapeutic avenues. Targeting newly discovere...
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Protocol
Acute Protein Depletion Strategies to Functionally Dissect the 3D Genome
The organization of the genome inside the nucleus facilitates many nuclear processes. Because the nuclear genome is highly dynamic and often regulated by essential proteins, rapid depletion strategies are nece...
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Article
WAPL maintains a cohesin loading cycle to preserve cell-type-specific distal gene regulation
The cohesin complex has an essential role in maintaining genome organization. However, its role in gene regulation remains largely unresolved. Here we report that the cohesin release factor WAPL creates a pool...
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Article
A transient absence of SMC-mediated loops after mitosis
After mitosis chromosomes are drastically reshaped. A study now charts the dynamics of this conformational change at high temporal resolution. During the shift from one loop-forming complex (condensin) to anot...
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Article
Open AccessBRD9 binds cell type-specific chromatin regions regulating leukemic cell survival via STAT5 inhibition
Leukemia is characterized by genetic and epigenetic mutations resulting in selection of cancer cells, which are unable to differentiate. Although genetic alterations are difficult to target, the epigenome is i...
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Article
Open AccessThe non-coding variant rs1800734 enhances DCLK3 expression through long-range interaction and promotes colorectal cancer progression
Genome-wide association studies have identified a great number of non-coding risk variants for colorectal cancer (CRC). To date, the majority of these variants have not been functionally studied. Identificatio...
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Article
Open AccessPrognostic significance of nuclear expression of UMP-CMP kinase in triple negative breast cancer patients
We have previously identified UMP-CMP kinase (CMPK1) as a prognostic marker for triple negative breast cancer (TNBC) by mass spectrometry (MS). In this study we evaluated CMPK1 association to prognosis in an i...
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Protocol
Use of Universal Stable Isotope Labeling by Amino Acids in Cell Culture (SILAC)-Based Selected Reaction Monitoring (SRM) Approach for Verification of Breast Cancer-Related Protein Markers
Mass spectrometry-based proteomics facilitates high-throughput discovery of protein markers for diagnosis and treatment of breast cancer patients. Hundreds of putative prognostic and predictive markers are bei...
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Article
Open AccessProteomics Pipeline for Biomarker Discovery of Laser Capture Microdissected Breast Cancer Tissue
Mass spectrometry (MS)-based label-free proteomics offers an unbiased approach to screen biomarkers related to disease progression and therapy-resistance of breast cancer on the global scale. However, multi-st...
