80 research outputs found
Probabilistic Inference for Nucleosome Positioning with MNase-Based or Sonicated Short-Read Data
We describe a model-based method, PING, for predicting nucleosome positions in MNase-Seq and MNase- or sonicated-ChIP-Seq data. PING compares favorably to NPS and TemplateFilter in scalability, accuracy and robustness to low read density. To demonstrate that PING predictions from widely available sonicated data can have sufficient spatial resolution to be to be useful for biological inference, we use Illumina H3K4me1 ChIP-seq data to detect changes in nucleosome positioning around transcription factor binding sites due to tamoxifen stimulation, to discriminate functional and non-functional transcription factor binding sites more effectively than with enrichment profiles, and to confirm that the pioneer transcription factor Foxa2 associates with the accessible major groove of nucleosomal DNA
Emphysematous cholecystitis presenting as gas-forming liver abscess and pneumoperitoneum in a dialysis patient: a case report and review of the literature
Occupancy by key transcription factors is a more accurate predictor of enhancer activity than histone modifications or chromatin accessibility
BIOMECHANICAL EFFECT OF DIFFERENT LAG SCREW LENGTHS WITH DIFFERENT BARREL LENGTHS IN DYNAMIC HIP SCREW SYSTEM: A FINITE ELEMENT ANALYSIS STUDY
Trametes versicolor Protein YZP Activates Regulatory B Lymphocytes â Gene Identification through De Novo Assembly and Function Analysis in a Murine Acute Colitis Model
Turnover of amyloid precursor protein family members determines their nuclear signaling capability
The amyloid precursor protein (APP) as well as its homologues, APP-like protein 1 and 2 (APLP1 and APLP2), are cleaved by α-, ÎČ-, and Îł-secretases, resulting in the release of their intracellular domains (ICDs). We have shown that the APP intracellular domain (AICD) is transported to the nucleus by Fe65 where they jointly bind the histone acetyltransferase Tip60 and localize to spherical nuclear complexes (AFT complexes), which are thought to be sites of transcription. We have now analyzed the subcellular localization and turnover of the APP family members. Similarly to AICD, the ICD of APLP2 localizes to spherical nuclear complexes together with Fe65 and Tip60. In contrast, the ICD of APLP1, despite binding to Fe65, does not translocate to the nucleus. In addition, APLP1 predominantly localizes to the plasma membrane, whereas APP and APLP2 are detected in vesicular structures. APLP1 also demonstrates a much slower turnover of the full-length protein compared to APP and APLP2. We further show that the ICDs of all APP family members are degraded by the proteasome and that the N-terminal amino acids of ICDs determine ICD degradation rate. Together, our results suggest that different nuclear signaling capabilities of APP family members are due to different rates of full-length protein processing and ICD proteasomal degradation. Our results provide evidence in support of a common nuclear signaling function for APP and APLP2 that is absent in APLP1, but suggest that APLP1 has a regulatory role in the nuclear translocation of APP family ICDs due to the sequestration of Fe65
Characteristics and overall survival in pediatric versus adult skull base chordoma: a population-based study
Evaluation of the Diagnostic Utility of the Traditional and Revised WHO Dengue Case Definitions
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