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Improved ChIP Sequencing for H3K27ac Profiling and Super-Enhancer Analysis Assisted by Fluorescence-Activated Sorting of Formalin-Fixed Paraffin-Embedded Tissues.
Biol Proced Online
January 2025
Department of Laboratory Medicine, West China Hospital of Sichuan University, Chengdu, 610041, China.
Archived clinical formalin-fixed paraffin-embedded tissue (FFPE) is valuable for the study of tumor epigenetics. Although protocol of chromatin immunoprecipitation coupled with next generation sequencing (NGS) (ChIP-seq) using FFPE samples has been established, removal of interference signals from non-target cell components in the samples is still needed. In this study, the protocol of ChIP-seq with purified cells from FFPE lymphoid tissue of nodal T follicular helper cell lymphoma, angioimmunoblastic type (nTFHL-AI) after fluorescence-activated cell sorting (FACS) was established and optimized.
View Article and Find Full Text PDFIsolation of proteins on chromatin (iPOC) reveals signaling pathway-dependent alterations in the DNA-bound proteome.
Mol Cell Proteomics
January 2025
Division of Proteomics of Stem Cell and Cancer, German Cancer Research Center (DKFZ), 69120 Heidelberg Germany; Medical Faculty, Heidelberg University, 69120 Heidelberg, Germany. Electronic address:
Signaling pathways often convergence on transcription factors (TFs) and other DNA-binding proteins (DBPs) that regulate chromatin structure and gene expression, thereby governing a broad range of essential cellular functions. However, the repertoire of DBPs is incompletely understood even for the best-characterized pathways. Here, we optimized a strategy for the isolation of Proteins on Chromatin (iPOC) exploiting tagged nucleoside analogues to label the DNA and capture associated proteins, thus enabling the comprehensive, sensitive, and unbiased characterization of the DNA-bound proteome.
View Article and Find Full Text PDFNon-Canonical TERT Activity Initiates Osteogenesis in Calcific Aortic Valve Disease.
Circ Res
January 2025
Division of Cardiology, Department of Medicine, Pittsburgh Heart, Lung, Blood and Vascular Medicine Institute, University of Pittsburgh, PA. (R.A.C., C.C.C., R.W., A.C., C.B., C.R., W.J.M., M.J. Bashline, A.P., A.M.P., P.B., M.J. Brown, C.S.H.).
Background: Calcific aortic valve disease is the pathological remodeling of valve leaflets. The initial steps in valve leaflet osteogenic reprogramming are not fully understood. As TERT (telomerase reverse transcriptase) overexpression primes mesenchymal stem cells to differentiate into osteoblasts, we investigated whether TERT contributes to the osteogenic reprogramming of valve interstitial cells.
View Article and Find Full Text PDFMaternal exposures are known to influence the risk of isolated cleft lip with or without cleft palate (CL/P) - a common and highly heritable birth defect with a multifactorial etiology. To identify new CL/P risk loci, we conducted a genome-wide gene-environment interaction (GEI) analysis of CL/P on a sample of 540 cases and 260 controls recruited from the Philippines, incorporating the interaction effects of genetic variants with maternal smoking and vitamin use. As GEI analyses are typically low in power and the results can be difficult to interpret, we used multiple testing frameworks to evaluate potential GEI effects: 1 degree-of-freedom (1df) GxE test, the 3df joint test, and the two-step EDGE approach.
View Article and Find Full Text PDFProduction, Isolation, and Characterization of Stable Isotope-Labeled Standards for Mass Spectrometric Measurements of Oxidatively-Damaged Nucleosides in RNA.
ACS Omega
January 2025
Biomolecular Measurement Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States.
RNA undergoes oxidatively induced damage in living organisms analogous to DNA. RNA is even more vulnerable to damage than DNA due to its greater abundance, single-strandedness, lack of repair and chromatin proteins shield, and instability, among other effects. RNA damage can adversely affect gene expression, leading to protein synthesis alterations, cell death, and other detrimental biological consequences.
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