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SPT5 regulates RNA polymerase II stability via Cullin 3-ARMC5 recognition.
Sci Adv
January 2025
Simpson Querrey Institute for Epigenetics, Department of Biochemistry and Molecular Genetics Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA.
The stability of RNA polymerase II (Pol II) is tightly regulated during transcriptional elongation for proper control of gene expression. Our recent studies revealed that promoter-proximal Pol II is destabilized via the ubiquitin E3 ligase cullin 3 (CUL3) upon loss of transcription elongation factor SPT5. Here, we investigate how CUL3 recognizes chromatin-bound Pol II as a substrate.
View Article and Find Full Text PDFEpiAge: a next-generation sequencing-based epigenetic clock for biological age assessment in saliva and blood across health and disease.
Aging (Albany NY)
January 2025
EpiMedTech Global, Singapore 409051, Singapore.
This study introduces EpiAgePublic, a new method to estimate biological age using only three specific sites on the gene known for its connection to aging. Unlike traditional methods that require complex and extensive data, our model uses a simpler approach that is well-suited for next-generation sequencing technology, which is a more advanced method of analyzing DNA methylation. This new model overcomes some of the common challenges found in older methods, such as errors due to sample quality and processing variations.
View Article and Find Full Text PDFDecoding the Epigenetic and Transcriptional Basis of Direct Cardiac Reprogramming.
Stem Cells
January 2025
Department of Biomedical Engineering, Heersink School of Medicine, School of Engineering, University of Alabama at Birmingham.
Heart disease, particularly resulting from myocardial infarction (MI), continues to be a leading cause of mortality, largely due to the limited regenerative capacity of the human heart. Current therapeutic approaches seek to generate new cardiomyocytes from alternative sources. Direct cardiac reprogramming, which converts fibroblasts into induced cardiomyocytes (iCMs), offers a promising alternative by enabling in situ cardiac regeneration and minimizing tumorigenesis concerns.
View Article and Find Full Text PDFDetection of reproducible liver cancer specific ligand-receptor signaling in blood.
Front Bioinform
January 2025
RNA Bioinformatics and High Throughput Analysis, Friedrich Schiller University Jena, Jena, Germany.
Cell-cell communication mediated by ligand-receptor interactions (LRI) is critical to coordinating diverse biological processes in homeostasis and disease. Lately, our understanding of these processes has greatly expanded through the inference of cellular communication, utilizing RNA extracted from bulk tissue or individual cells. Considering the challenge of obtaining tissue biopsies for these approaches, we considered the potential of studying cell-free RNA obtained from blood.
View Article and Find Full Text PDFExploring the utility of snRNA-seq in profiling human bladder tissue: A comprehensive comparison with scRNA-seq.
iScience
January 2025
Epigenetics & Molecular Carcinogenesis, M.D. Anderson Cancer Center, Houston, TX 77054, USA.
Single cell sequencing technologies have revolutionized our understanding of biology by mapping cell diversity and gene expression in healthy and diseased tissues. While single-cell RNA sequencing (scRNA-seq) has been widely used, interest in single-nucleus RNA sequencing (snRNA-seq) is growing due to its benefits, including the ability to analyze archival tissues and capture rare cell types that are challenging to dissociate. However, comparative studies across tissues have yielded mixed results, with some reporting enhanced cell type retention using snRNA-seq while others finding cell type identification to be challenging in snRNA-seq data.
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