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A unified framework for cell-type-specific eQTL prioritization by integrating bulk and scRNA-seq data.
Am J Hum Genet
January 2025
Shenzhen Research Institute of Big Data, Shenzhen 518172, China. Electronic address:
Genome-wide association studies (GWASs) have identified numerous genetic variants associated with complex traits, yet the biological interpretation remains challenging, especially for variants in non-coding regions. Expression quantitative trait locus (eQTL) studies have linked these variations to gene expression, aiding in identifying genes involved in disease mechanisms. Traditional eQTL analyses using bulk RNA sequencing (bulk RNA-seq) provide tissue-level insights but suffer from signal loss and distortion due to unaddressed cellular heterogeneity.
View Article and Find Full Text PDFImpact of rare non-coding variants on human diseases through alternative polyadenylation outliers.
Nat Commun
January 2025
Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, China.
Although rare non-coding variants (RVs) play crucial roles in complex traits and diseases, understanding their mechanisms and identifying disease-associated RVs continue to be major challenges. Here we constructed a comprehensive atlas of alternative polyadenylation (APA) outliers (aOutliers), including 1334 3' UTR and 200 intronic aOutliers, from 15,201 samples across 49 human tissues. These aOutliers exhibit unique characteristics from transcription or splicing outliers, with a pronounced RV enrichment.
View Article and Find Full Text PDFCentromere inactivation during aging can be rescued in human cells.
Mol Cell
January 2025
Center for Cancer Research, National Cancer Institute/NIH, Bethesda, MD 20892, USA. Electronic address:
Aging involves a range of genetic, epigenetic, and physiological alterations. A key characteristic of aged cells is the loss of global heterochromatin, accompanied by a reduction in canonical histone levels. In this study, we track the fate of centromeres in aged human fibroblasts and tissues and in various cellular senescent models.
View Article and Find Full Text PDFIdentification of Four New HLA-B Noncoding Variants by Next-Generation Sequencing.
HLA
January 2025
Kirov Hematology and Blood Transfusion Research Institute Under the Federal Medicine and Biology Agency, Federal State Budget Research Institution, Kirov, Russia.
Four novel HLA-B noncoding variants detected by next-generation sequencing: HLA-B*07:02:107, -B*08:01:78, -B*15:01:89 and -B*52:01:58.
View Article and Find Full Text PDFRNA splicing variants of the novel long non-coding RNA, CyKILR, possess divergent biological functions in non-small cell lung cancer.
Mol Ther Nucleic Acids
March 2025
Department of Medicine, Division of Hematology & Oncology, University of Virginia, Charlottesville, VA 22903, USA.
The CDKN2A gene, responsible for encoding the tumor suppressors p16(INK4A) and p14(ARF), is frequently inactivated in non-small cell lung cancer (NSCLC). Herein, an uncharacterized long non-coding RNA (lncRNA) (ENSG00000267053) on chromosome 19p13.12 was found to be overexpressed in NSCLC cells with an active, wild-type CDKN2A gene.
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