Introduction: Single-cell RNA-seq (scRNA-seq) technologies have been widely used to reveal the diversity and complexity of cells, and pioneering studies on scRNA-seq in plants began to emerge since 2019. However, existing studies on plants utilized scRNA-seq focused only on the gene expression regulation. As an essential post-transcriptional mechanism for regulating gene expression, alternative polyadenylation (APA) generates diverse mRNA isoforms with distinct 3' ends through the selective use of different polyadenylation sites in a gene. APA plays important roles in regulating multiple developmental processes in plants, such as flowering time and stress response.
Methods: In this study, we developed a pipeline to identify and integrate APA sites from different scRNA-seq data and analyze APA dynamics in single cells. First, high-confidence poly(A) sites in single root cells were identified and quantified. Second, three kinds of APA markers were identified for exploring APA dynamics in single cells, including differentially expressed poly(A) sites based on APA site expression, APA markers based on APA usages, and APA switching genes based on 3' UTR (untranslated region) length change. Moreover, cell type annotations of single root cells were refined by integrating both the APA information and the gene expression profile.
Results: We comprehensively compiled a single-cell APA atlas from five scRNA-seq studies, covering over 150,000 cells spanning four major tissue branches, twelve cell types, and three developmental stages. Moreover, we quantified the dynamic APA usages in single cells and identified APA markers across tissues and cell types. Further, we integrated complementary information of gene expression and APA profiles to annotate cell types and reveal subtle differences between cell types.
Discussion: This study reveals that APA provides an additional layer of information for determining cell identity and provides a landscape of APA dynamics during Arabidopsis root development.
Download full-text PDF |
Source |
---|---|
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC11449893 | PMC |
http://dx.doi.org/10.3389/fpls.2024.1437118 | DOI Listing |
Breast
December 2024
Population Health Sciences Institute, Newcastle University, Newcastle University Centre for Cancer, Newcastle upon Tyne, England, UK. Electronic address:
Breast cancer is the most commonly diagnosed cancer worldwide, with early detection and advanced treatments contributing to declining mortality rates. However, managing comorbid conditions, particularly mental illness, presents significant challenges for cancer treatment. This study systematically reviews and meta-analyses the impact of having a pre-existing mental illness on breast cancer treatment utilisation, focusing on specific treatments and comparing different mental illnesses.
View Article and Find Full Text PDFBMC Oral Health
December 2024
Dental Sciences Research Center, Department of Prosthodontics, School of Dentistry, Guilan University of Medical Sciences, Rasht, Iran.
BMC Health Serv Res
December 2024
RCSI University of Medicine and Health Sciences, Dublin, Ireland.
Background: Ireland is experiencing a general practitioner (GP) workforce crisis, facing an ageing workforce, a growing population with increased life expectancy, and increased complexity of patients. The GP crisis threatens access to primary care in Ireland, as well as Ireland's aim to transform into a primary-care centred system of universal healthcare via the proposed "Sláintecare" healthcare reforms. The challenges faced are common to many countries as health systems seek to expand their medical workforce post-pandemic.
View Article and Find Full Text PDFPsychon Bull Rev
December 2024
Queen Margaret University, Edinburgh, Scotland, EH21 6UU, UK.
Learning and remembering what things are used for is a capacity that is central to successfully living in any human culture. The current paper investigates whether functional facts (information about what an object is used for) are remembered more efficiently compared with nonfunctional facts. Experiment 1 presented participants with images of functionally ambiguous objects associated with a (made-up) name and a (made-up) fact that could relate either to the object's function or to something nonfunctional.
View Article and Find Full Text PDFCogn Affect Behav Neurosci
December 2024
Department of Psychology, Binghamton University, Binghamton, NY, USA.
Cognitive reserve (CR) and busyness can boost memory, whereas stress can impair memory. Nevertheless, extant research has not yet examined busyness in conjunction with CR and stress, nor whether CR or stress moderate the relationship between busyness and episodic memory. Middle-aged and older adult participants (N = 71; ages 50-74; 31% African-American) answered lifestyle questionnaires and completed a visual paired-associate memory fMRI task.
View Article and Find Full Text PDFEnter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!