A5032396845- RNA Research and Splicing
- RNA modifications and cancer
- Plant Molecular Biology Research
- RNA and protein synthesis mechanisms
- Genomics and Phylogenetic Studies
- Coastal wetland ecosystem dynamics
- Cancer-related gene regulation
- Chromosomal and Genetic Variations
- Lipid metabolism and biosynthesis
- Seed Germination and Physiology
- Synthetic Organic Chemistry Methods
- Acute Myeloid Leukemia Research
- Machine Learning in Bioinformatics
- Single-cell and spatial transcriptomics
- Plant responses to water stress
- Gene expression and cancer classification
- Cancer-related molecular mechanisms research
- Ubiquitin and proteasome pathways
- DNA Repair Mechanisms
- Bioinformatics and Genomic Networks
- Genetic Mapping and Diversity in Plants and Animals
- Glycosylation and Glycoproteins Research
- Immune Cell Function and Interaction
- T-cell and B-cell Immunology
- Plant Stress Responses and Tolerance
Xiamen University
2016-2025
Miami University
2014
Bentham Science Publishers (China)
2013
Bentham Science Publishers (United Arab Emirates)
2013
Alternative polyadenylation (APA) has been increasingly recognized as a crucial mechanism that contributes to transcriptome diversity and gene expression regulation. As RNA-seq become routine protocol for analysis, it is of great interest leverage such unprecedented collection data by new computational methods extract quantify APA dynamics in these transcriptomes. However, research progress this area relatively limited. Conventional rely on either transcript assembly determine 3' ends or...
Abstract Miniature inverted repeat transposable elements (MITEs) are prevalent in eukaryotic genomes, including plants and animals. Classified as a type of non-autonomous DNA elements, they play important roles genome organization evolution. Comprehensive accurate genome-wide detection MITEs various genomes can improve our understanding their origins, transposition processes, regulatory mechanisms biological relevance with regard to gene structures, expression regulation. In this paper, we...
Alternative polyadenylation (APA) has been discovered to play regulatory roles in the development of many cancer cells through preferential addition a poly(A) tail at specific sites pre-mRNA. A recent study found that APA was involved mediation acute myeloid leukaemia (AML). However, unlike gene expression heterogeneity, little attention directed toward variations single-cell for different cell types during AML development. Here, we used RNA-seq data massive population 16,843 bone marrow...
Vivipary is a rare sexual reproduction phenomenon where embryos germinate directly on the maternal plants. However, it common genetic event of woody mangroves in Rhizophoraceae family. The ecological benefits vivipary include nurturing seedlings harsh coastal and saline environments, but molecular mechanisms remain unclear. Here we investigate viviparous embryo development germination processes mangrove Kandelia obovata by transcriptomic approach. Many key biological pathways functional...
Auxin is widely involved in plant growth and development. However, the molecular mechanism on how auxin carries out this work unclear. In particular, effect of pre-mRNA post-transcriptional regulation mostly unknown. By using a poly(A) tag (PAT) sequencing approach, mRNA alternative polyadenylation (APA) profiles after treatment were revealed. We showed that hundreds site clusters (PACs) are affected by at transcriptome level, where reduces PAC distribution 5'-untranslated region (UTR), but...
Alternative cleavage and polyadenylation (APA) is increasingly recognized as an important regulatory mechanism in eukaryotic gene expression dynamically modulated a developmental, tissue-specific, or environmentally responsive manner. Given the functional importance of APA rapid accumulation sites plants, comprehensive easily accessible site database necessary for improved understanding APA-mediated regulation. We present called PlantAPAdb that catalogs most data derived from sequences...
Abstract Alternative polyadenylation (APA) generates diverse mRNA isoforms, which contributes to transcriptome diversity and gene expression regulation by affecting stability, translation localization in cells. The rapid development of 3′ tag-based single-cell RNA-sequencing (scRNA-seq) technologies, such as CEL-seq 10x Genomics, has led the emergence computational methods for identifying APA sites profiling dynamics at resolution. However, existing fail detect precise location poly(A) or...
Overlap of TCR repertoires among individuals provides the molecular basis for public T cell responses. By deep-sequencing TCRβ CD4+CD8+ thymocytes from three individual mice, we observed that a substantial degree overlap, comprising ∼10-15% all unique amino acid sequences and ∼5-10% nucleotide across any two individuals, is already present at this early stage development. The majority sharing between thymocyte could be attributed to process convergent recombination, with additional...
Highlights•U6/U2 snRNP inhibits global intronic PCPA (premature cleavage and polyadenylation)•U6/U2 regulates mRNA 3′-UTR (untranslated region) length for a subset of genes•Intronic is positively regulated by the 3′ processing activatorSummaryThe catalytic role U6 in pre-mRNA splicing has been well established. In this study, we utilize an antisense morpholino oligonucleotide (AMO) specifically targeting sites snRNA to achieve functional knockdown HeLa cells. The data show significant...
Abstract Mangrove plants adapt to coastal tidal mudflats with specially evolved viviparity seed development. However, very little is known about the genetic and molecular mechanisms of mangrove viviparity. Here, we tested a hypothesis that plant hormone abscisic acid (ABA) plays significant role in precocious germination viviparous Kandelia obovata seeds by exogenous applications. Through transcriptome analysis ABA treated seeds, it was found repressed fruit growth development, there were...
Abstract Motivation Alternative polyadenylation (APA) plays a key post-transcriptional regulatory role in mRNA stability and functions eukaryotes. Single cell RNA-seq (scRNA-seq) is powerful tool to discover cellular heterogeneity at gene expression level. Given 3′ enriched strategy library construction, the most commonly used scRNA-seq protocol—10× Genomics enables us improve study resolution of APA single However, currently there no computational available for investigating profiles from...
Transcriptional networks are tightly controlled in plant development and stress responses. Alternative polyadenylation (APA) has been found to regulate gene expression under abiotic by increasing the heterogeneity at mRNA 3'-ends. Heavy metals like cadmium pollute water soil due mining industry applications. Understanding how plants cope with heavy metal remains an interesting question. The Arabidopsis root hair was chosen as a single cell model investigate functional role of APA response....
Eukaryotic histone deacetylation, critical for maintaining nucleosome structure and regulating gene expression, is mediated by deacetylases (HDACs). Although nucleosomes have been reported to regulate mRNA polyadenylation in humans, the role of HDACs has not uncovered. Taking advantage phenotypic studies on Arabidopsis, HDA6 (one HDACs) was found be a part many biological processes. Here, we report that affects Arabidopsis Poly(A) sites up-regulated transcripts are closer acetylation peaks...
The essential role of U4 snRNP in pre-messenger RNA (mRNA) splicing has been well established. In this study, we utilized an antisense morpholino oligonucleotide (AMO) specifically targeting snRNA to achieve functional knockdown HeLa cells. Our results showed that resulted global intronic premature cleavage and polyadenylation (PCPA) events, comparable the effects observed with U1 AMO treatment, as demonstrated by mRNA 3′-seq analysis. Furthermore, our study suggested may be a common...
Plant species adapt to changing climates through phenotypic plasticity and natural selection, affecting invasive plants' niche breadth. However, our limited understanding of how temperature affects the relative importance selection contributes breadth across latitudes. Here, we used a model system, salt marsh grass Spartina alterniflora , native United States but was introduced into China in 1979, spreading over 20° latitude. We collected seeds S . from nine locations different latitudes...
Inverted repeats are present in abundance both prokaryotic and eukaryotic genomes can form DNA secondary structures – hairpins cruciforms that involved many important biological processes. Bioinformatics tools for efficient accurate detection of inverted desirable, because existing often less time consuming, sometimes incapable dealing with genome-scale input data. Here, we a MATLAB-based program called detectIR the perfect imperfect repeat utilizes complex numbers vector calculation allows...
Summary Alternative polyadenylation ( APA ) is a widespread post‐transcriptional mechanism that regulates gene expression through mRNA metabolism, playing pivotal role in modulating phenotypic traits rice Oryza sativa L.). However, little known about the ‐mediated regulation underlying distinct characteristics between two major subspecies, indica and japonica . Using poly(A)‐tag sequencing approach, (poly(A)) site profiles were investigated compared pairwise from germination to mature stage...
Despite a much higher proportion of intragenic heterochromatin-containing genes in crop genomes, the importance heterochromatin development remains unclear. Intragenic can be recognised by protein complex, ASI1-AIPP1-EDM2 (AAE) to regulate alternative polyadenylation. Here, we investigated impact rice ASI1 on global poly(A) site usage through sequencing and ASI1-dependent regulation development. We found that OsASI1 is essential for pollen flowering. dysfunction has an important usage, which...