A5001863695- RNA Research and Splicing
- Plant Molecular Biology Research
- RNA modifications and cancer
- Lipid metabolism and biosynthesis
- Plant-Microbe Interactions and Immunity
- Plant Stress Responses and Tolerance
- Electrocatalysts for Energy Conversion
- Bacteriophages and microbial interactions
- Gene expression and cancer classification
- Catalytic Processes in Materials Science
- Photosynthetic Processes and Mechanisms
- Plant Pathogenic Bacteria Studies
- RNA and protein synthesis mechanisms
- Vibrio bacteria research studies
- Genetic Mapping and Diversity in Plants and Animals
- Genomics and Phylogenetic Studies
- Plant Gene Expression Analysis
- Ubiquitin and proteasome pathways
- Polyamine Metabolism and Applications
- Cancer-related gene regulation
- Bacterial Genetics and Biotechnology
- Plant Reproductive Biology
- Algal biology and biofuel production
- Machine Learning in Materials Science
- Polysaccharides and Plant Cell Walls
University of Montana
2018-2023
Tsinghua University
2020-2022
Colorado State University
2013-2020
Miami University
2008-2014
Purdue University West Lafayette
2006-2008
Plant SR45 and its metazoan ortholog RNPS1 are serine/arginine-rich (SR)-like RNA binding proteins that function in splicing/postsplicing events regulate diverse processes eukaryotes. Interactions of with both RNAs crucial for regulating processing. However, vivo targets currently unclear. Using immunoprecipitation followed by high-throughput sequencing, we identified over 4000 Arabidopsis thaliana directly or indirectly associate SR45, designated as SR45-associated (SARs). Comprehensive...
Open AccessCCS ChemistryRESEARCH ARTICLE22 Apr 2022Computational Prediction of Graphdiyne-Supported Three-Atom Single-Cluster Catalysts Jin-Cheng Liu, Hai Xiao, Xiao-Kun Zhao, Nan-Nan Zhang, Yuan Deng-Hui Xing, Xiaohu Yu, Han-Shi Hu and Jun Li Liu Department Chemistry, Key Laboratory Organic Optoelectronics Molecular Engineering the Ministry Education, Tsinghua University, Beijing , Xiao Zhao Zhang Southern University Science Technology, Shenzhen, Guangdong Xing Yu Shaanxi Catalysis, School...
The polyadenylation of mRNA is one the critical processing steps during expression almost all eukaryotic genes. It tightly integrated with transcription, particularly its termination, as well other RNA events, i.e. capping and splicing. poly(A) tail protects from unregulated degradation, it required for nuclear export translation initiation. In recent years, has been demonstrated that process also involved in regulation gene expression. requires two components, cis-elements on a group...
Monitoring the extracellular environment for danger signals is a critical aspect of cellular survival. However, released by dying bacteria and mechanisms use threat assessment remain largely unexplored. Here, we show that lysis Pseudomonas aeruginosa cells releases polyamines are subsequently taken up surviving via mechanism relies on Gac/Rsm signaling. While intracellular spike in cells, duration this varies according to infection status cell. In bacteriophage-infected maintained at high...
Summary The timely transition from vegetative to reproductive growth is vital for success in plants. It has been suggested that messenger RNA 3′‐end processing plays a role this transition. Specifically, two autonomous factors the Arabidopsis thaliana flowering time control pathway, FY and FCA, are required alternative polyadenylation of FCA pre‐mRNA. In paper we provide evidence Pcf11p‐similar protein 4 (PCFS4), an homologue yeast factor Protein 1 Cleavage Factor (Pcf11p), regulates...
Abstract Background Polyadenylation, an essential step in eukaryotic gene expression, requires both cis -elements and a plethora of trans- acting polyadenylation factors. The factors are largely conserved across mammals fungi. conservation seems also extended to plants based on the analyses Arabidopsis To extend this observation, we systemically identified orthologs yeast human from 10 plant species chosen availability their genome sequences positions evolutionary tree, which render them...
Abstract Abiotic and biotic stresses cause significant yield losses in all crops. Acquisition of stress tolerance plants requires rapid reprogramming gene expression. SR1/CAMTA3, a member signal responsive transcription factors (TFs), functions both as positive negative regulator responses cold stress-induced Using high throughput RNA-seq, we identified ~3000 SR1-regulated genes. Promoters about 60% the differentially expressed genes have known DNA binding site for SR1, suggesting that they...
Summary Photoautotrophic growth in nature requires the accumulation of energy‐containing molecules via photosynthesis during daylight to fuel nighttime catabolism. Many diatoms store photosynthate as neutral lipid triacylglycerol (TAG). While pathways diatom fatty acid and TAG synthesis appear be well conserved with plants, catabolism downstream β‐oxidation have not been characterised diatoms. We identified a putative mitochondria‐targeted, bacterial‐type acyl‐CoA dehydrogenase (PtMACAD1)...
Abstract Polyadenylation factor CLP1 is essential for mRNA 3′-end processing in yeast and mammals. The Arabidopsis (Arabidopsis thaliana) CLP1-SIMILAR PROTEIN3 (CLPS3) an ortholog of human hCLP1. CLPS3 was previously found to be a subunit the affinity-purified PCFS4-TAP (tandem affinity purification) complex involved alternative polyadenylation FCA flowering time control Arabidopsis. In this article, we further explored components CLPS3-TAP complex, from which cleavage specificity (CPSF)...
Abstract Cleavage and polyadenylation of precursor mRNA is an essential process for maturation. Among the 15 to 20 protein factors required this process, a subgroup proteins needed both cleavage in plants animals. This known as specificity factor (CPSF). To explore vivo structural features plant CPSF, we used tandem affinity purification methods isolate interacting complexes each component CPSF subunits using Arabidopsis (Arabidopsis thaliana ecotype Landsberg erecta) suspension culture...
Soil salinity, a significant problem in agriculture, severely limits the productivity of crop plants. Plants respond to and cope with salt stress by reprogramming gene expression via multiple signaling pathways that converge on transcription factors. To develop strategies generate salt-tolerant crops, it is necessary identify factors modulate responses In this study, we investigated role VOZ (VASCULAR PLANT ONE-ZINC FINGER PROTEIN) (VOZs) response. Transcriptome analysis WT (wild-type),...
The yeast and human Pcf11 functions in both constitutive regulated transcription pre-mRNA processing. roles of PCF11 are largely mediated by its direct interaction with RNA Polymerase II C-terminal domain a polyadenylation factor, Clp1. However, little is known about the mechanism regulatory Pcf11. Though similar to multiple aspects, Arabidopsis Pcf11-similar-4 protein (PCFS4) plays only role gene expression. Towards understanding how PCFS4 regulates expression target genes genome level,...
The smallest bacterial genomes, in the range of about 0.1 to 0.5 million base pairs, are commonly found nutritional endosymbionts insects. These tiny genomes missing genes that encode proteins and RNAs required for translation mRNAs, one most highly conserved important cellular processes. In this study, we cicadas have which incomplete tRNA sets lack processing. Nevertheless, endosymbiont tRNAs correctly processed at their 5′ 3′ ends and, surprisingly, mostly exist as halves. We hypothesize...
Based on comparative genome analyses, the increases in protein-coding gene number could not account for of morphological and behavioral complexity higher eukaryotes. Transcriptional regulations, alternative splicing involvement non-coding RNA expression regulations have been credited drastic increase transcriptome complexity. However, an emerging theme another mechanism that contributes to formation alternatives mRNA 3'-ends is polyadenylation (APA). First, recent studies indicated APA a...
Background Alternative polyadenylation as a mechanism in gene expression regulation has been widely recognized recent years. Arabidopsis factor PCFS4 was shown to function leaf development and flowering time control. The of controlling correlated with the alternative FCA, regulator. However, genetic evidence suggested additional targets that may mediate its both development. Methodology/Principal Findings To identify further targets, we investigated whole transcriptome mutant using...
Abstract When eukaryotic cells are killed by pathogenic microorganisms, damage-associated and pathogen-associated signals generated that alert other of nearby danger. Bacteria can detect the death their kin; however, how bacteria make threat assessments cellular injury is largely unexplored. Here we show polyamines released lysed serve as molecules in Pseudomonas aeruginosa . In response to exogenous polyamines, Gac/Rsm cyclic-di-GMP signaling activated intracellular polyamine levels...
<p>While single-atom catalysts (SACs) have achieved great success in the past decade, their application is potentially limited by simplistic active centers, which makes single-cluster (SCCs) a natural extension. SCCs with precise numbers of atoms and structural configurations possess SAC’s merits, yet greater potentials for catalyzing complex reactions and/or bulky reactants. Through systematic quantum-chemical studies computational screening, we report here rational design transition...
Identification of gene structures is key to genome annotation, and analysis alternative RNA processing critical understand transcriptome diversity coding capacity. Tiling microarray has become an important tool for genome-wide expression due its high resolution, density throughput. However, the huge volume data limited probe design options, tiling neither easy nor effective. PROBER, a integrated massive data, developed identify analyze differential expression. In after normalization...