A5080163347- Plant Molecular Biology Research
- RNA Research and Splicing
- RNA modifications and cancer
- Photosynthetic Processes and Mechanisms
- Neuroscience and Neuropharmacology Research
- RNA and protein synthesis mechanisms
- Nuclear Receptors and Signaling
- Genomics and Phylogenetic Studies
- Plant Stress Responses and Tolerance
- Ubiquitin and proteasome pathways
- Light effects on plants
- Neurobiology and Insect Physiology Research
- Nitrogen and Sulfur Effects on Brassica
- Molecular Biology Techniques and Applications
- Microtubule and mitosis dynamics
- Plant nutrient uptake and metabolism
- SARS-CoV-2 and COVID-19 Research
- Gene Regulatory Network Analysis
- ATP Synthase and ATPases Research
- Cancer-related molecular mechanisms research
- Neurogenesis and neuroplasticity mechanisms
- Plant Reproductive Biology
- Nutrition, Genetics, and Disease
- Protein Kinase Regulation and GTPase Signaling
- Vaccine Coverage and Hesitancy
University of Glasgow
2007-2023
Government of the United Kingdom
2023
Public Health Scotland
2023
Glasgow Life
2012
Institute of Molecular and Cell Biology
2012
Genomics (United Kingdom)
2002
Alternative splicing plays crucial roles by influencing the diversity of transcriptome and proteome regulating protein structure/function gene expression. It is widespread in plants, alteration levels factors leads to a wide variety growth developmental phenotypes. The circadian clock complex piece cellular machinery that can regulate physiology behavior anticipate predictable environmental changes on revolving planet. We have performed system-wide analysis alternative components Arabidopsis...
Plants have adapted to tolerate and survive constantly changing environmental conditions by reprogramming gene expression The dynamics of the contribution alternative splicing (AS) stress responses are unknown. RNA-sequencing a time-series Arabidopsis thaliana plants exposed cold determines timing significant AS changes. This shows massive rapid response with coincident waves transcriptional activity occurring in first few hours temperature reduction further throughout cold. In particular,...
Alternative splicing generates multiple transcript and protein isoforms from the same gene thus is important in expression regulation. To date, RNA-sequencing (RNA-seq) standard method for quantifying changes alternative on a genome-wide scale. Understanding current limitations of RNA-seq crucial reliable analysis lack high quality, comprehensive transcriptomes most species, including model organisms such as Arabidopsis, major constraint accurate quantification isoforms. address this, we...
The circadian oscillator in eukaryotes consists of several interlocking feedback loops through which the expression clock genes is controlled. It generally assumed that all plant cells contain essentially identical and cell-autonomous multiloop clocks. Here, we show roots mature Arabidopsis plants differs markedly from shoots root synchronized by a photosynthesis-related signal shoot. Two are disengaged roots, because two key components, transcription factors CCA1 LHY, able to inhibit gene...
Plants re-programme their gene expression when responding to changing environmental conditions. Besides differential expression, extensive alternative splicing (AS) of pre-mRNAs and changes in long non-coding RNAs are associated with stress responses. RNA-sequencing a diel time-series the initial response Arabidopsis thaliana rosettes low temperature showed massive rapid waves both transcriptional AS activity protein-coding genes. We have now identified cold-dependent (lncRNAs) including...
Most forms of neuronal plasticity are associated with induction the transcription factor Zif268 (Egr1/Krox24/NGF-IA). In a genome-wide scan, we obtained evidence for potential modulation proteasome subunit and regulatory genes by in neurons, finding significance considering emerging that modulates synaptic function. Bioinformatic analysis indicated candidate target had rich concentration putative binding sites immediately upstream transcriptional start sites. Regulation mRNAs encoding psmb9...
Abstract The later phases of neuronal plasticity are invariably dependent on gene transcription. Induction the transcription factor Zif268 (Egr‐1) in neurones is closely associated with many forms functional plasticity, yet target genes modulated by have not been characterized. After transfection a cell line we identified that show altered expression using high density microarrays. Although some previously majority linked or action. Altered representative sample novel was confirmed...
Summary RNA ‐sequencing ( ‐seq) allows global gene expression analysis at the individual transcript level. Accurate quantification of variants generated by alternative splicing AS ) remains a challenge. We have developed comprehensive, nonredundant Arabidopsis reference dataset (At RTD containing over 74 000 transcripts for use with algorithms to quantify isoforms in ‐seq. The At was formed merging from TAIR 10 and novel identified an discovery project. estimated abundance ‐seq data using...
Abstract One of the ways in which plants can respond to temperature is via alternative splicing (AS). Previous work showed that changes affected several circadian clock gene transcripts. Here, we investigated role RNA‐binding factors (SFs) temperature‐sensitive AS LATE ELONGATED HYPOCOTYL ( LHY ). We characterized, wild type plants, temperature‐associated isoform switching and expression patterns for SF transcripts from a high‐resolution time series RNA‐seq experiment. In addition, employed...
In the March 2012 issue of The Plant Cell we describe extensive alternative splicing (AS) Arabidopsis circadian clock genes. Notably these distinct post-transcriptional events associate with different steady-state temperatures and also plants undergoing temperature transitions leading us to propose that temperature-associated AS is an additional mechanism involved in operation control plant clock. Here show associated extends REVEILLE 8 (RVE8), demonstrating a hitherto unrecognized link...
How plants perceive and respond to temperature remains an important question in the plant sciences. Temperature perception signal transduction may occur through temperature-sensitive intramolecular folding of primary mRNA transcripts. Recent studies suggested a role for retention first intron 5'UTR clock component LATE ELONGATED HYPOCOTYL (LHY) response changes temperature. Here, we identified set haplotypes LHY 5'UTR, examined their global spatial distribution, obtained evidence that...
Summary HAPPY mapping is an in vitro approach for defining the order and spacing of DNA markers directly on native genomic DNA. This cloning‐free technique based analysing segregation amplified from high molecular weight which has been broken randomly ‘segregated’ by limiting dilution into subhaploid samples. It a uniquely versatile tool, allowing construction genome maps with flexible ranges resolutions. Moreover, it applicable to plant genomes, many techniques pioneered animal genomes are...
Cold stress is one of the major environmental factors that limit growth and yield plants. However, it still not fully understood how plants account for daily temperature fluctuations, nor these changes are integrated with other regulatory systems such as circadian clock. We demonstrate REVEILLE2 undergoes alternative splicing after chilling increases accumulation a transcript isoform encoding MYB-like transcription factor. explore biological function in Arabidopsis thaliana using combination...
Abstract Background Alternative splicing is the major post-transcriptional mechanism by which gene expression regulated and affects a wide range of processes responses in most eukaryotic organisms. RNA-sequencing (RNA-seq) can generate genome-wide quantification individual transcript isoforms to identify changes alternative splicing. RNA-seq an essential modern tool but its ability accurately quantify depends on diversity, completeness quality information. Results We have developed new...
Most forms of neuronal plasticity are associated with induction the transcription factor zif268 (egr1). Down-regulation cdc20 (p55(cdc))--a regulatory protein for anaphase-promoting complex, which controls access specific substrates to proteasome--was observed after transfection a cell line zif268. Treatment cultured hippocampal neurones NMDA, elevates endogenous levels, also decreased levels. Conversely, levels were found be increased in cerebral cortex mice targeted deletion gene, when...
The regulation of synaptic glutamate receptor and GABAAR (γ-aminobutyric acid subtype A receptor) levels is a key component plasticity. Most forms neuronal plasticity are associated with the induction transcription factor zif268 (egr1). Hence, it predicted that may regulate genes receptors and/or GABAARs. It turns out by tends to be indirect. Induction in neurons leads altered expression proteasome subunit proteasome-regulatory genes, thereby changing capacity neuron degrade proteins,...
Abstract Background Plants have adapted to tolerate and survive constantly changing environmental conditions by re-programming gene expression. The scale of the contribution alternative splicing (AS) stress responses has been underestimated due limitations in RNA-seq analysis programs poor representation AS transcripts plant databases. Significantly, dynamics response not investigated but this is now possible with accurate transcript quantification AtRTD2, a new, comprehensive transcriptome...
Summary Cold stress is one of the major environmental factors that limit growth and yield plants. However, it still not fully understood how plants account for daily temperature fluctuations, nor these changes are integrated with other regulatory systems such as circadian clock. We demonstrate REVEILLE2, a MYB-like transcription factor, exhibits cold-induced alternative splicing switch from non-translatable isoform at ambient to translatable upon cold exposure. explore biological function...
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