A5041764276- RNA Research and Splicing
- RNA modifications and cancer
- Plant Molecular Biology Research
- RNA and protein synthesis mechanisms
- Photosynthetic Processes and Mechanisms
- Genomics and Phylogenetic Studies
- Molecular Biology Techniques and Applications
- Bioinformatics and Genomic Networks
- Biofuel production and bioconversion
- Light effects on plants
- Sugarcane Cultivation and Processing
- Wheat and Barley Genetics and Pathology
- Plant Disease Resistance and Genetics
- Gene Regulatory Network Analysis
- Antioxidant Activity and Oxidative Stress
- Education during COVID-19 pandemic
- Cancer-related molecular mechanisms research
- Genetic Mapping and Diversity in Plants and Animals
- Science and Education Research
- Magnetic and Electromagnetic Effects
- Growth and nutrition in plants
- Plant nutrient uptake and metabolism
- Plant Reproductive Biology
- Education and Digital Technologies
- Plant Stress Responses and Tolerance
Universidade de São Paulo
2009-2025
University of Dundee
2010-2022
James Hutton Institute
2015-2022
Instituto de Geociencias
2021
Plant (United States)
2017
John Innes Centre
2010
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...
RNA-sequencing (RNA-seq) analysis of gene expression and alternative splicing should be routine robust but is often a bottleneck for biologists because different complex programs reliance on specialized bioinformatics skills. We have developed the '3D RNA-seq' App, an R shiny App web-based pipeline comprehensive RNA-seq data from any organism. It represents easy-to-use, flexible powerful tool both transcript-level to identify differential gene/transcript expression, transcript usage (3D) as...
Accurate and comprehensive annotation of transcript sequences is essential for quantification differential gene expression analysis. Single-molecule long-read sequencing technologies provide improved integrity structures including alternative splicing, transcription start polyadenylation sites. However, accuracy significantly affected by errors, mRNA degradation, or incomplete cDNA synthesis.We present a new Arabidopsis thaliana Reference Transcript Dataset 3 (AtRTD3). AtRTD3 contains over...
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...
The circadian clock regulates a multitude of plant developmental and metabolic processes. In crop species, it contributes significantly to performance productivity the adaptation geographical range over which crops can be grown. To understand in barley how relates components Arabidopsis thaliana clock, we have performed systematic analysis core clock-associated genes barley, another eight species including tomato, potato, monocotyledonous moss, Physcomitrella patens. We identified...
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...
An alternative splicing isoform switch is where a pair of transcript isoforms reverse their relative expression abundances in response to external or internal stimuli. Although computational methods are available study differential splicing, few tools for detection switches exist and these based on pairwise comparisons. Here, we provide the TSIS R package, which first tool detecting significant time-series data. The main steps search points time-series, characterize filter results with user...
Abstract RNA-seq analysis of gene expression and alternative splicing should be routine robust but is often a bottleneck for biologists because reliance on specialized bioinformatics skills. Thus, we have developed “ 3D ”, an R shiny App web based service which provides easy-to-use, flexible powerful tool three-component data: Differential Expression, Alternative Splicing Transcript Usage. integrates state-of-the-art, highly rated differential tools adopts best practice analysis. It operates...
Small nucleolar RNAs (snoRNAs) and small Cajal body-specific (scaRNAs) are non-coding whose main function in eukaryotes is to guide the modification of nucleotides ribosomal spliceosomal nuclear RNAs, respectively. Full-length sequences Arabidopsis snoRNAs scaRNAs have been obtained from cDNA libraries capped uncapped using RNA isolated nucleoli cell cultures. We identified 31 novel snoRNA genes (9 box C/D 22 H/ACA) 15 new variants previously described snoRNAs. Three related with a distinct...
Alternative splicing (AS) is a regulated mechanism that generates multiple transcripts from individual genes. It widespread in eukaryotic genomes and provides an effective way to control gene expression. At low temperatures, AS regulates Arabidopsis clock genes through dynamic changes the levels of productive mRNAs. We examined barley assess whether temperature-dependent responses also occur monocotyledonous crop species. identify various core including orthologues AtLHY AtPRR7 which showed...
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...
Alternative Splicing (AS) is a mechanism that generates different mature transcripts from precursor mRNAs (pre-mRNAs) of the same gene. In plants, wide range physiological and metabolic events are related to AS, as well fast responses changes in temperature. AS present around 60% intron-containing genes Arabidopsis, 46% rice, 38% maize it widespread among circadian clock genes. Little known about how influences C4 like commercial sugarcane, crop with complex hybrid genome. This work aims...
ABSTRACT Protein translation programs often select the longest open reading frame (ORF) in a transcript leading to numerous inaccurate and mis-annotated ORFs databases. Unproductive isoforms containing premature termination codons (PTCs) are potential substrates for nonsense-mediated decay (NMD). These transcripts contain truncated but incorrectly annotated due selection of long ORF beginning at an AUG downstream PTC despite authentic start AUG. In gene expression alternative splicing...
Rice (Oryza sativa L.) is a major food crop but heat stress affects its yield and grain quality. To identify mechanistic solutions to improve rice under rising temperatures, molecular responses of thermotolerance must be understood. Transcriptional post-transcriptional controls are involved in wide range plant environmental responses. Alternative splicing (AS), particular, widespread mechanism impacting the defence plants it has been completely overlooked genome-wide studies. In this...
Co-expression has been widely used to identify novel regulatory relationships using high throughput measurements, such as microarray and RNA-seq data. Evaluation studies on co-expression network analysis methods mostly focus networks of small or medium size up a few hundred nodes. For large networks, simulated expression data usually consist hundreds thousands profiles with different perturbations knock-outs, which is uncommon in real experiments due their cost the amount work required....
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...
Abstract Background Accurate and comprehensive annotation of transcript sequences is essential for quantification differential gene expression analysis. Single molecule long read sequencing technologies provide improved integrity structures including alternative splicing, transcription start polyadenylation sites. However, accuracy significantly affected by errors, mRNA degradation or incomplete cDNA synthesis. Results We present a new Arabidopsis thaliana Reference Transcript Dataset 3...
To identify novel solutions to improve rice yield under rising temperatures, molecular components of thermotolerance must be better understood. Alternative splicing (AS) is a major post-transcriptional mechanism impacting plant tolerance against stresses, including heat stress (HS). AS largely regulated by factors (SFs) and recent studies have shown their involvement in temperature response. However, little known about the networks between SFs transcripts HS expand this knowledge, we...