A5083142859- RNA Research and Splicing
- RNA modifications and cancer
- Molecular Biology Techniques and Applications
- RNA and protein synthesis mechanisms
- Plant Molecular Biology Research
- Photosynthetic Processes and Mechanisms
- Genomics and Phylogenetic Studies
- Cancer-related molecular mechanisms research
James Hutton Institute
2018-2022
University of Dundee
2016-2022
Plant (United States)
2017
Despite the many approaches to study differential splicing from RNA-seq, challenges remain unsolved, including computing capacity and sequencing depth requirements. Here we present SUPPA2, a new method that addresses these challenges, enables streamlined analysis across multiple conditions taking into account biological variability. Using experimental simulated data, show SUPPA2 achieves higher accuracy compared other methods, especially at low short read length. We use identify novel...
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...
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...
SUMMARY Accurate characterisation of splice junctions (SJs) as well transcription start and end sites in reference transcriptomes allows precise quantification transcripts from RNA‐seq data, enables detailed investigations transcriptional post‐transcriptional regulation. Using novel computational methods a combination PacBio Iso‐seq Illumina short‐read sequences 20 diverse tissues conditions, we generated comprehensive highly resolved barley transcript dataset the European 2‐row spring...
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...
Abstract Despite the many approaches to study differential splicing from RNA-seq, challenges remain unsolved, including computing capacity and sequencing depth requirements. Here we present SUPPA2, a new method for analysis that addresses these enables streamlined across multiple conditions taking into account biological variability. Using experimental simulated data SUPPA2 achieves higher accuracy compared other methods; especially at low short read length, with important implications...
ABSTRACT Accurate characterization of splice junctions as well transcription start and end sites in reference transcriptomes allows precise quantification transcripts from RNA-seq data enable detailed investigations transcriptional post-transcriptional regulation. Using novel computational methods a combination PacBio Iso-seq Illumina short read sequences 20 diverse tissues conditions, we generated comprehensive highly resolved barley transcript dataset (RTD) the European 2-row spring...
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...
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...