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Open accessJournal ArticleDOI: 10.1093/BIOINFORMATICS/BTAB141

ASpli: integrative analysis of splicing landscapes through RNA-Seq assays

02 Mar 2021-Bioinformatics (Oxford University Press)-Vol. 37, Iss: 17, pp 2609-2616
Abstract: Fil: Mancini, Estefania. Centro de Regulacion Genomica; Espana. Consejo Nacional de Investigaciones Cientificas y Tecnicas. Oficina de Coordinacion Administrativa Parque Centenario. Instituto de Investigaciones Bioquimicas de Buenos Aires. Fundacion Instituto Leloir. Instituto de Investigaciones Bioquimicas de Buenos Aires; Argentina

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7 results found


Open accessJournal ArticleDOI: 10.1093/PLPHYS/KIAB112
11 Jun 2021-Plant Physiology
Abstract: Plants are plastic organisms that optimize growth in response to a changing environment. This adaptive capability is regulated by external cues, including light, which provides vital information about the habitat. Phytochrome photoreceptors detect far-red light, indicative of nearby vegetation, and elicit the adaptive shade-avoidance syndrome (SAS), which is critical for plant survival. Plants exhibiting SAS are typically more elongated, with distinctive, small, narrow leaf blades. By applying SAS-inducing end-of-day far-red (EoD FR) treatments at different times during Arabidopsis (Arabidopsis thaliana) leaf 3 development, we have shown that SAS restricts leaf blade size through two distinct cellular strategies. Early SAS induction limits cell division, while later exposure limits cell expansion. This flexible strategy enables phytochromes to maintain control of leaf size through the proliferative and expansion phases of leaf growth. mRNAseq time course data, accessible through a community resource, coupled to a bioinformatics pipeline, identified pathways that underlie these dramatic changes in leaf growth. Phytochrome regulates a suite of major development pathways that control cell division, expansion, and cell fate. Further, phytochromes control cell proliferation through synchronous regulation of the cell cycle, DNA replication, DNA repair, and cytokinesis, and play an important role in sustaining ribosome biogenesis and translation throughout leaf development.

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Topics: Arabidopsis (52%), Arabidopsis thaliana (50%), Cytokinesis (50%) ... show more

4 Citations


Open accessPosted ContentDOI: 10.1101/2021.06.27.450092
V. Vern Lee1, V. Vern Lee2, Seizova S1, Paul J. McMillan2  +4 moreInstitutions (2)
27 Jun 2021-bioRxiv
Abstract: The splicing of mRNA constitutes a major source of co- and post-transcriptional regulation in metazoans. In particular, members of the serine/arginine (SR) protein family are essential splicing factors that are implicated in the regulation of gene expression and RNA metabolism. However, very little is known about these proteins in apicomplexans, a phylum that includes some of the most important global parasites. In this study, we investigated the suite of three uncharacterised SR proteins in Toxoplasma gondii and show that all three are found localised to nuclear speckles. We show, by genetic ablation, that TgSR1 is particularly important for T. gondii growth. Using RNA-seq, we also characterised the global gene expression and splicing regulation of these proteins. We find that the SR proteins regulate several types of alternative splicing of distinct but overlapping subsets of transcripts, as well as impacting transcript abundance. Most of the alternative splicing events are non-productive intron retention events that do not appear to affect transcript abundance. The splicing sites of the impacted transcripts are enriched in characteristic SR binding motifs. We also identified and conditionally knocked down two putative kinases of SR proteins. The kinases are localised to nuclear speckles and are essential to parasite survival. Their perturbation resulted in widespread changes to splicing, but the affected transcripts did not mirror the patterns seen in knockouts of individual SRs, suggesting an absence of a simple relationship between SRs and these putative kinase regulators. Overall, this study reveals a complex system of splicing factors and kinases that post-transcriptionally regulate gene expression in T. gondii.

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Topics: SR protein (68%), Alternative splicing (67%), RNA splicing (63%) ... show more

1 Citations


Open accessBook ChapterDOI: 10.5772/INTECHOPEN.97500
29 Apr 2021-
Abstract: RNA sequencing (RNA-Seq) is the leading, routine, high-throughput, and cost-effective next-generation sequencing (NGS) approach for mapping and quantifying transcriptomes, and determining the transcriptional structure. The transcriptome is a complete collection of transcripts found in a cell or tissue or organism at a given time point or specific developmental or environmental or physiological condition. The emergence and evolution of RNA-Seq chemistries have changed the landscape and the pace of transcriptome research in life sciences over a decade. This chapter introduces RNA-Seq and surveys its recent food and agriculture applications, ranging from differential gene expression, variants calling and detection, allele-specific expression, alternative splicing, alternative polyadenylation site usage, microRNA profiling, circular RNAs, single-cell RNA-Seq, metatranscriptomics, and systems biology. A few popular RNA-Seq databases and analysis tools are also presented for each application. We began to witness the broader impacts of RNA-Seq in addressing complex biological questions in food and agriculture.

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Topics: RNA (55%)

Open accessPosted ContentDOI: 10.1101/2020.10.19.345900
Takamasa Suzuki1, Tomomi Shinagawa1, Tomoko Niwa1, Hibiki Akeda1  +7 moreInstitutions (3)
19 Oct 2020-bioRxiv
Abstract: An Arabidopsis mutant named defective repression of OLE3::LUC 1 (drol1) was originally isolated as a mutant with defects in the repression of OLEOSIN3 (OLE3) after seed germination. In this study, we show that DROL1 is an Arabidopsis homolog of yeast DIB1, a subunit of U5 snRNP in the spliceosome, but comprises a subfamily specific to a certain class of eukaryotes. Comprehensive analysis of intron splicing by RNA-Seq analysis of drol1 mutants revealed reduced splicing of most of the minor introns with AT-AC dinucleotide termini. Thirty-nine genes, including those playing important roles in the response to abiotic stress, exhibited reduced splicing of AT-AC-type introns in drol1 mutants. In addition, drol1 mutant seedlings showed growth arrest, similar to that caused by the activation of abscisic acid signaling, as a result of reduced splicing of AT-AC-type introns in some genes. These results indicate that DROL1 is specifically involved in the splicing of introns with AT-AC termini, and splicing of these minor introns plays an important role in plant growth and development.

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Topics: RNA splicing (71%), Spliceosome (63%), Intron (62%) ... show more

Open accessPosted ContentDOI: 10.1101/2021.10.08.463671
08 Oct 2021-bioRxiv
Abstract: During CART-19 immunotherapy for B-cell acute lymphoblastic leukaemia (B-ALL), many patients relapse due to loss of the cognate CD19 epitope. Since epitope loss can be caused by aberrant CD19 exon 2 processing, we herein investigate the regulatory code that controls CD19 splicing. We combine high-throughput mutagenesis with mathematical modelling to quantitatively disentangle the effects of all mutations in the region comprising CD19 exons 1-3. Thereupon, we identify ~200 single point mutations that alter CD19 splicing and thus could predispose B-ALL patients to CART-19 resistance. Furthermore, we report almost 100 previously unknown splice isoforms that emerge from cryptic splice sites and likely encode non-functional CD19 proteins. We further identify cis-regulatory elements and trans-acting RNA-binding proteins that control CD19 splicing (e.g., PTBP1 and SF3B4) and validate that loss of these factors leads to enhanced CD19 mis-splicing. Our dataset represents a comprehensive resource for potential prognostic factors predicting success of CART-19 therapy. HighlightsO_LIMutations in relapsed CART-19 patients lead to CD19 mis-splicing C_LIO_LIHigh-throughput mutagenesis uncovers ~200 single point mutations with a potential role in CART-19 therapy resistance C_LIO_LIMany mutations generate non-functional CD19 proteins by activating cryptic splice sites C_LIO_LIRNA-binding proteins such as PTBP1 are key to the expression of properly spliced, CART-19 immunotherapy-sensitive isoforms C_LI

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Topics: RNA splicing (56%), Exon (55%), RNA-binding protein (52%) ... show more

References
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40 results found


Open accessJournal ArticleDOI: 10.1093/BIOINFORMATICS/BTP616
01 Jan 2010-Bioinformatics
Abstract: Summary: It is expected that emerging digital gene expression (DGE) technologies will overtake microarray technologies in the near future for many functional genomics applications. One of the fundamental data analysis tasks, especially for gene expression studies, involves determining whether there is evidence that counts for a transcript or exon are significantly different across experimental conditions. edgeR is a Bioconductor software package for examining differential expression of replicated count data. An overdispersed Poisson model is used to account for both biological and technical variability. Empirical Bayes methods are used to moderate the degree of overdispersion across transcripts, improving the reliability of inference. The methodology can be used even with the most minimal levels of replication, provided at least one phenotype or experimental condition is replicated. The software may have other applications beyond sequencing data, such as proteome peptide count data. Availability: The package is freely available under the LGPL licence from the Bioconductor web site (http://bioconductor.org).

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Topics: Bioconductor (64%)

21,575 Citations


Open accessJournal ArticleDOI: 10.1038/NRG2484
Zhong Wang1, Mark Gerstein1, Michael Snyder1Institutions (1)
Abstract: RNA-Seq is a recently developed approach to transcriptome profiling that uses deep-sequencing technologies. Studies using this method have already altered our view of the extent and complexity of eukaryotic transcriptomes. RNA-Seq also provides a far more precise measurement of levels of transcripts and their isoforms than other methods. This article describes the RNA-Seq approach, the challenges associated with its application, and the advances made so far in characterizing several eukaryote transcriptomes.

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Topics: De novo transcriptome assembly (53%), RNA-Seq (51%), Transcriptome (50%)

10,295 Citations


Open accessJournal ArticleDOI: 10.1038/NPROT.2012.016
Cole Trapnell1, Adam Roberts2, Loyal A. Goff3, Loyal A. Goff1  +11 moreInstitutions (7)
01 Mar 2012-Nature Protocols
Abstract: Recent advances in high-throughput cDNA sequencing (RNA-seq) can reveal new genes and splice variants and quantify expression genome-wide in a single assay. The volume and complexity of data from RNA-seq experiments necessitate scalable, fast and mathematically principled analysis software. TopHat and Cufflinks are free, open-source software tools for gene discovery and comprehensive expression analysis of high-throughput mRNA sequencing (RNA-seq) data. Together, they allow biologists to identify new genes and new splice variants of known ones, as well as compare gene and transcript expression under two or more conditions. This protocol describes in detail how to use TopHat and Cufflinks to perform such analyses. It also covers several accessory tools and utilities that aid in managing data, including CummeRbund, a tool for visualizing RNA-seq analysis results. Although the procedure assumes basic informatics skills, these tools assume little to no background with RNA-seq analysis and are meant for novices and experts alike. The protocol begins with raw sequencing reads and produces a transcriptome assembly, lists of differentially expressed and regulated genes and transcripts, and publication-quality visualizations of analysis results. The protocol's execution time depends on the volume of transcriptome sequencing data and available computing resources but takes less than 1 d of computer time for typical experiments and ∼1 h of hands-on time.

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Topics: MRNA Sequencing (61%), RNA-Seq (54%)

9,549 Citations


Journal ArticleDOI: 10.1038/NBT.3519
Abstract: We present kallisto, an RNA-seq quantification program that is two orders of magnitude faster than previous approaches and achieves similar accuracy. Kallisto pseudoaligns reads to a reference, producing a list of transcripts that are compatible with each read while avoiding alignment of individual bases. We use kallisto to analyze 30 million unaligned paired-end RNA-seq reads in <10 min on a standard laptop computer. This removes a major computational bottleneck in RNA-seq analysis.

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4,396 Citations


Open accessJournal ArticleDOI: 10.1038/NMETH.4197
Rob Patro1, Geet Duggal, Michael I. Love2, Rafael A. Irizarry2  +1 moreInstitutions (3)
01 Apr 2017-Nature Methods
Abstract: We introduce Salmon, a lightweight method for quantifying transcript abundance from RNA-seq reads. Salmon combines a new dual-phase parallel inference algorithm and feature-rich bias models with an ultra-fast read mapping procedure. It is the first transcriptome-wide quantifier to correct for fragment GC-content bias, which, as we demonstrate here, substantially improves the accuracy of abundance estimates and the sensitivity of subsequent differential expression analysis.

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3,535 Citations


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