SUPPA2: fast, accurate, and uncertainty-aware differential splicing analysis across multiple conditions

Genome biology, Год журнала: 2018, Номер 19(1)

Опубликована: Март 23, 2018

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 Transformer2-regulated exons, microexons induced during differentiation of bipolar neurons, intron retention events erythroblast differentiation.

Язык: Английский

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Nanopore direct RNA sequencing maps the complexity of Arabidopsis mRNA processing and m6A modification

eLife, Год журнала: 2020, Номер 9

Опубликована: Янв. 14, 2020

Understanding genome organization and gene regulation requires insight into RNA transcription, processing modification. We adapted nanopore direct sequencing to examine from a wild-type accession of the model plant Arabidopsis thaliana mutant defective in mRNA methylation (m6A). Here we show that m6A can be mapped full-length mRNAs transcriptome-wide reveal combinatorial diversity cap-associated transcription start sites, splicing events, poly(A) site choice tail length. Loss 3’ untranslated regions is associated with decreased relative transcript abundance 3′ end formation. A functional consequence disrupted lengthening circadian period. conclude complexity modification single molecule reads. These findings refine annotation. Further, applying this approach less well-studied species could transform our understanding what their genomes encode.

Язык: Английский

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Rapid and Dynamic Alternative Splicing Impacts the Arabidopsis Cold Response Transcriptome

The Plant Cell, Год журнала: 2018, Номер 30(7), С. 1424 - 1444

Опубликована: Май 15, 2018

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, hundreds genes showed changes due rapidly ("early AS" genes); these included numerous novel cold-responsive transcription factors factors/RNA binding proteins regulated only AS. speed sensitivity small some suggest that fine-tuning via pathways contributes thermo-plasticity expression. Four early regulatory been shown previously be required for freezing tolerance acclimation; we provide evidence fifth gene, U2B"-LIKE Such likely drive cascades downstream that, alongside transcription, modulate transcriptome together govern physiological survival low temperature.

Язык: Английский

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Activation of TIR signalling boosts pattern-triggered immunity

Nature, Год журнала: 2021, Номер 598(7881), С. 500 - 503

Опубликована: Сен. 20, 2021

Язык: Английский

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Alternative Splicing and Protein Diversity: Plants Versus Animals

Frontiers in Plant Science, Год журнала: 2019, Номер 10

Опубликована: Июнь 12, 2019

Plants, unlike animals, exhibit a very high degree of plasticity in their growth and development employ diverse strategies to cope with the variations during diurnal cycles stressful conditions. Plants despite remarkable morphological physiological differences, share many basic cellular processes regulatory mechanisms. Alternative Splicing (AS) is one such gene mechanism that modulates expression multiple ways. It now well established AS prevalent all multicellular eukaryotes including plants humans. Emerging evidence indicates plants, as transcription splicing are coupled. Here, we reviewed recent support co-transcriptional highlighted similarities differences between An unsettled question field extent which splice isoforms contribute protein diversity. To take critical look at this question, presented comprehensive summary current status research area both humans, discussed limitations currently used approaches suggested improvements methods alternative approaches. We end discussion on potential role epigenetic modifications chromatin state memory primed stresses.

Язык: Английский

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The changing paradigm of intron retention: regulation, ramifications and recipes

Nucleic Acids Research, Год журнала: 2019, Номер unknown

Опубликована: Окт. 30, 2019

Abstract Intron retention (IR) is a form of alternative splicing that has long been neglected in mammalian systems although it studied for decades non-mammalian species such as plants, fungi, insects and viruses. It was generally assumed mis-splicing, leading to the introns, would have no physiological consequence other than reducing gene expression by nonsense-mediated decay. Relatively recent landmark discoveries highlighted pivotal role IR serves normal disease-related human biology. Significant technical hurdles overcome, thereby enabling robust detection quantification IR. Still, relatively little known about cis- trans-acting modulators controlling this phenomenon. The fate an intron be, or not retained mature transcript direct result influence exerted numerous intrinsic extrinsic factors at multiple levels regulation. These altered current biological paradigms provided unexpected insights into transcriptional landscape. In review, we discuss regulators methods identify them. Our focus primarily on mammals, however, broaden scope organisms which shown be biologically relevant.

Язык: Английский

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Alternative splicing landscapes in Arabidopsis thaliana across tissues and stress conditions highlight major functional differences with animals

Genome biology, Год журнала: 2021, Номер 22(1)

Опубликована: Янв. 14, 2021

Abstract Background Alternative splicing (AS) is a widespread regulatory mechanism in multicellular organisms. Numerous transcriptomic and single-gene studies plants have investigated AS response to specific conditions, especially environmental stress, unveiling substantial amounts of intron retention that modulate gene expression. However, comprehensive study contrasting stress-response tissue-specific patterns directly comparing them with those animal models still missing. Results We generate massive resource for Arabidopsis thaliana , PastDB comprising expression quantifications across tissues, development including abiotic biotic stresses. Harmonized analysis these datasets reveals A. shows high levels AS, similar fruitflies, that, compared animals, disproportionately uses stress responses. identify core sets genes regulated specifically by either or transcription upon stresses among specialization tightly mirrored the genomic features genes. Unexpectedly, non-intron events, exon skipping, are overrepresented being also largely involved modulating through NMD uORF inclusion. Conclusions Non-intron events likely been functionally underrated plants. constitutes distinct layer controlling internal external stimuli whose target master regulators hardwired at level undergo post-transcriptional regulation. Given higher relevance different when this molecular hardwiring required proper .

Язык: Английский

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The evolutionary emergence of land plants

Current Biology, Год журнала: 2021, Номер 31(19), С. R1281 - R1298

Опубликована: Окт. 1, 2021

Язык: Английский

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Gene Body Methylation in Plants: Mechanisms, Functions, and Important Implications for Understanding Evolutionary Processes

Genome Biology and Evolution, Год журнала: 2022, Номер 14(4)

Опубликована: Март 16, 2022

Gene body methylation (gbM) is an epigenetic mark where gene exons are methylated in the CG context only, as opposed to CHG and CHH contexts (where H stands for A, C, or T). transmitted transgenerationally plants, opening possibility that gbM may be shaped by adaptation. This presupposes, however, has a function affects phenotype, which been topic of debate literature. Here, we review our current knowledge plants. We start presenting well-elucidated mechanisms plant establishment maintenance. then more controversial topics: evolution potential selective pressures act on it. Finally, discuss functions affect organismal phenotypes: expression stabilization upregulation, inhibition aberrant transcription (reverse internal), prevention intron retention, protection against TE insertions. To bolster these topics, include novel analyses assess effect transcripts. Overall, growing literature finds correlates with levels patterns expression. It not clear, if this causal relationship. Altogether, functional work suggests effects gbM, any, must relatively small, but there nonetheless evidence it natural selection. conclude discussing adaptive character its implications updated view adaptation

Язык: Английский

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A barley pan-transcriptome reveals layers of genotype-dependent transcriptional complexity

Nature Genetics, Год журнала: 2025, Номер unknown

Опубликована: Фев. 3, 2025

Abstract A pan-transcriptome describes the transcriptional and post-transcriptional consequences of genome diversity from multiple individuals within a species. We developed barley using 20 inbred genotypes representing domesticated by generating analyzing short- long-read RNA-sequencing datasets tissues. To overcome single reference bias in transcript quantification, we constructed genotype-specific (RTDs) integrated these into linear pan-genome framework to create pan-RTD, allowing categorization as core, shell or cloud. Focusing on core (expressed all genotypes), observed significant abundance variation among tissues between driven partly RNA processing, gene copy number, structural rearrangements conservation promotor motifs. Network analyses revealed conserved co-expression module::tissue correlations frequent functional diversification. complement pan-transcriptome, comprehensive cultivar (cv.) Morex gene-expression atlas illustrate how combined can be used guide biological inquiry.

Язык: Английский

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