Large-scale analysis of the cassava transcriptome reveals the impact of cold stress on alternative splicing

2019 ◽  
Author(s):  
Shuxia Li ◽  
Xiang Yu ◽  
Zhihao Cheng ◽  
Changying Zeng ◽  
Wenbin Li ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
Drought Stress ◽  
Cold Stress ◽  
Large Scale ◽  
Intron Retention ◽  
Global Analysis ◽  
Premature Termination Codon ◽  
Alternatively Spliced ◽  
Alternative Splicing Events ◽  
The Impact

Abstract Alternative splicing is an essential post-transcriptional regulatory mechanism that can impact mRNA stability and protein diversity of eukaryotic genomes. Although numerous forms of stress-responsive alternative splicing have been identified in model plants, a large-scale study of alternative splicing dynamics under abiotic stress conditions in cassava has not been conducted. Here, we report the parallel employment of isoform-Seq, ssRNA-Seq, and Degradome-Seq to investigate the diversity, abundance, and fate of alternatively spliced isoforms in response to cold and drought stress. We identified 38 164 alternative splicing events, among which 3292 and 1025 events were significantly regulated by cold and drought stress, respectively. Intron retention was the most abundant subtype of alternative splicing. Global analysis of splicing regulators revealed that the number of their alternatively spliced isoforms and the corresponding abundance were specifically modulated by cold stress. We found that 58.5% of cold-regulated alternative splicing events introduced a premature termination codon into the transcripts, and 77.6% of differential alternative splicing events were detected by Degradome-Seq. Our data reveal that cold intensely affects both quantitative and qualitative aspects of gene expression via alternative splicing pathways, and advances our understanding of the high complexity and specificity of gene regulation in response to abiotic stresses. Alternative splicing is responsible for reprogramming of the transcriptome and the sensitivity of cassava plants to cold.

scholarly journals PacBio and Illumina RNA Sequencing Identify Alternative Splicing Events in Response to Cold Stress in Two Poplar Species

2021 ◽  
Vol 12 ◽  
Author(s):  
Jingli Yang ◽  
Wanqiu Lv ◽  
Liying Shao ◽  
Yanrui Fu ◽  
Haimei Liu ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
Stress Response ◽  
Cold Stress ◽  
Rna Sequencing ◽  
Single Molecule ◽  
Intron Retention ◽  
Global Analysis ◽  
Populus Trichocarpa ◽  
Rna Seq ◽  
Long Read

In eukaryotes, alternative splicing (AS) is a crucial regulatory mechanism that modulates mRNA diversity and stability. The contribution of AS to stress is known in many species related to stress, but the posttranscriptional mechanism in poplar under cold stress is still unclear. Recent studies have utilized the advantages of single molecular real-time (SMRT) sequencing technology from Pacific Bioscience (PacBio) to identify full-length transcripts. We, therefore, used a combination of single-molecule long-read sequencing and Illumina RNA sequencing (RNA-Seq) for a global analysis of AS in two poplar species (Populus trichocarpa and P. ussuriensis) under cold stress. We further identified 1,261 AS events in P. trichocarpa and 2,101 in P. ussuriensis among which intron retention, with a frequency of more than 30%, was the most prominent type under cold stress. RNA-Seq data analysis and annotation revealed the importance of calcium, abscisic acid, and reactive oxygen species signaling in cold stress response. Besides, the low temperature rapidly induced multiple splicing factors, transcription factors, and differentially expressed genes through AS. In P. ussuriensis, there was a rapid occurrence of AS events, which provided a new insight into the complexity and regulation of AS during cold stress response in different poplar species for the first time.

Transcriptome-wide analysis of alternative splicing events in bladder cancer: Novel biomarkers discovery for early diagnosis.

2018 ◽  
Vol 36 (6_suppl) ◽  
pp. 483-483
Author(s):  
Claudio Jeldres ◽  
Sabrina Bouchard ◽  
Michel Carmel ◽  
Patrick O Richard ◽  
Robert Sabbagh ◽  
...  
Keyword(s):  
Bladder Cancer ◽  
Alternative Splicing ◽  
Large Scale ◽  
Structural Changes ◽  
The Cancer Genome Atlas ◽  
P Value ◽  
Normal Tissues ◽  
Normal Bladder ◽  
Alternative Splicing Events ◽  
The Impact

483 Background: Cystoscopy, an invasive, painful and expensive method, is currently the main clinical tool for new diagnosis and disease recurrence detection of bladder cancer (BCa). The need for new biomarkers discovery that is costless, sensitive and specific is urgent. This project aims to study and compare alternative splicing events (ASE) in BCa tissues and normal bladder tissues and ultimately, identify specific spliced events coding for proteins detectable in urine by liquid chromatography–mass spectrometry. Methods: In this study, alterations to the global RNA splicing landscape of cellular genes were investigated in a large-scale screen from 408 BCa tissues and 19 normal tissues provided by The Cancer Genome Atlas (TCGA). Three statistical thresholds were used to determine substantial modifications. All events showing a p-value<0.05 and a level of expression ≥ 50 transcripts per million; -10 ≥ Δ percent splice index ≤10; and a q-value<0.05 were conserved. Next, mRNA expression levels between cancer and normal tissues were compared for all splicing factors and the spliceosome to determine the impact of gene dysregulation on alternative splicing events. Using multiple bioinformatic platforms such as EASANA, MultAlin, ExPasy, NLS Mapper and Pfam, splicing events responsible for significant protein structural changes between cancer and healthy tissue were selected. From this sample chosen, ASEs coding for proteins that could be detected in urine were conserved. Results: Our study identifies modifications in the alternative splicing patterns of 107 transcripts encoded by 97 genes. STRING analysis revealed that many of the gene products interact either directly or indirectly with each other (enrichment p-value = 1x10-10). 61 ASEs are causing important protein changes from which 27 can be detected in urine. Finally, 16 ASEs coding for easily recognizable peptide sequences in urine represented significant targets for potential BCa biomarkers. Conclusions: The TCGA data show the relevance to investigate alternative splicing events in bladder cancer. 16 significant events were detectable in urine and may potentially discriminate between presence or absence of bladder cancer.

scholarly journals PacBio and Illumina RNA sequencing identify alternative splicing events in response to cold stress in two poplar species

2020 ◽  
Author(s):  
Jingli Yang ◽  
Wanqiu Lv ◽  
Minzhen Zeng ◽  
Yanrui Fu ◽  
Chenghao Li
Keyword(s):  
Alternative Splicing ◽  
Stress Response ◽  
Cold Stress ◽  
Rna Sequencing ◽  
Single Molecule ◽  
Intron Retention ◽  
Global Analysis ◽  
Populus Trichocarpa ◽  
Rna Seq ◽  
Long Read

In eukaryotes, alternative splicing (AS) is a crucial regulatory mechanism that modulates mRNA diversity and stability. The contribution of AS to stress are known in many species related to stress. But the post-transcriptional mechanism in poplar under cold stress is still unclear. Recent studies have utilized the advantages of Single Molecular Real Time (SMRT) sequencing technology from Pacific Bioscience (PacBio) to identify full-length transcripts. We, therefore, used a combination of single-molecule long-read sequencing and Illumina RNA sequencing (RNA-Seq) for a global analysis of AS in two poplar species (Populus trichocarpa and P. ussuriensis) under cold stress. We further identified 1261 AS events in P. trichocarpa and 2101 in P. ussuriensis, among which intron retention, with a frequency of more than 30%, was the most prominent type under cold stress. RNA-Seq data analysis and annotation revealed the importance of calcium, abscisic acid, and reactive oxygen species signaling in cold stress response. Besides, the low temperature rapidly induced multiple splicing factors, transcription factors, and differentially expressed genes through AS. In P. ussuriensis, there was a rapid occurrence of AS events. This study provides new insight into the complexity and regulation of AS during cold stress response in two poplar species.

scholarly journals Alternative Splicing of Transcription Factors' Genes: Beyond the Increase of Proteome Diversity

2009 ◽  
Vol 2009 ◽  
pp. 1-6 ◽  
Author(s):  
David Talavera ◽  
Modesto Orozco ◽  
Xavier de la Cruz
Keyword(s):  
Transcription Factors ◽  
Alternative Splicing ◽  
Expression Patterns ◽  
Developmental Changes ◽  
Functional Families ◽  
Transcription Regulators ◽  
Alternatively Spliced ◽  
The Impact ◽  
Human And Mouse

Functional modification of transcription regulators may lead to developmental changes and phenotypical differences between species. In this work, we study the influence of alternative splicing on transcription factors in human and mouse. Our results show that the impact of alternative splicing on transcription factors is similar in both species, meaning that the ways to increase variability should also be similar. However, when looking at the expression patterns of transcription factors, we observe that they tend to diverge regardless of the role of alternative splicing. Finally, we hypothesise that transcription regulation of alternatively spliced transcription factors could play an important role in the phenotypical differences between species, without discarding other phenomena or functional families.

scholarly journals Determining the impact of alternative splicing events on transcriptome dynamics

2008 ◽  
Vol 1 (1) ◽  
pp. 94 ◽  
Author(s):  
Emmanuelle Wilhelm ◽  
François-Xavier Pellay ◽  
Arndt Benecke ◽  
Brendan Bell
Keyword(s):  
Alternative Splicing ◽  
Alternative Splicing Events ◽  
The Impact

scholarly journals Alternative Splicing in the Obligate Biotrophic Oomycete Pathogen Pseudoperonospora cubensis

2015 ◽  
Vol 28 (3) ◽  
pp. 298-309 ◽  
Author(s):  
Alyssa Burkhardt ◽  
Alex Buchanan ◽  
Jason S. Cumbie ◽  
Elizabeth A. Savory ◽  
Jeff H. Chang ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
Intron Retention ◽  
Draft Genome ◽  
Pseudoperonospora Cubensis ◽  
Rna Seq ◽  
Transcriptome Regulation ◽  
Oomycete Pathogen ◽  
Alternatively Spliced ◽  
Genome Annotations ◽  
Obligate Pathogen

Pseudoperonospora cubensis is an obligate pathogen and causative agent of cucurbit downy mildew. To help advance our understanding of the pathogenicity of P. cubensis, we used RNA-Seq to improve the quality of its reference genome sequence. We also characterized the RNA-Seq dataset to inventory transcript isoforms and infer alternative splicing during different stages of its development. Almost half of the original gene annotations were improved and nearly 4,000 previously unannotated genes were identified. We also demonstrated that approximately 24% of the expressed genome and nearly 55% of the intron-containing genes from P. cubensis had evidence for alternative splicing. Our analyses revealed that intron retention is the predominant alternative splicing type in P. cubensis, with alternative 5′- and alternative 3′-splice sites occurring at lower frequencies. Representatives of the newly identified genes and predicted alternatively spliced transcripts were experimentally validated. The results presented herein highlight the utility of RNA-Seq for improving draft genome annotations and, through this approach, we demonstrate that alternative splicing occurs more frequently than previously predicted. In total, the current study provides evidence that alternative splicing plays a key role in transcriptome regulation and proteome diversification in plant-pathogenic oomycetes.

scholarly journals The Emergence of the Metabolic Signaling of the Nucleoredoxin-like Genes during Evolution

2022 ◽  
Author(s):  
Najate Ait-Ali ◽  
Frederic Blond ◽  
Emmanuelle Clerin ◽  
Ala Morshedian ◽  
Quenol Cesar ◽  
...  
Keyword(s):  
Biological Activity ◽  
Alternative Splicing ◽  
Intron Retention ◽  
Hydra Vulgaris ◽  
Metabolic Signaling ◽  
Retinal Degenerations ◽  
Animal Phyla ◽  
Alternatively Spliced ◽  
Early Vertebrates ◽  
Rod And Cone Photoreceptors

The nucleoredoxin-like genes NXNL1 and NXNL2 were identified through the biological activity of rod-derived cone viability factors (RdCVF and RdCVF2), the alternatively spliced variants produced by intron retention, that mediate signaling between rod and cone photoreceptors by stimulating glucose uptake. These therapeutic genes for inherited retinal degenerations also produce by splicing thioredoxin-like proteins that reduce oxidized cysteines in photoreceptor proteins. The first NXNL genes date from the first animal phyla. Intron retention produces an active RdCVF protein in the tentacles of Hydra vulgaris, a species without eyes. A Scallop RdCVF protein is produced by ciliated photoreceptors of the retina and binds its receptor, BSG1. In the lamprey, a descendent of early vertebrates, RdCVF metabolic signaling between rod and cones is fully established. In the mouse, the production of BSG1 by photoreceptors is regulated by cell-specific splicing inhibition. RdCVF signaling predates photoreceptors and evolved through two alternative splicing events.

scholarly journals Temporal regulation of alternative splicing events in rice memory under drought stress

2020 ◽  
Author(s):  
Hong Yang ◽  
Ping Li ◽  
Guihua Jin ◽  
Daping Gui ◽  
Li Liu ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
Drought Stress ◽  
Temporal Regulation ◽  
Alternative Splicing Events

The RNA Environment Of Hematopoietic Stem Cells

Blood ◽  
2013 ◽  
Vol 122 (21) ◽  
pp. 1171-1171
Author(s):  
George R Wendt ◽  
Motohiko Oshima ◽  
Atsushi Iwama
Keyword(s):  
Stem Cells ◽  
Alternative Splicing ◽  
Hematopoietic Stem Cells ◽  
Rna Editing ◽  
Critical Role ◽  
Hematopoietic Stem ◽  
Rna Biology ◽  
Alternatively Spliced ◽  
Non Coding Rnas ◽  
Alternative Splicing Events

Abstract Recent reports in RNA biology have suggested that long non-coding RNAs, edited RNAs, and alternatively spliced RNAs (henceforth referred to as non-canonical RNAs) play a relatively unclear but critical role in numerous cells, tissues, and diseases. Of interest to hematology, several recent studies have also shown that these non-canonical RNAs all play various roles in both normal and malignant hematopoiesis, but no study yet has comprehensively examined these non-canonical RNAs in hematopoietic stem cells (HSCs). To this end, we conducted microarray and RNAseq analyses of mouse hematopoietic cells at various stages of differentiation. Microarray analysis detected several thousand possible lincRNAs expressed in hematopoietic stem and progenitor cells (HSPCs), several hundred of which were significantly enriched in CD34-LSKs compared to more differentiated populations. RNAseq analysis provided a more detailed look at these non-coding RNAs, as well as a slightly more conservative estimate of the abundance and structure of the long non-coding RNAs expressed and significantly enriched in HSPCs. In addition to examining lincRNAs, RNAseq data allowed us to profile alternative splicing events and RNA editing events in HSPCs. Interestingly, several hundred potentially significant HSC-specific alternative splicing events and RNA editing events were also discovered. In order to test whether these non-canonical RNAs play a functional role in HSPCs we performed shRNA mediated knockdown of several interesting HSC-specific lincRNAs and alternatively-spliced transcripts. We found that knockdown of several of these candidates was incompatible with hematopoiesis, both in vitro and in vivo. To better understand how these particular non-canonical RNAs function in HSCs, we are currently carrying out RNA FISH studies. In this study, we explored the RNA environment of HSCs and compared it to their downstream progenitors. We discovered several hundred novel non-coding transcripts, hundreds of alternative splicing events and hundreds of RNA editing events unique to HSCs. Functional investigation of some of these events revealed that these non-canonical RNAs do indeed play a critical role in HSC maintenance. The data presented here should eventually be an asset to other HSC researchers interested in the RNA biology of HSCs. Disclosures: No relevant conflicts of interest to declare.

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