scholarly journals Analysis of Alternative Splicing and Alternative Polyadenylation in Populus alba var. pyramidalis by Single-Molecular Long-Read Sequencing

2020 ◽  
Vol 11 ◽  
Author(s):  
Hongyin Hu ◽  
Wenlu Yang ◽  
Zeyu Zheng ◽  
Zhimin Niu ◽  
Yongzhi Yang ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
Alternative Polyadenylation ◽  
Populus Alba ◽  
Long Read

scholarly journals Elav-mediated exon skipping and alternative polyadenylation of the Dscam1 gene is required for axon outgrowth

2019 ◽  
Author(s):  
Z. Zhang ◽  
K. So ◽  
R. Peterson ◽  
M. Bauer ◽  
H. Ng ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
Neural Development ◽  
Rna Binding ◽  
Axon Growth ◽  
Alternative Polyadenylation ◽  
Axon Outgrowth ◽  
List Type ◽  
Long Read ◽  
Upstream Exon ◽  
Exon 19

SummaryMany metazoan genes express alternative long 3′ UTR isoforms in the nervous system, but their functions remain largely unclear. In Drosophila melanogaster, the Dscam1 gene generates short and long (Dscam1-L) 3′ UTR isoforms due to alternative polyadenylation (APA). Here, we found that the RNA-binding protein Embryonic Lethal Abnormal Visual System (Elav) impacts Dscam1 biogenesis at two levels, including regulation of long 3′ UTR biogenesis and skipping of an upstream exon (exon 19). MinION long-read sequencing confirmed the connectivity of this alternative splicing event to the long 3′ UTR. Knockdown or CRISPR deletion of Dscam1-L impaired axon growth in Drosophila. The Dscam1 long 3′ UTR was found to be required for correct Elav-mediated skipping of exon 19. Elav thus co-regulates APA and alternative splicing to generate specific Dscam1 transcripts that are essential for neural development. This coupling of APA to alternative splicing might represent a new class of regulated RNA processing. Graphical AbstractHighlightsElav regulates Dscam1 long 3′ UTR (Dscam1-L) biogenesisLong-read sequencing reveals connectivity of long 3′ UTR to skipping of upstream exon 19Loss of Dscam1-L impairs axon outgrowthDscam1 long 3′ UTR is required for correct splicing of exon 19

scholarly journals Single-Molecule Long-Read Sequencing Reveals the Diversity of Full-Length Transcripts in Leaves of Gnetum (Gnetales)

2019 ◽  
Vol 20 (24) ◽  
pp. 6350 ◽  
Author(s):  
Nan Deng ◽  
Chen Hou ◽  
Fengfeng Ma ◽  
Caixia Liu ◽  
Yuxin Tian
Keyword(s):  
Single Molecule ◽  
Developmental Stages ◽  
Alternative Polyadenylation ◽  
Full Length ◽  
Stomatal Development ◽  
Rna Seq ◽  
Leaf Transcriptome ◽  
Long Read ◽  
Non Coding Rnas ◽  
A Site

The limitations of RNA sequencing make it difficult to accurately predict alternative splicing (AS) and alternative polyadenylation (APA) events and long non-coding RNAs (lncRNAs), all of which reveal transcriptomic diversity and the complexity of gene regulation. Gnetum, a genus with ambiguous phylogenetic placement in seed plants, has a distinct stomatal structure and photosynthetic characteristics. In this study, a full-length transcriptome of Gnetum luofuense leaves at different developmental stages was sequenced with the latest PacBio Sequel platform. After correction by short reads generated by Illumina RNA-Seq, 80,496 full-length transcripts were obtained, of which 5269 reads were identified as isoforms of novel genes. Additionally, 1660 lncRNAs and 12,998 AS events were detected. In total, 5647 genes in the G. luofuense leaves had APA featured by at least one poly(A) site. Moreover, 67 and 30 genes from the bHLH gene family, which play an important role in stomatal development and photosynthesis, were identified from the G. luofuense genome and leaf transcripts, respectively. This leaf transcriptome supplements the reference genome of G. luofuense, and the AS events and lncRNAs detected provide valuable resources for future studies of investigating low photosynthetic capacity of Gnetum.

scholarly journals Comparative transcriptome analysis of male and female flowers in Spinacia oleracea L

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Ning Li ◽  
Ziwei Meng ◽  
Minjie Tao ◽  
Yueyuan Wang ◽  
Yulan Zhang ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
Transcriptome Analysis ◽  
Spinacia Oleracea ◽  
Sex Differentiation ◽  
Alternative Polyadenylation ◽  
Gender Development ◽  
Comparative Transcriptome ◽  
Male And Female ◽  
First Time ◽  
Female Flowers

Abstract Background Dioecious spinach (Spinacia oleracea L.), a commercial and nutritional vegetable crop, serves as a model for studying the mechanisms of sex determination and differentiation in plants. However, this mechanism is still unclear. Herein, based on PacBio Iso-seq and Illumina RNA-seq data, comparative transcriptome analysis of male and female flowers were performed to explore the sex differentiation mechanism in spinach. Results Compared with published genome of spinach, 10,800 transcripts were newly annotated; alternative splicing, alternative polyadenylation and lncRNA were analyzed for the first time, increasing the diversity of spinach transcriptome. A total of 2965 differentially expressed genes were identified between female and male flowers at three early development stages. The differential expression of RNA splicing-related genes, polyadenylation-related genes and lncRNAs suggested the involvement of alternative splicing, alternative polyadenylation and lncRNA in sex differentiation. Moreover, 1946 male-biased genes and 961 female-biased genes were found and several candidate genes related to gender development were identified, providing new clues to reveal the mechanism of sex differentiation. In addition, weighted gene co-expression network analysis showed that auxin and gibberellin were the common crucial factors in regulating female or male flower development; however, the closely co-expressed genes of these two factors were different between male and female flower, which may result in spinach sex differentiation. Conclusions In this study, 10,800 transcripts were newly annotated, and the alternative splicing, alternative polyadenylation and long-noncoding RNA were comprehensively analyzed for the first time in spinach, providing valuable information for functional genome study. Moreover, candidate genes related to gender development were identified, shedding new insight on studying the mechanism of sex determination and differentiation in plant.

scholarly journals DSCAM-AS1-Driven Proliferation of Breast Cancer Cells Involves Regulation of Alternative Exon Splicing and 3′-End Usage

Cancers ◽  
2020 ◽  
Vol 12 (6) ◽  
pp. 1453 ◽  
Author(s):  
Jamal Elhasnaoui ◽  
Valentina Miano ◽  
Giulio Ferrero ◽  
Elena Doria ◽  
Antonette E. Leon ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
Clinical Data ◽  
Noncoding Rna ◽  
Estrogen Receptor Alpha ◽  
Exon Skipping ◽  
Alternative Polyadenylation ◽  
Luminal A ◽  
Her2 Positive ◽  
Public Datasets ◽  
Nuclear Ribonucleoprotein

DSCAM-AS1 is a cancer-related long noncoding RNA with higher expression levels in Luminal A, B, and HER2-positive Breast Carcinoma (BC), where its expression is strongly dependent on Estrogen Receptor Alpha (ERα). DSCAM-AS1 expression is analyzed in 30 public datasets and, additionally, by qRT-PCR in tumors from 93 BC patients, to uncover correlations with clinical data. Moreover, the effect of DSCAM-AS1 knockdown on gene expression and alternative splicing is studied by RNA-Seq in MCF-7 cells. We confirm DSCAM-AS1 overexpression in high grade Luminal A, B, and HER2+ BCs and find a significant correlation with disease relapse. In total, 908 genes are regulated by DSCAM-AS1-silencing, primarily involved in the cell cycle and inflammatory response. Noteworthily, the analysis of alternative splicing and isoform regulation reveals 2085 splicing events regulated by DSCAM-AS1, enriched in alternative polyadenylation sites, 3′UTR (untranslated region) shortening and exon skipping events. Finally, the DSCAM-AS1-interacting splicing factor heterogeneous nuclear ribonucleoprotein L (hnRNPL) is predicted as the most enriched RBP for exon skipping and 3′UTR events. The relevance of DSCAM-AS1 overexpression in BC is confirmed by clinical data and further enhanced by its possible involvement in the regulation of RNA processing, which is emerging as one of the most important dysfunctions in cancer.

scholarly journals Long-read transcriptome sequencing analysis with IsoTools

2021 ◽  
Author(s):  
Matthias Lienhard ◽  
Twan van den Beucken ◽  
Florian Claiment ◽  
Stefan Boerno ◽  
Myriam Hochradel ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
Transcriptome Sequencing ◽  
Sequencing Analysis ◽  
Differential Splicing ◽  
Accurate Analysis ◽  
Extensive Documentation ◽  
Long Read ◽  
Potential Applications ◽  
Transcriptional Changes ◽  
Analysis Package

Long-read transcriptome sequencing (LRTS) holds the promise to boost our understanding of alternative splicing. Recent advances in accuracy and throughput have diminished the major limitations and enabled the direct quantification of isoforms. Considering the complexity of the data and the broad range of potential applications, it is clear that highly flexible, accurate analysis tools are crucial. Here, we present IsoTools, a comprehensive Python-based analysis package, for the improvement of alternative and differential splicing analysis. IsoTools provides a comprehensive data structure that integrates genomic information from LRTS transcripts together with the reference annotation, and enables broad functionality to quality control, visualize and analyze the data. Additionally, we implemented a graph-based method for the identification of alternative splicing events and a statistical approach based on the beta binomial distribution for the detection of differential events. To demonstrate our methods, we generated PacBio Iso-Seq data of human hepatocytes treated with the HDAC inhibitor valproic acid, a compound known to induce widespread transcriptional changes. Contrasted with short read RNA-Seq of the same samples, this analysis shows that LRTS provides valuable additional insights for a better understanding of alternative splicing, in particular with respect to complex novel and differential splicing events. IsoTools is made available for the community along with extensive documentation at https://github.com/MatthiasLienhard/isotools.

scholarly journals Coupling between alternative polyadenylation and alternative splicing is limited to terminal introns (560.2)

2014 ◽  
Vol 28 (S1) ◽  
Author(s):  
Maliheh Movassat ◽  
Tara Crabb ◽  
Anke Busch ◽  
Yongsheng Shi ◽  
Klemens Hertel
Keyword(s):  
Alternative Splicing ◽  
Alternative Polyadenylation

scholarly journals Full-length Transcriptome Analysis of Pecan (Carya illinoinensis) Kernels

2021 ◽  
Author(s):  
Chengcai Zhang ◽  
Huadong Ren ◽  
Xiaohua Yao ◽  
Kailiang Wang ◽  
Jun Chang
Keyword(s):  
Single Molecule ◽  
Molecular Mechanisms ◽  
Draft Genome ◽  
Alternative Polyadenylation ◽  
Full Length ◽  
Functional Annotations ◽  
Predominant Type ◽  
Long Read ◽  
Non Coding Rnas ◽  
Novel Isoforms

Abstract Pecan is rich in bioactive components such as fatty acids and flavonoids and is an important nut type worldwide. Therefore, the molecular mechanisms of phytochemical biosynthesis in pecan are a focus of research. Recently, a draft genome and several transcriptomes have been published. However, the full-length mRNA transcripts remain unclear, and the regulatory mechanisms behind the quality components biosynthesis and accumulation have not been fully investigated. In this study, single-molecule long read sequencing technology was used to obtain full-length transcripts of pecan kernels. In total, 37 504 isoforms of 16 702 genes were mapped to the reference genome. The numbers of known isoforms, new isoforms, and novel isoforms were 9013 (24.03%), 26 080 (69.54%), and 2411 (6.51%), respectively. Over 80% of the transcripts (30 751, 81.99%) had functional annotations. A total of 15 465 alternative splicing (AS) events and 65 761 alternative polyadenylation events were detected; wherein, the retained intron was the predominant type (5652, 36.55%) of AS. Furthermore, 1894 long non-coding RNAs and 1643 transcription factors were predicted using bioinformatics methods. Finally, the structural genes associated with fatty acid (FA) and flavonoid biosynthesis were characterized. A high frequency of AS accuracy (70.31%) was observed in FA synthesis-associated genes. The present study provides a full-length transcriptome dataset of pecan kernels, which will significantly enhance the understanding of the regulatory basis of phytochemical biosynthesis during pecan kernel maturation.

scholarly journals Long read sequencing reveals novel isoforms and insights into splicing regulation during cell state changes

BMC Genomics ◽  
2022 ◽  
Vol 23 (1) ◽  
Author(s):  
David J. Wright ◽  
Nicola A. L. Hall ◽  
Naomi Irish ◽  
Angela L. Man ◽  
Will Glynn ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
Cellular Differentiation ◽  
Neuroblastoma Cell ◽  
Transcript Level ◽  
Neuroblastoma Cell Line ◽  
Future Research ◽  
Human Neuroblastoma Cell ◽  
Human Neuroblastoma ◽  
Cell State ◽  
Long Read

Abstract Background Alternative splicing is a key mechanism underlying cellular differentiation and a driver of complexity in mammalian neuronal tissues. However, understanding of which isoforms are differentially used or expressed and how this affects cellular differentiation remains unclear. Long read sequencing allows full-length transcript recovery and quantification, enabling transcript-level analysis of alternative splicing processes and how these change with cell state. Here, we utilise Oxford Nanopore Technologies sequencing to produce a custom annotation of a well-studied human neuroblastoma cell line SH-SY5Y, and to characterise isoform expression and usage across differentiation. Results We identify many previously unannotated features, including a novel transcript of the voltage-gated calcium channel subunit gene, CACNA2D2. We show differential expression and usage of transcripts during differentiation identifying candidates for future research into state change regulation. Conclusions Our work highlights the potential of long read sequencing to uncover previously unknown transcript diversity and mechanisms influencing alternative splicing.

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