CATANA: a tool for generating comprehensive annotations of alternative transcript events

Shiau, Cheng-Kai; Huang, Jia-Hsin; Tsai, Huai-Kuang

doi:10.1093/bioinformatics/bty795

Cited by 5 publications

(8 citation statements)

References 9 publications

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“…Details of each step and additional filtering steps are described in Supplementary Note 1. ParasiTE further classifies altTE-Gis into TE-associated alternative splicing (TE-AS) and TE-associated alternative transcript production (TE-ATP) according to the associated RNA processing events detected by the tool CATANA 48 . TE-AS events include TE-A5SS, TE-A3SS, TE-ES, and TE-IR.…”

Section: Resultsmentioning

confidence: 99%

“…TE-AS events include TE-A5SS, TE-A3SS, TE-ES, and TE-IR. TE-ATP events include TE-ATSS and TE-ATTS, and ParasiTE further distinguishes TE-associated alternative first exon (TE-AFE) from TE-ATSS and TE-ALE TE-associated alternative last exon (TE-ALE) from TE-ATTS 51 (Supplementary Note 1). Validation of ParasiTE with Araport11 transcript annotation and manual inspection of the output data demonstrated that ParasiTE could detect TE-ATP events with higher accuracy than TE-AS events (Supplementary Note 1).…”

Section: Resultsmentioning

confidence: 99%

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Long-read direct RNA sequencing reveals epigenetic regulation of chimeric gene-transposon transcripts in Arabidopsis thaliana

Berthelier

Furci

Asai

et al. 2022

Preprint

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Transposable elements (TEs) are accumulated in both intergenic and intragenic regions in plant genomes. Intragenic TEs often act as regulatory elements of associated genes, and are also co-transcribed with genes, generating chimeric TE-gene transcripts. Despite its potential impacts on mRNA regulation and gene function, the prevalence and transcriptional regulation of TE-gene transcripts remain elusive. By the long-read Direct RNA Sequencing (DRS) and a dedicated bioinformatic pipeline ParasiTE, we investigated transcription and RNA processing of TE-gene transcripts in Arabidopsis thaliana. We identified that thousands of Arabidopsis gene loci generate TE-gene transcripts, where in many loci TEs are associated with alternative Transcription Start Sites (ATSS) or Transcription Termination Sites (ATTS). Epigenetic state of intragenic TE affects PolII elongation and usage of alternative polyA signals in TE sequences, regulating alternative TE-gene isoform production. Co-transcription and inclusion of TE-derived sequence into gene transcripts impacts regulation of RNA stability and environmental responses in some loci. Our study provides novel insights into TE-gene interaction that contributes to mRNA regulation and transcriptome diversity in plants.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Long-read direct RNA sequencing reveals epigenetic regulation of chimeric gene-transposon transcripts in Arabidopsis thaliana

Berthelier

Furci

Asai

et al. 2022

Preprint

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“…The v94 human and mouse genome annotations were downloaded from Ensembl. CATANA [ 25 ] was used upon the human and mouse genome annotation to obtain the latest version of AS annotation. The latest AS annotation and the mapped bam files (from data preparation) were used for MISO [ 26 ] to compute percent splice in (PSI), which is an inclusion index based on the number of junction reads [ 27 ].…”

Section: Methodsmentioning

confidence: 99%

Genome-wide identification of associations between enhancer and alternative splicing in human and mouse

et al. 2021

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Background Alternative splicing (AS) increases the diversity of transcriptome and could fine-tune the function of genes, so that understanding the regulation of AS is vital. AS could be regulated by many different cis-regulatory elements, such as enhancer. Enhancer has been experimentally proved to regulate AS in some genes. However, there is a lack of genome-wide studies on the association between enhancer and AS (enhancer-AS association). To bridge the gap, here we developed an integrative analysis on a genome-wide scale to identify enhancer-AS associations in human and mouse. Result We collected enhancer datasets which include 28 human and 24 mouse tissues and cell lines, and RNA-seq datasets which are paired with the selected tissues. Combining with data integration and statistical analysis, we identified 3,242 human and 7,716 mouse genes which have significant enhancer-AS associations in at least one tissue. On average, for each gene, about 6% of enhancers in human (5% in mouse) are associated to AS change and for each enhancer, approximately one gene is identified to have enhancer-AS association in both human and mouse. We found that 52% of the human significant (34% in mouse) enhancer-AS associations are the co-existence of homologous genes and homologous enhancers. We further constructed a user-friendly platform, named Visualization of Enhancer-associated Alternative Splicing (VEnAS, http://venas.iis.sinica.edu.tw/), to provide genomic architecture, intuitive association plot, and contingency table of the significant enhancer-AS associations. Conclusion This study provides the first genome-wide identification of enhancer-AS associations in human and mouse. The results suggest that a notable portion of enhancers are playing roles in AS regulations. The analyzed results and the proposed platform VEnAS would provide a further understanding of enhancers on regulating alternative splicing.

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“…Isoform events were identified among novel isoforms and reference transcripts using the CATANA tool [97] with default settings. The transcript annotation (.gtf) file together with the PlasmoDB-53 annotation were used as inputs for CATANA.…”

Section: Characterization Of Isoform Eventsmentioning

confidence: 99%

“…(XLSX) S3 Table . Isoform events in the transcriptomic catalog. Isoform events identified by CAT-ANA [97] among reference transcripts (S3A) and novel isoforms (S3B). Event identifier is shown in column 1 (event).…”

Section: S8mentioning

confidence: 99%

Transcriptomic complexity of the human malaria parasite Plasmodium falciparum revealed by long-read sequencing

et al. 2022

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The Plasmodium falciparum human malaria parasite genome is incompletely annotated and does not accurately represent the transcriptomic diversity of this species. To address this need, we performed long-read transcriptomic sequencing. 5′ capped mRNA was enriched from samples of total and nuclear-fractionated RNA from intra-erythrocytic stages and converted to cDNA library. The cDNA libraries were sequenced on PacBio and Nanopore long-read platforms. 12,495 novel isoforms were annotated from the data. Alternative 5′ and 3′ ends represent the majority of isoform events among the novel isoforms, with retained introns being the next most common event. The majority of alternative 5′ ends correspond to genomic regions with features similar to those of the reference transcript 5′ ends. However, a minority of alternative 5′ ends showed markedly different features, including locations within protein-coding regions. Alternative 3′ ends showed similar features to the reference transcript 3′ ends, notably adenine-rich termination signals. Distinguishing features of retained introns could not be observed, except for a tendency towards shorter length and greater GC content compared with spliced introns. Expression of antisense and retained intron isoforms was detected at different intra-erythrocytic stages, suggesting developmental regulation of these isoform events. To gain insights into the possible functions of the novel isoforms, their protein-coding potential was assessed. Variants of P. falciparum proteins and novel proteins encoded by alternative open reading frames suggest that P. falciparum has a greater proteomic repertoire than the current annotation. We provide a catalog of annotated transcripts and encoded alternative proteins to support further studies on gene and protein regulation of this pathogen.

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CATANA: a tool for generating comprehensive annotations of alternative transcript events

Abstract: Supplementary data are available at Bioinformatics online.

Cited by 5 publications

References 9 publications

Long-read direct RNA sequencing reveals epigenetic regulation of chimeric gene-transposon transcripts in Arabidopsis thaliana

Long-read direct RNA sequencing reveals epigenetic regulation of chimeric gene-transposon transcripts in Arabidopsis thaliana

Genome-wide identification of associations between enhancer and alternative splicing in human and mouse

Transcriptomic complexity of the human malaria parasite Plasmodium falciparum revealed by long-read sequencing

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