Updated and enhanced pig cardiac transcriptome based on long-read RNA sequencing and proteomics

Müller, Torsten; Boileau, Etienne; Talyan, Sweta; Kehr, Dorothea; Varadi, Karl; Busch, Martin; Most, Patrick; Krijgsveld, Jeroen; Dieterich, Christoph

doi:10.1016/j.yjmcc.2020.10.005

Cited by 15 publications

(19 citation statements)

References 25 publications

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“…TNF-α, IL-1β, and IL-6 are the major pro-inflammatory cytokines that aggravate the inflammatory response after ischemia injury. Our results also confirmed that acupuncture could decrease the level of these inflammatory In recent years, alternative splicing, another factor that causes protein diversity, has also been widely studied in many fields [4,27,33]. The pre-mRNA generated by gene transcription has many splicing methods.…”

Section: Discussionsupporting

confidence: 82%

Full-length transcriptome analysis reveals the mechanism of acupuncture at PC6 improves cardiac function in myocardial ischemia model

Yuan

Wang

et al. 2021

Chin Med

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Background The pathological process of myocardial ischemia (MI) is very complicated. Acupuncture at PC6 has been proved to be effective against MI injury, but the mechanism remains unclear. This study investigated the mechanism that underlies the effect of acupuncture on MI through full-length transcriptome. Methods Adult male C57/BL6 mice were randomly divided into control, MI, and PC6 groups. Mice in MI and PC6 group generated MI model by ligating the left anterior descending (LAD) coronary artery. The samples were collected 5 days after acupuncture treatment. Results The results showed that treatment by acupuncture improved cardiac function, decreased myocardial infraction area, and reduced the levels of cTnT and cTnI. Based on full-length transcriptome sequencing, 5083 differential expression genes (DEGs) and 324 DEGs were identified in the MI group and PC6 group, respectively. These genes regulated by acupuncture were mainly enriched in the inflammatory response pathway. Alternative splicing (AS) is a post-transcriptional action that contributes to the diversity of protein. In all samples, 8237 AS events associated with 1994 genes were found. Some differential AS-involved genes were enriched in the pathway related to heart disease. We also identified 602 new genes, 4 of which may the novel targets of acupuncture in MI. Conclusions Our findings suggest that the effect of acupuncture on MI may be based on the multi-level regulation of the transcriptome.

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Section: Discussionsupporting

confidence: 82%

Full-length transcriptome analysis reveals the mechanism of acupuncture at PC6 improves cardiac function in myocardial ischemia model

Yuan

Wang

et al. 2021

Chin Med

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“…An alternative long-read sequencing technology, ONT sequencing, measures changes in ionic current as fragments move through protein nanopores, and does not depend on enzyme-based nucleotide incorporation or detection of fluorescence ( Ip et al, 2015 ). Due to its affordability and higher throughput – the ONT PromethION generates 20 times more reads per flow cell than the PacBio Sequel II ( Garalde et al, 2018 ) – ONT has been widely used for transcriptome annotation in organisms ranging from yeast to humans ( Sharon et al, 2013 ; Tilgner et al, 2014 ; Oikonomopoulos et al, 2016 ; Byrne et al, 2017 ; Jenjaroenpun et al, 2018 ; Kadobianskyi et al, 2019 ; Seki et al, 2019 ; Sessegolo et al, 2019 ; Workman et al, 2019 ; Müller et al, 2020 ; Sahoo et al, 2020 ), permitting the discovery of isoforms that were difficult to observe from short-read sequencing alone ( Steijger et al, 2013 ; Venturini et al, 2018 ).…”

Section: Introductionmentioning

confidence: 99%

Large-Scale Multiplexing Permits Full-Length Transcriptome Annotation of 32 Bovine Tissues From a Single Nanopore Flow Cell

et al. 2021

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A comprehensive annotation of transcript isoforms in domesticated species is lacking. Especially considering that transcriptome complexity and splicing patterns are not well-conserved between species, this presents a substantial obstacle to genomic selection programs that seek to improve production, disease resistance, and reproduction. Recent advances in long-read sequencing technology have made it possible to directly extrapolate the structure of full-length transcripts without the need for transcript reconstruction. In this study, we demonstrate the power of long-read sequencing for transcriptome annotation by coupling Oxford Nanopore Technology (ONT) with large-scale multiplexing of 93 samples, comprising 32 tissues collected from adult male and female Hereford cattle. More than 30 million uniquely mapping full-length reads were obtained from a single ONT flow cell, and used to identify and characterize the expression dynamics of 99,044 transcript isoforms at 31,824 loci. Of these predicted transcripts, 21% exactly matched a reference transcript, and 61% were novel isoforms of reference genes, substantially increasing the ratio of transcript variants per gene, and suggesting that the complexity of the bovine transcriptome is comparable to that in humans. Over 7,000 transcript isoforms were extremely tissue-specific, and 61% of these were attributed to testis, which exhibited the most complex transcriptome of all interrogated tissues. Despite profiling over 30 tissues, transcription was only detected at about 60% of reference loci. Consequently, additional studies will be necessary to continue characterizing the bovine transcriptome in additional cell types, developmental stages, and physiological conditions. However, by here demonstrating the power of ONT sequencing coupled with large-scale multiplexing, the task of exhaustively annotating the bovine transcriptome – or any mammalian transcriptome – appears significantly more feasible.

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“…The read length (average reads length 1,153 bp) ( Supplementary Table 1 ) contained in our study was longer than that obtained by NGS in a large animal model of HF (e.g., dog model of HF, average reads length 93 bp) ( 38 ). Recently, full-length transcript sequencing was also used in a pig model of HF ( 7 ). Our work focused on the identification of lncRNAs and AS events, and GO and KEGG analyses of DETs, providing more detailed information on HF research.…”

Section: Discussionmentioning

confidence: 99%

“…Transcriptome analysis in large animal model of HF is widely used in HF research ( 6 , 7 ). In recent years, transcript data in HF model have been analyzed by the next-generation sequencing (NGS) or Affymetrix exon arrays (Santa Clara, CA, USA), such as prediction of alternative splicing (AS) events and lncRNAs ( 8 , 9 ).…”

Section: Introductionmentioning

confidence: 99%

Full-Length Transcriptome Sequencing: An Insight Into the Dog Model of Heart Failure

Liang

Bai

Wang

et al. 2021

Front. Cardiovasc. Med.

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Heart failure (HF) leads to a progressive increase in morbidity and mortality rates. This study aimed to explore the transcriptional landscape during HF and identify differentially expressed transcripts (DETs) and alternative splicing events associated with HF. We generated a dog model of HF (n = 3) using right ventricular pacemaker implantation. We performed full-length transcriptome sequencing (based on nanopore platform) on the myocardial tissues and analyzed the transcripts using differential expression analysis and functional annotation methods [Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses]. Additionally, we estimated the expression of the selected genes by quantitative real-time PCR (qRT-PCR) and detected the proportion of immune cells using flow cytometry. We found that increased B-type natriuretic peptide reduced ejection fraction, and apparent clinical signs were observed in the dog model of HF. We identified 67,458 transcripts using full-length transcriptome sequencing. A total of 785 DETs were obtained from the HF and control groups. These DETs were mainly enriched in the immune responses, especially Th1, Th2, and Th17 cell differentiation processes. Furthermore, flow cytometry results revealed that the proportion of Th1 and Th17 cells increased in patients with HF compared to controls, while the proportion of Th2 cells decreased. Differentially expressed genes in the HF and control groups associated with Th1, Th2, and Th17 cell differentiation were quantified using qRT-PCR. We also identified variable splicing events of sarcomere genes (e.g., MYBPC3, TNNT2, TTN, FLNC, and TTNI3). In addition, we detected 4,892 transcription factors and 406 lncRNAs associated with HF. Our analysis based on full-length transcript sequencing provided an analysis perspective in a dog model of HF, which is valuable for molecular research in an increasingly relevant large animal model of HF.

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Updated and enhanced pig cardiac transcriptome based on long-read RNA sequencing and proteomics

Cited by 15 publications

References 25 publications

Full-length transcriptome analysis reveals the mechanism of acupuncture at PC6 improves cardiac function in myocardial ischemia model

Full-length transcriptome analysis reveals the mechanism of acupuncture at PC6 improves cardiac function in myocardial ischemia model

Large-Scale Multiplexing Permits Full-Length Transcriptome Annotation of 32 Bovine Tissues From a Single Nanopore Flow Cell

Full-Length Transcriptome Sequencing: An Insight Into the Dog Model of Heart Failure

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