De novo characterization of placental transcriptome in the Eurasian beaver (Castor fiber L.)

Lipka, Aleksandra; Paukszto, Łukasz; Majewska, Marta; Jastrzebski, J; Panasiewicz, Grzegorz; Szafrańska, Bożena

doi:10.1007/s10142-019-00663-6

Cited by 4 publications

(6 citation statements)

References 69 publications

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“…The assembly comprised 342,910 contigs and exhibited BUSCO transcriptome completeness of 79.1% (Figure 2C). Previous studies on de novo transcriptome assembly using Trinity reported 64.7%, 77.1%, 80%, and 87% complete BUSCO genes in higher animals such as Homo sapiens ( 36 ), Castor fiber L.( 37 ), Mirounga angustirostris ( 39 ), and Dromiciops gliroides ( 40 ), respectively. We successfully obtained a de novo transcriptome with standard quality.…”

Section: Resultsmentioning

confidence: 99%

“…Moreover, de novo transcriptome assembly technology can address the dependency problem of reference genomes. The de novo transcriptome assembly can generate transcriptome sequences without the reference genome using RNA-seq data( [36][37][38][39][40] ). We identified factual genomic sequences in mRNA-transcribed regions using de novo transcriptome assembly from geneedited organisms and cells.…”

Section: Introductionmentioning

confidence: 99%

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Danger Analysis: Risk-Averse on/Off-Target Assessment for Crispr Editing Without a Reference Genome

Nakamae

Bono

2023

Preprint

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The CRISPR-Cas9 system has successfully achieved site-specific gene editing in organisms ranging from humans to bacteria. The technology efficiently generates mutants, allowing for phenotypic analysis of the on-target gene. However, some conventional studies did not investigate whether deleterious off-target effects partially affect the phenotype. Herein, we present a novel phenotypic assessment of CRISPR-mediated gene editing: Deleterious and ANticipatable Guides Evaluated by RNA-sequencing (DANGER) analysis. Using RNA-seq data, this bioinformatics pipeline can elucidate genomic on/off-target sites on mRNA-transcribed regions related to expression changes and then quantify phenotypic risk at the gene ontology (GO) term level. We demonstrated the risk-averse on/off-target assessment in RNA-seq data from gene-edited samples of human cells and zebrafish brains. Our DANGER analysis successfully detected off-target sites, and it quantitatively evaluated the potential contribution of deleterious off-targets to the transcriptome phenotypes of the edited mutants. Notably, DANGER analysis harnessed de novo transcriptome assembly to perform risk-averse on/off-target assessments without a reference genome. Thus, our resources would help assess genome editing in non-model organisms, individual human genomes, and atypical genomes from diseases and viruses. In conclusion, DANGER analysis facilitates the safer design of genome editing in all organisms with a transcriptome.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Danger Analysis: Risk-Averse on/Off-Target Assessment for Crispr Editing Without a Reference Genome

Nakamae

Bono

2023

Preprint

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“…We performed GO enrichment analysis for the host genes of DE circRNAs to better understand how circRNA may be involved in flower development. GOseq (version 2.12) was used to annotate the function of the parent genes of the differentially expressed circRNAs’ host genes ( Young et al., 2010 ) using the Wallenius non-central hyper-geometric distribution method ( Kang and Liu, 2015 ; Bedre et al., 2019 ; Lipka et al., 2019 ; Li et al., 2021 ). The Benjamini Hochberg method was used to correct the p-value, with a smaller value being more significant.…”

Section: Methodsmentioning

confidence: 99%

Comprehensive identification and analysis of circRNAs during hickory (Carya cathayensis Sarg.) flower bud differentiation

Jin

Yang²,

Luo³

et al. 2023

Front. Plant Sci.

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Flower bud differentiation represents a crucial transition from vegetative growth to reproductive development. Carya cathayensis (hickory) is an important economic species in China, with a long juvenile period that hinders its commercial development. In recent years, circular RNAs (circRNAs) have been widely studied and identified as sponges for miRNA regulation of mRNA expression. However, little is known regarding the role of circRNAs in flower buds. In this study, we sequenced circRNAs at three developmental stages (undifferentiated, differentiating, and fully differentiated) in both female and male buds. A total of 6,931 circRNAs were identified in the three developmental stages and 4,449 and 2,209 circRNAs were differentially expressed in female and male buds, respectively. Gene ontology demonstrated that many circRNA host genes participated in various processes, for example, cellular and intracellular pH regulation. Function annotation identified 46 differentially expressed circRNAs involved in flowering regulation, with 28 circRNAs found only in female buds, 4 found only in male buds, and 11 found in both female and male buds. A circRNA-miRNA-mRNA network was predicted based on 13 flowering-related circRNAs and their seven putative interacting miRNAs to describe the regulatory mechanism. Our preliminary results demonstrated a potential involvement of circRNA in bud differentiation. They provided a preliminary theoretical basis for how circRNA might participate in flower development in hickory, perhaps in woody plants.

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“…Moreover, de novo transcriptome assembly technology can address the dependency problem of reference genomes. The de novo transcriptome assembly can generate transcriptome sequences without the reference genome using RNA-seq data ( Grabherr et al 2011 , Khudyakov et al 2017 , Nespolo et al 2018 , Hölzer and Marz 2019 , Lipka et al 2019 ). We identified factual genomic sequences in mRNA-transcribed regions using de novo transcriptome assembly from gene-edited organisms and cells.…”

Section: Introductionmentioning

confidence: 99%

DANGER analysis: risk-averse on/off-target assessment for CRISPR editing without a reference genome

Nakamae,

Bono

2023

Bioinformatics Advances

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Motivation The CRISPR-Cas9 system has successfully achieved site-specific gene editing in organisms ranging from humans to bacteria. The technology efficiently generates mutants, allowing for phenotypic analysis of the on-target gene. However, some conventional studies did not investigate whether deleterious off-target effects partially affect the phenotype. Results Herein, we present a novel phenotypic assessment of CRISPR-mediated gene editing: Deleterious and ANticipatable Guides Evaluated by RNA-sequencing (DANGER) analysis. Using RNA-seq data, this bioinformatics pipeline can elucidate genomic on/off-target sites on mRNA-transcribed regions related to expression changes and then quantify phenotypic risk at the gene ontology (GO) term level. We demonstrated the risk-averse on/off-target assessment in RNA-seq data from gene-edited samples of human cells and zebrafish brains. Our DANGER analysis successfully detected off-target sites, and it quantitatively evaluated the potential contribution of deleterious off-targets to the transcriptome phenotypes of the edited mutants. Notably, DANGER analysis harnessed de novo transcriptome assembly to perform risk-averse on/off-target assessments without a reference genome. Thus, our resources would help assess genome editing in non-model organisms, individual human genomes, and atypical genomes from diseases and viruses. In conclusion, DANGER analysis facilitates the safer design of genome editing in all organisms with a transcriptome. Availability The Script for the DANGER analysis pipeline is available at https://github.com/KazukiNakamae/DANGER_analysis. In addition, the software provides a tutorial on reproducing the results presented in this article on the Readme page. The Docker image of DANGER_analysis is also available at https://hub.docker.com/repository/docker/kazukinakamae/dangeranalysis/general. Supplementary information Supplementary data are available at Bioinformatics Advances online.

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De novo characterization of placental transcriptome in the Eurasian beaver (Castor fiber L.)

Cited by 4 publications

References 69 publications

Danger Analysis: Risk-Averse on/Off-Target Assessment for Crispr Editing Without a Reference Genome

Danger Analysis: Risk-Averse on/Off-Target Assessment for Crispr Editing Without a Reference Genome

Comprehensive identification and analysis of circRNAs during hickory (Carya cathayensis Sarg.) flower bud differentiation

DANGER analysis: risk-averse on/off-target assessment for CRISPR editing without a reference genome

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