Comparative transcriptome and co-expression analysis reveal key genes involved in leaf margin serration in Perilla frutescens

Shen, Qi; Zhang, Dong; Zhang, Tianyuan; Xu, Yangyang; Zhao, Degang

doi:10.1016/j.chmed.2019.10.001

Cited by 3 publications

(3 citation statements)

References 38 publications

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“…A total of 8767 unigenes were upregulated and 8379 unigenes were downregulated in the comparison of two Betula pendula plants with different leaf shapes at the transcriptome level [ 24 ]. Researchers have identified 43 differentially expressed genes (DEGs) that potentially regulate leaf shape in Perilla frutescens using transcriptome sequencing and co-expression analysis, which may potentially regulate leaf shape [ 25 ]. In this study, the Corset hierarchical clustering method was used to select unigenes, which not only achieved the goal of aggregating redundant transcripts, but also improved the detection rate of differentially expressed genes [ 26 , 27 , 28 ].…”

Section: Discussionmentioning

confidence: 99%

The Role of PnTCP2 in the Lobed Leaf Formation of Phoebe neurantha var. lobophylla

Sun

Long

et al. 2022

IJMS

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A lobed leaf is a common trait in plants, but it is very rare in Lauraceae plants, including species of Phoebe. In the study of germplasm resources of Phoebe neurantha, we found lobed leaf variant seedlings, and the variation could be inherited stably. Studying the lobed leaf mechanism of P. neurantha var. lobophylla can offer insight into the leaf development mechanism of woody plants. RNA-seq and small RNA-seq analysis results showed that a total of 8091 differentially expressed genes (DEGs) and 16 differentially expressed miRNAs were identified in P. neurantha var. lobophylla. Considering previous research results, a leaf margin morphological development related miRNA, pne-miRNA319a, was primary identified as a candidate miRNA. Target gene prediction showed that a total of 2070 genes were predicted to be the target genes of differentially expressed miRNAs. GO enrichment analysis of differentially expressed target genes suggested that PnTCP2 is related to lobed leaf formation. The TRV-VIGS gene silencing of PnTCP2 led to lobed leaves in P. neurantha seedlings. The downregulation of PnTCP2 led to lobed leaves. The yeast two-hybrid test and bimolecular fluorescence complementation test confirmed that the PnTCP2 protein interacted with the PnLBD41 protein. Based on the expression analysis of gene-silenced leaves and RNA-seq and small RNA-seq analysis results, pne- miRNA319a and PnLBD41 might also play important roles in this process. In conclusion, PnTCP2 plays an important and vital role in the formation of the lobed leaves of P. neurantha var. lobophylla.

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Section: Discussionmentioning

confidence: 99%

The Role of PnTCP2 in the Lobed Leaf Formation of Phoebe neurantha var. lobophylla

Sun

Long

et al. 2022

IJMS

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“…Differential expression and bioinformatics analyses were performed to identify lncRNAs, miRNAs, and mRNAs with differential expression between 5×FAD and WT mice using the “edgeR” packages in R [ 42 ]. To make the lncRNA and mRNA expression levels comparable across samples and experiments, we represented the expression levels of lncRNAs and mRNAs in units of TPM, a superior measure when considering the sequencing depth and gene length along with the effect of samples on the counts of reads [ 43 ].…”

Section: Methodsmentioning

confidence: 99%

The Relationship between the Aberrant Long Non-Coding RNA-Mediated Competitive Endogenous RNA Network and Alzheimer’s Disease Pathogenesis

Cai

Zhao

Zeng

et al. 2022

IJMS

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Alzheimer’s disease (AD) is a common neurodegenerative disorder characterized by cognitive dysfunction. The role of long non-coding RNAs (lncRNAs) with the action of competitive endogenous RNA (ceRNA) in AD remains unclear. The present study aimed to identify significantly differentially expressed lncRNAs (SDELs) and establish lncRNA-associated ceRNA networks via RNA sequencing analysis and a quantitative real-time Polymerase Chain Reaction (qPCR) assay using transgenic mice with five familial AD mutations. A total of 53 SDELs in the cortex and 51 SDELs in the hippocampus were identified, including seven core SDELs common to both regions. The functions and pathways were then investigated through the potential target genes of SDELs via Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses, which indicate biological effects, action distributions, and pathological transductions associated with AD. Based on the ceRNA hypothesis, integrated ceRNA networks in the cortex and hippocampus of lncRNA-miRNA-mRNA were constructed. The core SDEL-mediated ceRNA relationship was established and the expression of these RNAs was verified by qPCR. The results identified lncRNA ENSMUST00000127786 and highlighted miRNAs and mRNAs as potential key mediators in AD. These findings provide AD-derived lncRNA-mediated ceRNA profiles, and further experimental evidence is needed to confirm these identified ceRNA regulatory relationships.

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“…KEGG enrichment was performed to analyze the enriched pathways associated with circRNA target genes ( Chen et al, 2020 ; Shen et al, 2020 ). The GO knowledge base was used to describe information on the functions of genes, including biological processes (BP), molecular functions (MF), and cellular components (CC).…”

Section: Methodsmentioning

confidence: 99%

Comprehensive analysis of dysregulated circular RNAs and construction of a ceRNA network involved in the pathology of Alzheimer’s disease in a 5 × FAD mouse model

Sun

Zeng

Cai

et al. 2022

Front. Aging Neurosci.

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IntroductionAlzheimer’s disease (AD) causes a decline in cognitive function that poses a significant hazard to human health. However, the exact pathogenesis of AD and effective treatment have both proven elusive. Circular RNAs (circRNAs), which were initially deemed as meaningless non-coding RNAs, have been shown to participate in a variety of physiological and pathological processes. However, the variations and characteristics of circRNAs are not fairly well understood during the occurrence and development of AD.MethodsIn this study, we performed RNA sequencing analyses, identified circRNA expression profiles, and explored the circRNA-associated competing endogenous RNA (ceRNA) relationship in the hippocampus of five familial AD (5 × FAD) mice with cognitive dysfunction.ResultsThe RNA sequencing results identified 34 dysregulated circRNAs in the hippocampus of 5 × FAD mice, including 17 upregulated and 17 downregulated circRNAs. The circRNA-miRNA interaction network for the dysregulated circRNAs was generated, and it was found to include 34 circRNAs and 711 miRNAs. Next, 2067 mRNAs potentially modulated by upregulated circRNA-interacting miRNAs and 2297 mRNAs potentially modulated by downregulated circRNA-interacting miRNAs were identified. Pathway enrichment analyses revealed that the circRNA-miRNA-mRNA network modulated AD development via multiple pathways, such as axon guidance, mitogen-activated protein kinase, and neurotrophin. The associated biological processes were mainly related to neuron projection development, cell morphogenesis, and head development. Their corresponding distributions were especially high in the axon, postsynapse, and neuronal body. We constructed a ceRNA network that included five circRNAs, four miRNAs, and 188 mRNAs. In this network, the differential expressions of three circRNAs (circRNA04655, circRNA00723, and circRNA01891), two miRNAs (miR-3470b and miR-6240), and 13 mRNAs (Vgll3, Nhsl2, Rab7, Tardbp, Vps33b, Fam107a, Tacr1, Ankrd40, Creb1, Snap23, Csnk1a1, Bmi1, and Bfar) in the hippocampus of 5 × FAD mice using qRT-PCR analyses were consistent with the RNA sequencing results. Another one circRNAs (circRNA00747) and two mRNAs (Zfp37 and Polr1e) had similar expression trends to the sequencing data, while circRNA03723 and Mapk10 had deviated expression trends to the sequencing data.ConclusionsIn conclusion, our study uncovered dysregulated circRNA expression profiles in the hippocampus of 5 × FAD mice, stretched comprehension of ceRNA biology, investigated the potential role of this ceRNA network in pathogenesis and progression, and identified potential biomarkers and therapeutic targets for AD.

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Comparative transcriptome and co-expression analysis reveal key genes involved in leaf margin serration in Perilla frutescens

Cited by 3 publications

References 38 publications

The Role of PnTCP2 in the Lobed Leaf Formation of Phoebe neurantha var. lobophylla

The Role of PnTCP2 in the Lobed Leaf Formation of Phoebe neurantha var. lobophylla

The Relationship between the Aberrant Long Non-Coding RNA-Mediated Competitive Endogenous RNA Network and Alzheimer’s Disease Pathogenesis

Comprehensive analysis of dysregulated circular RNAs and construction of a ceRNA network involved in the pathology of Alzheimer’s disease in a 5 × FAD mouse model

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