Analysis of miRNAs Targeted Storage Regulatory Genes during Soybean Seed Development Based on Transcriptome Sequencing

Yu, Jingquan; Zhang, Zhanguo; Huang, Shi-Yu; Han, Xue; Wang, Xinyu; Pan, Wenjing; Qin, Hui; Qi, Hongbo; Yin, Zhan; Qu, Kun; Zhang, Zexin; Liu, Shanshan; Jiang, Hongwei; Liu, Chunyan; Hu, Zhenbang; Wu, Xiaoxia; Chen, Qingshan; Xin, Dawei; Qi, Zhaoming

doi:10.3390/genes10060408

Cited by 19 publications

(17 citation statements)

References 38 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Another novelty of our study is that we further explored the functional relevance of target genes between tissues and functional divergence of isoforms by building an isoform-based co-expression network. Meanwhile, the reason why we selected WGCNA for co-expression analysis is its diverse functions and maturity of data processing which has been successfully applied in many gene network and functional genomic studies [37,47,48]. Our findings revealed the case that some isoforms from the same gene appear to be divergent in the isoform coexpression network and selectively targeted by miRNAs due to their difference of sequence structure, suggesting the coordination of both structural and expression alteration during gene regulation.…”

Section: Discussionmentioning

confidence: 91%

“…Further, our another study on lotus transcript isoforms has been facilitated by full-length transcript sequencing using a combination of PacBio and Illumina [28]. The strategy of the combination of miRNAs and mRNA by deep sequencing has been successfully applied in many plant species, such as soybean [37], peanut [38] and cotton [39]. Therefore, in this study, we focused on how the expression of miRNAs in different lotus tissues influences the expression dynamics of their target genes and especially targeted isoforms.…”

Section: Discussionmentioning

confidence: 99%

See 1 more Smart Citation

Integrative expression network analysis of microRNA and gene isoforms in sacred lotus

Zhang

Rahmani

Yang

et al. 2020

Preprint

View full text Add to dashboard Cite

Background Gene expression is complex and regulated by multiple molecular mechanisms, such as miRNA-mediated gene inhibition and alternative-splicing of pre-mRNAs. However, the coordination of interaction between miRNAs with different splicing isoforms, and the change of splicing isoform in response to different cellular environments are largely unexplored in plants. In this study, we analyzed the miRNA and mRNA transcriptome from lotus ( Nelumbo nucifera ), an economically important flowering plant. Results Through RNA-seq analyses on miRNAs and their target genes (isoforms) among six lotus tissues, expression of most miRNAs seem to be negatively correlated with their targets, and tend to be tissue-specific. Further, our results showed that frequent interactions between miRNAs and hub gene isoforms highlight the critical roles of miRNAs in the gene network. Intriguingly, for many genes, their corresponding isoforms were assigned to different co-expressed modules, and they exhibited more divergent mRNA structures including presence and absence of miRNA binding sites, suggesting functional divergence for many isoforms is escalated by both structural and expression divergence. Further detailed functional enrichment analysis of miRNA targets revealed that miRNAs are involved in the regulation of lotus growth and development by regulating plant hormone-related pathway genes. Conclusions Taken together, our comprehensive analyses of miRNA and mRNA transcriptome elucidate the coordination of interaction between miRNAs and different splicing isoforms, and highlight the functional divergence of many transcript isoforms from the same locus in lotus.

show abstract

Section: Discussionmentioning

confidence: 91%

Section: Discussionmentioning

confidence: 99%

Integrative expression network analysis of microRNA and gene isoforms in sacred lotus

Zhang

Rahmani

Yang

et al. 2020

Preprint

View full text Add to dashboard Cite

show abstract

“…Another novelty of our study is that we further explored the functional relevance of target genes between tissues and functional divergence of isoforms by building an isoform-based co-expression network. Meanwhile, the reason why we selected WGCNA for co-expression analysis is its diverse functions and maturity of data processing which has been successfully applied in many gene network and functional genomic studies [38,48,49]. Our ndings revealed the case that some isoforms from the same gene appear to be divergent in the isoform coexpression network and selectively targeted by miRNAs due to their difference in sequence structure, suggesting the coordination of both structural and expression alteration during gene regulation.…”

Section: Discussionmentioning

confidence: 97%

“…Further, our other study on lotus transcript isoforms has been facilitated by full-length transcript sequencing using a combination of PacBio and Illumina [28]. The strategy of the combination of miRNAs and mRNA by deep sequencing has been successfully applied in many plant species, such as soybean [38], peanut [39] and cotton [40]. Therefore, in this study, we focused on how the expression of miRNAs in different lotus tissues in uences the expression dynamics of their target genes and especially targeted isoforms.…”

Section: Discussionmentioning

confidence: 99%

Integrative expression network analysis of microRNA and gene isoforms in sacred lotus

Zhang

Rahmani

Yang

et al. 2020

Preprint

View full text Add to dashboard Cite

Background: Gene expression is complex and regulated by multiple molecular mechanisms, such as miRNA-mediated gene inhibition and alternative-splicing of pre-mRNAs. However, the coordination of interaction between miRNAs with different splicing isoforms, and the change of splicing isoform in response to different cellular environments are largely unexplored in plants. In this study, we analyzed the miRNA and mRNA transcriptome from lotus (Nelumbo nucifera), an economically important flowering plant.Results: Through RNA-seq analyses on miRNAs and their target genes (isoforms) among six lotus tissues, expression of most miRNAs seem to be negatively correlated with their targets and tend to be tissue-specific. Further, our results showed that preferential interactions between miRNAs and hub gene isoforms in one coexpression module which is highly correlated with leaf. Intriguingly, for many genes, their corresponding isoforms were assigned to different co-expressed modules, and they exhibited more divergent mRNA structures including presence and absence of miRNA binding sites, suggesting functional divergence for many isoforms is escalated by both structural and expression divergence. Further detailed functional enrichment analysis of miRNA targets revealed that miRNAs are involved in the regulation of lotus growth and development by regulating plant hormone-related pathway genes.Conclusions: Taken together, our comprehensive analyses of miRNA and mRNA transcriptome elucidate the coordination of interaction between miRNAs and different splicing isoforms, and highlight the functional divergence of many transcript isoforms from the same locus in lotus.

show abstract

“…Further, our other study on lotus transcript isoforms has been facilitated by full-length transcript sequencing using a combination of PacBio and Illumina [28]. The strategy of the combination of miRNAs and mRNA by deep sequencing has been successfully applied in many plant species, such as soybean [38], peanut [39] and cotton [40]. Therefore, in this study, we focused on how the expression of miR-NAs in different lotus tissues influences the expression dynamics of their target genes and especially targeted isoforms.…”

Section: Discussionmentioning

confidence: 99%

Integrative expression network analysis of microRNA and gene isoforms in sacred lotus

et al. 2020

View full text Add to dashboard Cite

Background: Gene expression is complex and regulated by multiple molecular mechanisms, such as miRNAmediated gene inhibition and alternative-splicing of pre-mRNAs. However, the coordination of interaction between miRNAs with different splicing isoforms, and the change of splicing isoform in response to different cellular environments are largely unexplored in plants. In this study, we analyzed the miRNA and mRNA transcriptome from lotus (Nelumbo nucifera), an economically important flowering plant. Results: Through RNA-seq analyses on miRNAs and their target genes (isoforms) among six lotus tissues, expression of most miRNAs seem to be negatively correlated with their targets and tend to be tissue-specific. Further, our results showed that preferential interactions between miRNAs and hub gene isoforms in one coexpression module which is highly correlated with leaf. Intriguingly, for many genes, their corresponding isoforms were assigned to different coexpressed modules, and they exhibited more divergent mRNA structures including presence and absence of miRNA binding sites, suggesting functional divergence for many isoforms is escalated by both structural and expression divergence. Further detailed functional enrichment analysis of miRNA targets revealed that miRNAs are involved in the regulation of lotus growth and development by regulating plant hormone-related pathway genes. Conclusions: Taken together, our comprehensive analyses of miRNA and mRNA transcriptome elucidate the coordination of interaction between miRNAs and different splicing isoforms, and highlight the functional divergence of many transcript isoforms from the same locus in lotus.

show abstract

Analysis of miRNAs Targeted Storage Regulatory Genes during Soybean Seed Development Based on Transcriptome Sequencing

Cited by 19 publications

References 38 publications

Integrative expression network analysis of microRNA and gene isoforms in sacred lotus

Integrative expression network analysis of microRNA and gene isoforms in sacred lotus

Integrative expression network analysis of microRNA and gene isoforms in sacred lotus

Integrative expression network analysis of microRNA and gene isoforms in sacred lotus

Contact Info

Product

Resources

About