Back to Search
Start Over
Integrative expression network analysis of microRNA and gene isoforms in sacred lotus
- Source :
- BMC Genomics, Vol 21, Iss 1, Pp 1-13 (2020), BMC GENOMICS, BMC Genomics
- Publication Year :
- 2020
- Publisher :
- BMC, 2020.
-
Abstract
- 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.
- Subjects :
- Gene isoform
lcsh:QH426-470
lcsh:Biotechnology
MiRNA binding
Nelumbo
Biology
Transcriptome
Transcript isoforms
ANALYSIS REVEALS
Gene Expression Regulation, Plant
TARGETS
lcsh:TP248.13-248.65
Gene expression
Genetics
Protein Isoforms
Gene Regulatory Networks
PLANT
TRANSCRIPTOME
ADAPTATION
Gene
Plant Proteins
Co-expression network
microRNA
Sequence Analysis, RNA
Gene Expression Profiling
fungi
Biology and Life Sciences
PATHWAYS
food and beverages
EVOLUTION
Sacred lotus
MicroRNAs
INSIGHTS
lcsh:Genetics
Organ Specificity
MIRNAS
RNA splicing
DNA microarray
CAMELLIA
Functional divergence
Research Article
Biotechnology
Subjects
Details
- Language :
- English
- ISSN :
- 14712164
- Volume :
- 21
- Issue :
- 1
- Database :
- OpenAIRE
- Journal :
- BMC Genomics
- Accession number :
- edsair.doi.dedup.....d7d8aebd12b64a8d90690ee9890b7419