Integration of miRNA weighted gene co-expression network and miRNA-mRNA co-expression analyses reveals potential regulatory functions of miRNAs in calf rumen development

Ngoc, Duy; Dudemaine, Pier-Luc; Fomenky, Bridget E.; Ibeagha‐Awemu, Eveline M.

doi:10.1016/j.ygeno.2018.05.009

Cited by 33 publications

(36 citation statements)

References 58 publications

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“…Accompanied by the development of rumen size, rumen papillae and muscular tissues, gene expression were also remarkably altered though transcriptional and post-transcriptional regulation. Plenty of differential expressed genes (DEGs) have been identi ed in cattle between pre-and post-weaning [2,35,36].…”

Section: Discussionmentioning

confidence: 99%

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Analysis of MicroRNA Transcriptomes Insights into the miR-148a-3p Inducer of Rumen Development in Goats

Zhong

Wang

et al. 2020

Preprint

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Abstract Background: Rumen is an important digestive organ of ruminant. From fetal to adult stage, the morphology, structure and function of rumen have changed significantly. But the intrinsic genetic regulation is still limited. We previously reported a genome-wide expression profile of miRNAs in prenatal goat rumens. In the present study, we rejoined analyzed the transcriptomes of rumen miRNAs during prenatal (E60 and E135) and postnatal (D30 and D150) stages.Results: A total of 66 differentially expressed miRNAs (DEMs) were identified in the rumen tissues from D30 and D150 goats. Of these, 17 DEMs were consistently highly expressed in the rumens at the preweaning stages (E60, E135 and D30), while down-regulated at D150. Noteworthy, annotation analysis revealed that the target genes regulated by the DEMs were mainly enriched in MAPK signaling pathway, Jak-STAT signaling pathway and Ras signaling pathway. Interestingly, the expression of miR-148a-3p was significantly high in the embryonic stage and down-regulated at D150. The potential binding sites between miR-148a-3p and QKI were predicted by the TargetScan and verified by the dual luciferase report assay. The co-localization of miR-148a-3p and QKI was observed not in intestinal tracts but in rumen tissues by in situ hybridization. Moreover, the expression of miR-148a-3p in the epithelium was significantly higher than that in the other layers, suggesting that miR-148a-3p involve in the development of rumen epithelial cells by targeting QKI. Subsequently, miR-148a-3p inhibitor was found to induce the proliferation of GES-1 cells.Conclusions: Taken together, these results identified the DEMs involved in the development of rumen and provided an insight into the regulation mechanism of goat rumens during development.

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Section: Discussionmentioning

confidence: 99%

“…Subsequently, 122 DEMs were identi ed from 260 known and 35 novel miRNAs in the same rumen tissues. Among them, six miRNAs (miR-143, miR-29b, miR-145, miR-493, miR-26a and miR-199) were identi ed as the key regulators of rumen development in cattle [36]. However, the studies about miRNAs in goat rumens still limited.…”

Section: Discussionmentioning

confidence: 99%

Analysis of MicroRNA Transcriptomes Insights into the miR-148a-3p Inducer of Rumen Development in Goats

Zhong

Wang

et al. 2020

Preprint

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“…Experimental details have been described in our previous studies [ 23 , 24 ]. Briefly, sixteen 2–7 days-old Holstein calves were raised for a period of 96 days in individual pens.…”

Section: Methodsmentioning

confidence: 99%

“…Recently, we characterized the long non-coding RNA (lncRNA) expression in ileum tissues of calves and functional inference of identified lncRNA (623 known and 1505 novel) cis target genes revealed potential roles in growth and development as well as in posttranscriptional gene silencing by RNA or miRNA processing processes and in disease resistance mechanisms [ 23 ]. Moreover, we also observed that 122 miRNAs were significantly differentially expressed between the pre- and post-weaning periods in the rumen, suggesting important roles of miRNAs in calf gut during early life [ 24 ]. Therefore, we hypothesize that miRNAs might play important roles in ileum development during the pre- and post-weaning periods.…”

Section: Introductionmentioning

confidence: 99%

Integration of miRNA and mRNA Co-Expression Reveals Potential Regulatory Roles of miRNAs in Developmental and Immunological Processes in Calf Ileum during Early Growth

Ngoc

Dudemaine

Fomenky

et al. 2018

Cells

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This study aimed to investigate the potential regulatory roles of miRNAs in calf ileum developmental transition from the pre- to the post-weaning period. For this purpose, ileum tissues were collected from eight calves at the pre-weaning period and another eight calves at the post-weaning period and miRNA expression characterized by miRNA sequencing, followed by functional analyses. A total of 388 miRNAs, including 81 novel miRNAs, were identified. A total of 220 miRNAs were differentially expressed (DE) between the two periods. The potential functions of DE miRNAs in ileum development were supported by significant enrichment of their target genes in gene ontology terms related to metabolic processes and transcription factor activities or pathways related to metabolism (peroxisomes), vitamin digestion and absorption, lipid and protein metabolism, as well as intracellular signaling. Integration of DE miRNAs and DE mRNAs revealed several DE miRNA-mRNA pairs with crucial roles in ileum development (bta-miR-374a—FBXO18, bta-miR-374a—GTPBP3, bta-miR-374a—GNB2) and immune function (bta-miR-15b—IKBKB). This is the first integrated miRNA-mRNA analysis exploring the potential roles of miRNAs in calf ileum growth and development during early life.

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“…Still, large information about DPC roles in growth and e resistance to stress regulation is unknown. Herein, we used Weighted Gene Co-expression Network Analysis (WGCNA), a mathematical method to identify key gene network and hub genes [38][39][40]. The present study was conducted which focused on the transcriptome changes by DPC treatment using Illumina Hiseq 4000 platform.…”

Section: Introductionmentioning

confidence: 99%

Global Transcriptome Changes of Elongating Internode of Sugarcane in Response to Mepiquat Chloride

Chen

Fan

Zhou

et al. 2020

Preprint

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Background: Mepiquat chloride (DPC) is an extensively used chemical to control internode growth and compact canopies in cultured plants. Previous studies suggested that DPC could inhibit gibberellin biosynthesis in sugarcane. Unfortunately, the molecular mechanism underlying the suppressive effects of DPC on plant growth is still largely unknown. Results: In the present study, we first obtained the high-quality long transcripts from internode of sugarcane by PacBio Sequel System. A total of 72,671 isoforms with N50 as 3,073 were generated. These long isoforms were used for the following RNA-seq as reference. Subsequently, short reads generated from Illumina Hiseq 4000 platform were used for comparing the differentially expressed genes in DPC and control groups. The transcriptome profiling showed the 6 days post DPC treatment had the most significant changed genes. These genes were related to plant hormone signal transduction and biosynthesis of several metabolites, indicating DPC affected multiple pathways beside depressed gibberellin biosynthesis. The network of DPC on the key stage was illustrated by weighted gene co-expression network analysis (WGCNA). Among the constructed 36 modules, the top positive correlated module with stage of 6 day post spraying DPC was sienna3. Stf0 sulphotransferase, cyclin-like F-box and HOX12 were the hub genes in sienna3 that had high correlation with other genes in this module. The qPCR demonstrated the high accuracy of RNA-seq result. Conclusion: Taken together, we demonstrated the key role of these genes in DPC-induced growth inhibition in sugarcane.

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Integration of miRNA weighted gene co-expression network and miRNA-mRNA co-expression analyses reveals potential regulatory functions of miRNAs in calf rumen development

Cited by 33 publications

References 58 publications

Analysis of MicroRNA Transcriptomes Insights into the miR-148a-3p Inducer of Rumen Development in Goats

Analysis of MicroRNA Transcriptomes Insights into the miR-148a-3p Inducer of Rumen Development in Goats

Integration of miRNA and mRNA Co-Expression Reveals Potential Regulatory Roles of miRNAs in Developmental and Immunological Processes in Calf Ileum during Early Growth

Global Transcriptome Changes of Elongating Internode of Sugarcane in Response to Mepiquat Chloride

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