Abstract
Holarrhena pubescens is an effective medicinal plant from the Apocynaceae family, widely distributed over the Indian subcontinent and extensively used by Ayurveda and ethno-medicine systems without apparent side effects. We postulated that miRNAs, endogenous non-coding small RNAs that regulate gene expression at the post-transcriptional level, may, after ingestion into the human body, contribute to the medicinal properties of plants of this species by inducing regulated human gene expression to modulate. However, knowledge is scarce about miRNA in Holarrhena. In addition, to test the hypothesis on the potential pharmacological properties of miRNA, we performed a high-throughput sequencing analysis using the Next Generation Sequencing Illumina platform; 42,755,236 raw reads have been generated from H. pubescens stems from a library of small RNA isolated, identifying 687 known and 50 new miRNAs led. The novel H. pubescens miRNAs were predicted to regulate specific human genes, and subsequent annotations of gene functions suggested a possible role in various biological processes and signaling pathways, such as Wnt, MAPK, PI3K-Akt, and AMPK signaling pathways and endocytosis. The association of these putative targets with many diseases, including cancer, congenital malformations, nervous system disorders, and cystic fibrosis, has been demonstrated. The top hub proteins STAT3, MDM2, GSK3B, NANOG, IGF1, PRKCA, SNAP25, SRSF1, HTT, and SNCA show their interaction with human diseases, including cancer and cystic fibrosis. To our knowledge, this is the first report of uncovering H. pubescens miRNAs based on high-throughput sequencing and bioinformatics analysis. This study has provided new insight into a potential cross-species control of human gene expression. The potential for miRNA transfer should be evaluated as one possible mechanism of action to account for the beneficial properties of this valuable species.
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Data availability
The datasets used and/or analyzed during the current study are available from the corresponding author upon reasonable request.
Abbreviations
- H. pubescens :
-
Holarrhena pubescens
- miRNA:
-
MicroRNA
- nt:
-
Nucleotide
- STAT3 :
-
Signal transducer and activator of transcription 3
- MDM2 :
-
Murine double minute 2
- GSK3B :
-
Glycogen synthase kinase-3 beta
- NANOG :
-
Nanog homeobox
- IGF1 :
-
Insulin-like growth factor 1
- PRKCA :
-
Protein kinase C alpha
- SNAP25 :
-
Synaptosome-associated protein 25
- SRSF1 :
-
Serine and arginine-rich splicing factor 1
- HTT :
-
Huntingtin
- SNCA :
-
Synuclein alpha
- CF:
-
Cystic fibrosis
- CFTR :
-
Cystic fibrosis transmembrane conductance regulator
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Acknowledgements
We acknowledge GUJCOST, Dept. of Science and Technology, Govt. of Gujarat and GSBTM, Dept. of Science and Technology, Govt. of Gujarat for providing the super-computing facility and Bioinformatics Node facility respectively. Author Tithi S. Trivedi would like to acknowledge the ScHeme Of Developing High-quality research (SHODH), Education Department, Government of Gujarat, INDIA, for providing the student support fellowship.We acknowledge GUJCOST, DST, Government of Gujarat, for the super-computing facility provision and Financial Assistance Program (Bioinformatics Node facility) Department of Science and Technology. Author Tithi S. Trivedi would like to acknowledge the ScHeme Of Developing High-quality research (SHODH), Education Department, Government of Gujarat, INDIA, for providing the student support fellowship. Author Tithi S. Trivedi acknowledges Ms. Harsha Motwani for being a helpful classmate during the study. Author Tithi S. Trivedi acknowledges Mrs. Sukanya P. Raval, Ms. Sandhya Verma, Ms. Neha Jha, Ms. Mansi Bhavsar, and Mr. Naman Mangukia for resolving the queries. Author Tithi S. Trivedi sincerely acknowledges the assistance of Ms. Kinjal Bhadresha and Afzal A. who helped in performing the chord plot.
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Tithi S. Trivedi: conceptualization, software, methodology, data analysis, writing – original draft, writing – review and editing. Maulikkumar P. Patel: conceptualization, software, data analysis. Vishal Nanavaty: small RNA sequencing experiment, writing – review and editing. Archana U. Mankad: visualization, supervision, investigation, funding acquisition, writing – review and editing. Rakesh M. Rawal: visualization, supervision, investigation. Saumya K. Patel: visualization, supervision, investigation, funding acquisition, writing – review and editing.
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Trivedi, T.S., Patel, M.P., Nanavaty, V. et al. MicroRNAs from Holarrhena pubescens stems: Identification by small RNA Sequencing and their Potential Contribution to Human Gene Targets. Funct Integr Genomics 23, 149 (2023). https://doi.org/10.1007/s10142-023-01078-0
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DOI: https://doi.org/10.1007/s10142-023-01078-0