Integrated Analysis of microRNA Targets Reveals New Insights into Transcriptional–Post-Transcriptional Regulatory Cross-Talk
It is becoming increasingly clear that microRNAs are key players in gene regulatory networks, modulating gene expression at post-transcriptional level. Their involvement in almost all cellular processes predicts their role in diseases, and several microRNA-based therapeutics are currently undergoing...
Saved in:
| Main Authors: | , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2025-01-01
|
| Series: | Biology |
| Subjects: | |
| Online Access: | https://www.mdpi.com/2079-7737/14/1/43 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1832589081764167680 |
|---|---|
| author | Simona Panni Roberto Pizzolotto |
| author_facet | Simona Panni Roberto Pizzolotto |
| author_sort | Simona Panni |
| collection | DOAJ |
| description | It is becoming increasingly clear that microRNAs are key players in gene regulatory networks, modulating gene expression at post-transcriptional level. Their involvement in almost all cellular processes predicts their role in diseases, and several microRNA-based therapeutics are currently undergoing clinical testing. Despite their undeniable relevance and the substantial body of literature demonstrating their role in cancer and other pathologies, the identification of functional interactions is still challenging. To address this issue, several resources have been developed to collect information from the literature, according to different criteria and reliability scores. In the present study, we have constructed a network of verified microRNA-mRNA interactions by integrating strong-evidence couples from different resources. Our analysis of the resulting network reveals that only one-fifth of the human genes exhibits experimental validated regulation by microRNAs. A very small subset of them is controlled by more than 20 microRNAs, and these hubs are highly enriched of pivotal transcription factors and regulatory proteins, strongly suggesting a complex interplay and a combinatorial effect between transcriptional and post-transcriptional gene control. Data analysis also reveals that several microRNAs control multiple targets involved in the same pathway or biological process, likely contributing to the coordinated control of the protein levels. |
| format | Article |
| id | doaj-art-e107351862c547d489d46e9632f84240 |
| institution | Kabale University |
| issn | 2079-7737 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Biology |
| spelling | doaj-art-e107351862c547d489d46e9632f842402025-01-24T13:23:24ZengMDPI AGBiology2079-77372025-01-011414310.3390/biology14010043Integrated Analysis of microRNA Targets Reveals New Insights into Transcriptional–Post-Transcriptional Regulatory Cross-TalkSimona Panni0Roberto Pizzolotto1Dipartimento di Biologia Ecologia Scienze della Terra (DiBEST), Università della Calabria, 87036 Rende, CS, ItalyDipartimento di Biologia Ecologia Scienze della Terra (DiBEST), Università della Calabria, 87036 Rende, CS, ItalyIt is becoming increasingly clear that microRNAs are key players in gene regulatory networks, modulating gene expression at post-transcriptional level. Their involvement in almost all cellular processes predicts their role in diseases, and several microRNA-based therapeutics are currently undergoing clinical testing. Despite their undeniable relevance and the substantial body of literature demonstrating their role in cancer and other pathologies, the identification of functional interactions is still challenging. To address this issue, several resources have been developed to collect information from the literature, according to different criteria and reliability scores. In the present study, we have constructed a network of verified microRNA-mRNA interactions by integrating strong-evidence couples from different resources. Our analysis of the resulting network reveals that only one-fifth of the human genes exhibits experimental validated regulation by microRNAs. A very small subset of them is controlled by more than 20 microRNAs, and these hubs are highly enriched of pivotal transcription factors and regulatory proteins, strongly suggesting a complex interplay and a combinatorial effect between transcriptional and post-transcriptional gene control. Data analysis also reveals that several microRNAs control multiple targets involved in the same pathway or biological process, likely contributing to the coordinated control of the protein levels.https://www.mdpi.com/2079-7737/14/1/43microRNAbiocurationmiRNA interaction networkgene regulationtranscription factors |
| spellingShingle | Simona Panni Roberto Pizzolotto Integrated Analysis of microRNA Targets Reveals New Insights into Transcriptional–Post-Transcriptional Regulatory Cross-Talk Biology microRNA biocuration miRNA interaction network gene regulation transcription factors |
| title | Integrated Analysis of microRNA Targets Reveals New Insights into Transcriptional–Post-Transcriptional Regulatory Cross-Talk |
| title_full | Integrated Analysis of microRNA Targets Reveals New Insights into Transcriptional–Post-Transcriptional Regulatory Cross-Talk |
| title_fullStr | Integrated Analysis of microRNA Targets Reveals New Insights into Transcriptional–Post-Transcriptional Regulatory Cross-Talk |
| title_full_unstemmed | Integrated Analysis of microRNA Targets Reveals New Insights into Transcriptional–Post-Transcriptional Regulatory Cross-Talk |
| title_short | Integrated Analysis of microRNA Targets Reveals New Insights into Transcriptional–Post-Transcriptional Regulatory Cross-Talk |
| title_sort | integrated analysis of microrna targets reveals new insights into transcriptional post transcriptional regulatory cross talk |
| topic | microRNA biocuration miRNA interaction network gene regulation transcription factors |
| url | https://www.mdpi.com/2079-7737/14/1/43 |
| work_keys_str_mv | AT simonapanni integratedanalysisofmicrornatargetsrevealsnewinsightsintotranscriptionalposttranscriptionalregulatorycrosstalk AT robertopizzolotto integratedanalysisofmicrornatargetsrevealsnewinsightsintotranscriptionalposttranscriptionalregulatorycrosstalk |