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MicroRNA (miRNA) are short, regulatory RNA transcribed from introns—non-coding regions of a gene—or intergenic regions—stretches of DNA present between genes. Several processing steps are required to form biologically active, mature miRNA. The initial transcript, called primary miRNA (pri-mRNA), base-pairs with itself forming a stem-loop structure. Within the nucleus, an endonuclease enzyme, called Drosha, shortens the stem-loop structure into hairpin-shaped pre-miRNA. After...
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mirMachine: A One-Stop Shop for Plant miRNA Annotation
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CmirC update 2024: a multi-omics database for clustered miRNAs.

Akshay Pramod Ware1,2, Kapaettu Satyamoorthy3, Bobby Paul4

  • 1Department of Bioinformatics, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India.

Functional & Integrative Genomics
|July 31, 2024
PubMed
Summary
This summary is machine-generated.

Clustered microRNAs (miRNAs) play a key role in cancer progression. The updated CmirC database now integrates DNA methylation data, revealing regulatory roles in 14 cancer types.

Keywords:
Cancer informaticsDNA methylationEpigenomicsIntegrated data analysis

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Area of Science:

  • Genomics
  • Epigenetics
  • Cancer Biology

Background:

  • Clustered microRNAs (miRNAs) are transcribed together and can coordinately regulate gene expression, impacting cancer progression.
  • Previous work identified copy number variation (CNV) driven clustered miRNAs in cancer using the CmirC database.
  • Differential expression of clustered miRNAs is influenced by genetic and epigenetic mechanisms.

Purpose of the Study:

  • To update the CmirC database with DNA methylation analysis of clustered miRNAs.
  • To identify regulatory roles of DNA methylation in clustered miRNA expression across various cancer types.
  • To enhance data browsing and analysis functionalities for user convenience.

Main Methods:

  • Utilized The Cancer Genome Atlas (TCGA) methylation datasets from 9,639 samples.
  • Analyzed 215,435 methylation sites and 27,949 CpG islands associated with miRNA clusters.
  • Integrated copy number variation (CNV) and DNA methylation data for comprehensive analysis.

Main Results:

  • Identified three miRNAs (mir-96, mir-183, mir-21) significantly upregulated in 17 cancer types.
  • Discovered 34 miRNA clusters with differentially methylated CpG sites across 14 cancer types.
  • Found CpG islands in the promoter regions of 20 miRNA clusters potentially involved in regulation.

Conclusions:

  • The updated CmirC database provides insights into epigenetic regulation of clustered miRNAs in cancer.
  • DNA methylation significantly impacts clustered miRNA expression and may play a regulatory role in oncogenesis.
  • The enhanced CmirC database serves as a valuable resource for understanding miRNA-targeted oncogenes and tumor suppressors.