Evolutionary conservation and function of the human embryonic stem cell specific miR-302/367 cluster

Area of Science:

• Genomics
• Developmental Biology
• Molecular Evolution

Background:

• MicroRNA (miRNA) clusters are genomic regions containing related miRNAs with poorly understood evolutionary histories.
• The miR-302/367 cluster, a polycistronic transcript essential for human embryonic stem cell maintenance, is highly expressed.
• This cluster's evolutionary trajectory and regulatory mechanisms remain largely unexplored.

Purpose of the Study:

• To investigate the evolutionary conservation and dynamics of the miR-302/367 miRNA cluster.
• To identify regulatory mechanisms and functional implications of the miR-302/367 cluster, including its role in stem cell maintenance and cancer.
• To explore the generation of sequence diversity within the cluster through isomiR expression.

Main Methods:

• Comparative genomics to assess conservation across mammalian species.
• Bioinformatic analysis of miRNA seed sequences, structures, and inter-precursor regions.
• Identification of transcription factor binding sites and miRNA target sites in flanking regions.
• Gene expression analysis using kidney tumor datasets to evaluate miR-302 family member expression in normal versus tumor tissues.
• Correlation analysis between miRNA expression and validated target genes.

Main Results:

• The miR-302/367 cluster is highly conserved in most mammals, with conserved miRNA structures in primates but evolving inter-precursor sequences.
• Evidence of active evolution includes miRNA insertions/deletions and cluster duplication in different species.
• Stem cell-specific transcription factors (NANOG, OCT-4) bind upstream, and flanking regions are targeted by other miRNAs, suggesting feedback regulation.
• Analysis revealed concordance in gene ontology levels for miR-302 and miR-367 targets, and isomiRs contribute to sequence diversity.
• Kidney tumor datasets showed decreased miR-302 family expression in tumors compared to normal tissue, with correlated expression of target genes.

Conclusions:

• The miR-302/367 cluster is a highly conserved yet actively evolving genomic entity.
• Its regulation involves key stem cell transcription factors and feedback mechanisms via miRNA targeting.
• Dysregulation of the miR-302/367 cluster in kidney tumors highlights its potential role in oncogenesis.
• The cluster's conserved nature and evolving dynamics suggest broader, potentially unrecognized functions in mammalian biology.